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2014-10-18T03:51:48Z
<p>Hlx1996: </p>
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<p style="font-size:64px;height:100%;line-height:100%;color:rgb(144,144,144)">Meet Biopano</p><br />
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<p></p><br />
<h4 id="overview">Overview</h4><br />
<div class="underline-small"></div><br />
<p>Designed specifically for biological research, BioPano is a software platform targeted for visualisation of biological relationships as well as cooperative net-building. You can set up your own network of biological relationship by adding information about genetic regulation and metabolic system to the network we already provided for you. Also, the software allows you to explore the links among the substances by just several clicks, and you can even look into the details of the interaction between the exogenous gene and the host. What is even more exciting is that our software will end your loneliness and frustration in research, since it is providing you with cloud cooperating system so that you can view massive amounts of resources in databases, together with build up groups to share information and set up mutual network with others.<br />
</p><br />
<br />
<h4 id="motivation">Motivation</h4><br />
<div class="underline-small"></div><br />
<p><br />
In recent years, people has made a lot of remarkable achievements <br />
in synthetic biology. However, scientists are often faced with <br />
many unpredictable problems when carrying out experiments. <br />
Each kind of biological substance is inextricably linked to the <br />
biological environment to which it belongs, so we have to consider <br />
a question: Can we attain the desired goal, if we simply follow the traditional ideas of synthetic biology and avoid the problem merely by engineering?<br />
</p><br />
<p><br />
A synthetic biologist, Chris Voigt, has successfully transferred a<br />
Toggle Switch, which usually works in the Bacillus <br />
subtilis, into E. coli. Unfortunately, it did not function properly. In <br />
fact, in experiments, due to the unexpected interactions between <br />
BioBrick and the host, it is very common that the designed path do <br />
not work as anticipated.<br />
</p><br />
<p><br />
In fact, the life system is so complex that there are many sorts of <br />
biological substance to support it with complex interations in it. <br />
In order to understand a phenomenon, we keep using new and <br />
sophisticated methods to refine our research and to explore every <br />
detail of life. However, if we widen our perspective, by looking at <br />
our research objectives from a more comprehensive perspective, <br />
we may have some unexpected discoveries.<br />
</p><br />
<br />
<h4 id="features">Features</h4><br />
<div class="underline-small"><br />
</div><br />
<p>Our software has many marvelous features, with which your biology research will become extremely easy and joyful.</p><br />
<ul><br />
<br />
<h5>1. Expansion of single node</h5><br />
<div class="row"><br />
<div class="large-6 columns"><p>In Biopano, every biology part of E.coli K-12 will be displayed as a node of different types and regulation relationship <br />
will be displayed as arc of different types. They are displayed in the biological network in a visualizational way. <br />
You just need to select a node and click “Expand”, and the nodes associated with it will be “expanded”. <br />
Nodes are connected to each other by all kinds of relationship, so users can see how biological parts are connected clearly, <br />
such as LacI Operon. </p></div><br />
<div class="large-6 columns"><img src="https://static.igem.org/mediawiki/2014/4/46/2014ustc-Feature-a.png"></div><br />
</div><br />
<br />
<div class="row"><br />
<div class="large-6 columns"><img src="https://static.igem.org/mediawiki/2014/9/9e/2014ustc-Feature-b.png"></div><br />
<div class="large-6 columns"><p>However, since there are so many biological parts connected to each other in various convoluted, <br />
the expansion of all nodes will give rise to extremely involved nets, which will fail to convey useful information to the users, <br />
even interfere their thoughts. So you can choose to expand the nodes in a way you see fit. Take Transcription factor CRP as an example. </p><br />
<p>Biopano displays the network dynamically, which makes you able to tease out the relationship among thousands of materials of <br />
E.coli K-12, satisfies your curiosity and helps you discover unknown biological field.</p></div><br />
</div><br />
<div class="underline-tiny"></div><br />
<br />
<br />
<br />
<h5>2. Link Finder</h5><br />
<div class="row"><br />
<div class="large-6 columns"><p>You can input two nodes that seem irrelevant, such as gene A and Transcription FactorB, and the software will <br />
search the route connecting the two nodes for you. Since some routes are too sinuous for further analysis or does not make sense, <br />
you can set a specific number k, Biopano will search and show the k shortest routes for you.</p></div><br />
<div class="large-6 columns"><img src="https://static.igem.org/mediawiki/2014/7/79/2014ustc-Feature-c.png"></div><br />
</div><br />
<div class="underline-tiny"></div><br />
<br />
<br />
<h5>3. BLAST</h5><br />
<div class="row"><br />
<div class="large-6 columns"><img src="https://static.igem.org/mediawiki/2014/7/71/2014ustc-Feature-e.png"></div><br />
<div class="large-6 columns"><p>By BLAST method, Biopano finds E.coli K-12 gene highly similar to the injected sequence. <br />
These genes are regulated by other parts in E.coli K-12, so can provide information of the host environment’s impact on injected <br />
exogenous sequence. Biopano also offers BioBrick helper, enabling you search all kinds of BioBricks on iGEM’s official website. <br />
By BLAST analysis, it helps you design correct gene route with appropriate BioBricks.</p></div><br />
</div><br />
<div class="underline-tiny"></div><br />
<br />
<br />
<h5>4. Data Sharing</h5><br />
<p>Hence, while offering various functions, Biopano also serves as a cooperative network building platform. When you create a project, you can add new nodes, name new biological parts and link them with respect to your comprehension to build a brand new net gradually. Meanwhile, Biopano provides log in service. You can sign up with Google or Baidu account and upload your network to the main database to make it more plentiful. Biopano also supports data importing in batch. You can even import data of a species and a database.</p><br />
<ul class="small-block-grid-2"><br />
<li><img src="https://static.igem.org/mediawiki/2014/2/2a/2014ustc-Feature-f.png"></li><br />
<li><img src="https://static.igem.org/mediawiki/2014/5/57/2014ustc-Feature-g.png"></li><br />
</ul><br />
<div class="underline-tiny"></div><br />
<br />
<h5>5. Details and Reference</h5><br />
<p>When you have already got the entire view and want to know more about the details, double-click the nodes and arcs and the details will be shown. More surprisingly, Biopano supports literature reading in the network. You can view literature corresponding to every node and arc along any gene route in the network, and you will understand how the nodes in the net are associated with each other in depth. If you cast doubt on the reliability of our database, you can verify your thought with authoritative literature.</p><br />
<br />
</ul><br />
<p></p><br />
<h4 id="demos">Demo</h4><br />
<div class="underline-small"><br />
</div><br />
<div><br />
<h4>Next we will demonstrate some common modules of E.coli k-12:</h4><br />
<br />
<h5>1, Lac Operon: When you input LacZYA, a Transcription Unit(TU) of Lac Operon and Expand the node:</h5><br />
<p>You will see four promoters, acZp1, lacZp2, lacZp3 and lacZp4 as<br />
upstream sequences and three structure genes, lacZ, lacY and lacA as <br />
downstream sequences. Meanwhile, you can see the TU belongs to <br />
the Operon lacZYA.<br />
</p><br />
<p>Above the node lacZYA, you also see three Transcription<br />
Factors, namely, CRP, H-NS and lacl. They suppress the expression of <br />
lazZYA.</p><br />
<p>Expand lacZ, lacY and lacA, and we get BgaL, LacY and ThgA<br />
respectively, of which Bgal and ThgA are Enzymes. They catalyze<br />
corresponding reactions. Expand Lacl and we get the gene lacl which<br />
codes it.</p><br />
<ul class="small-block-grid-2"><br />
<li><img src="https://static.igem.org/mediawiki/2014/4/47/2014ustc-B.png"></li><br />
<li><img src="https://static.igem.org/mediawiki/2014/e/ee/C.png"></li><br />
</ul><br />
<br />
<p>Continue to Expand lacZYA and lacl and we find more materials’<br />
connected with them. You can select and drag the nodes to arrange the <br />
network neatly; you can also click Full Screen and the network will be <br />
displayed in full screen.</p><br />
<ul class="small-block-grid-2"><br />
<li><img src="https://static.igem.org/mediawiki/2014/c/c5/2014ustc-D.png"></li><br />
<li><img src="https://static.igem.org/mediawiki/2014/3/3a/2014ustc-E.png"></li><br />
</ul><br />
<br />
<h5>2, Following the same steps, we can also get the regulation network of<br />
the Operon Trp.</h5><br />
<img src="https://static.igem.org/mediawiki/2014/9/9d/2014ustc-F.png"><br />
</div><br />
<br />
<br />
<h4 id="why">Why choose BioPano?</h4><br />
<div class="underline-small"></div><br />
<div><br />
<p> Biopano, do the experiment as you do in the lab.</p><br />
<p>In experiment, synthetic biologists always find gene circuits formed by BioBricks are incompatible with the host cell, thus cannot work as expected. However, Biopano uses sequence alignment to analyze the possible reasons of the failure and design more acute gene circuit for your consideration.</p><br />
<p>Our Blast algorism derives from NCBI. However, the original version only offers sequence alignment and fails to analyze what impact the host environment might have on the injected gene circuit, let along predicts whether it will work.</p><br />
<p>Firstly, Biopano offers BioBrick searching to make it convenient for you to study all standardized biological parts on the official website of iGEM. Secondly, you can input a BioBrick and even construct a brand new sequence. Biopano will find the gene nodes of E.coli K-12 sharing the deepest homology with it based on authoritative Blast algorithm. Then you can Expand these nodes to find out the possible regulation on them. In this way, Biopano helps you analyze whether the injected gene circuit will actually work.</p><br />
<p>Biopano abstracts biological parts and the regulation among them into nodes and arcs to realize data visualization, and displays gene regulation and metabolism network of E.coli K-12 dynamically by continually Expanding nodes. Single database cannot make an entire material network, so our back end combines Regulon DB, KEGG, Uniprot and abundant data. You can ceaselessly Expand the nodes in the network to comb the relationship among them and satisfy your curiosity.</p><br />
<br />
<p>Compared with Biopano, Cytoscape and Netscience mainly support file importing and network displaying without powerful database from the back end. Hence you cannot search for biological parts online and view the certain part of the biological network you need with them.</p><br />
<br />
<p>Now that there is enormous astonishing material relationship in biological body, more and more biologists hope to find the specific function route between two biological parts or even two biological blocks that seem not related to each other, such as c-di-GMP signalling and Quorum Sensing. Unfortunately, the interactions of the biological parts are saved in database as records and it is almost impossible to find the route in thousands of records. There haven’t been any software to offer any help before. Luckily, Biopano brings hope to this.</p><br />
<br />
<p>You can input two biological parts and set several shortest routes, then you will find their relationship. We used this powerful function to find the specific relationship betweem c-di-GMP signalling and Quorum Sensing, which was corroborated by corresponding literature. How amazing!</p><br />
<br />
<p>We have to admit that Biopano may show you wrong gene route. However, it provides you with direction of studying the relationship of two fields. It not only makes your goal for experiment designing clearer, but enables you to understand the connection inside body is so close as well.</p><br />
<br />
<p>While offering function services, Biopano serves as a platform for collaborative network building. You can define new nodes and arcs yourself and sign in with your Google or Baidu account to upload the network you build to our database. You can also invite several companions to complete a project together. Common biological software, such as Cytoscape and Netscience, doesn’t provide a good platform for communication, while Biopano enhances the communication of biological areas by data sharing.</p><br />
<br />
<p>Biopano, your right hand for biological research. Get it now!</p><br />
</div><br />
<br />
<h4 id="futurework">Future Work</h4><br />
<div class="underline-small"></div><br />
<div><br />
<h4>It is undeniable that we still have a lot to do to improve Biopano in many aspects in order to make it even better. We need to think more and develop it as we can. In the future, we hope to:<br />
</h4><br />
<br />
<p>1. Integrate more data in it. Currently, Biopano only integrates data of E.coli k-12 from Regulon DB, KEGG and Uniprot, and our data in regulatory interaction lack accurate numerical data to indicate its strength. etc. Therefore, not only will we update the existing data in the original species, we will also make complement of high-throughput data through other databases and papers, as well as expand information of other species, so that more biological researchers can benefit from our software.</p><br />
<br />
<p>2. Normalize users' rights, improve quality of data. With the increase of the number of users, the data synchronized every day become not only massive, but also in many different forms, and some of them have nevitable errors or redundant information, or there may be different kinds of comprehension of certain regulatory relations. So we want the machine to automatically recognize the validity of the data submitted by the user, and establish a evaluation criteria of credibility. Thus, only those reliable users will be selected, and only their data can be synchronized to the main database, and the redundancy or errors will be eliminated, and they also continue to enhance the credibility and value of the main database.</p><br />
<br />
<p>3. Enhance network analysis functions. When we add the high-throughput kinetic data for biological networks, we can build a variety of mathematical models on the network and carry out quantitative simulation analysis. For example, we can put the nodes that are closely related to one another together in a group. We can make out software automatically arrange the modules for different functions in the organism. We can even do things that are analogic to those in an electric circult. The network provides the entrance and the exit of the signals, and all you need to do is to enter the target product and we will help you find the substance needed for synthesizing it. </p><br />
<br />
<p>4. Supports more file formats. Currently, the file formats we provide to the users are only XML and SBOL. In the future we will make our software support more file formats, such as sif, EMBL, etc., and we will develop its ability to be capable with other biological softwares such as cytoscape and Netscience, seamlessly. You can import and export any file that are constantly used. From this aspect, we will greatly broadens the scope of the functions of the software.</p><br />
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Hlx1996
http://2014.igem.org/Team:USTC-Software/biopano.php
Team:USTC-Software/biopano.php
2014-10-18T03:51:14Z
<p>Hlx1996: </p>
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<p style="font-size:64px;height:100%;line-height:100%;color:rgb(144,144,144)">Meet Biopano</p><br />
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</div><br />
<div class="row"><br />
<div class="large-12 columns large-centered"><br />
<br />
<p></p><br />
<h4 id="overview">Overview</h4><br />
<div class="underline-small"></div><br />
<p>Designed specifically for biological research, BioPano is a software platform targeted for visualisation of biological relationships as well as cooperative net-building. You can set up your own network of biological relationship by adding information about genetic regulation and metabolic system to the network we already provided for you. Also, the software allows you to explore the links among the substances by just several clicks, and you can even look into the details of the interaction between the exogenous gene and the host. What is even more exciting is that our software will end your loneliness and frustration in research, since it is providing you with cloud cooperating system so that you can view massive amounts of resources in databases, together with build up groups to share information and set up mutual network with others.<br />
</p><br />
<br />
<h4 id="motivation">Motivation</h4><br />
<div class="underline-small"></div><br />
<p><br />
In recent years, people has made a lot of remarkable achievements <br />
in synthetic biology. However, scientists are often faced with <br />
many unpredictable problems when carrying out experiments. <br />
Each kind of biological substance is inextricably linked to the <br />
biological environment to which it belongs, so we have to consider <br />
a question: Can we attain the desired goal, if we simply follow the traditional ideas of synthetic biology and avoid the problem merely by engineering?<br />
</p><br />
<p><br />
A synthetic biologist, Chris Voigt, has successfully transferred a<br />
Toggle Switch, which usually works in the Bacillus <br />
subtilis, into E. coli. Unfortunately, it did not function properly. In <br />
fact, in experiments, due to the unexpected interactions between <br />
BioBrick and the host, it is very common that the designed path do <br />
not work as anticipated.<br />
</p><br />
<p><br />
In fact, the life system is so complex that there are many sorts of <br />
biological substance to support it with complex interations in it. <br />
In order to understand a phenomenon, we keep using new and <br />
sophisticated methods to refine our research and to explore every <br />
detail of life. However, if we widen our perspective, by looking at <br />
our research objectives from a more comprehensive perspective, <br />
we may have some unexpected discoveries.<br />
</p><br />
<br />
<h4 id="features">Features</h4><br />
<div class="underline-small"><br />
</div><br />
<p>Our software has many marvelous features, with which your biology research will become extremely easy and joyful.</p><br />
<ul><br />
<br />
<h5>1. Expansion of single node</h5><br />
<div class="row"><br />
<div class="large-6 columns"><p>In Biopano, every biology part of E.coli K-12 will be displayed as a node of different types and regulation relationship <br />
will be displayed as arc of different types. They are displayed in the biological network in a visualizational way. <br />
You just need to select a node and click “Expand”, and the nodes associated with it will be “expanded”. <br />
Nodes are connected to each other by all kinds of relationship, so users can see how biological parts are connected clearly, <br />
such as LacI Operon. </p></div><br />
<div class="large-6 columns"><img src="https://static.igem.org/mediawiki/2014/4/46/2014ustc-Feature-a.png"></div><br />
</div><br />
<br />
<div class="row"><br />
<div class="large-6 columns"><img src="https://static.igem.org/mediawiki/2014/9/9e/2014ustc-Feature-b.png"></div><br />
<div class="large-6 columns"><p>However, since there are so many biological parts connected to each other in various convoluted, <br />
the expansion of all nodes will give rise to extremely involved nets, which will fail to convey useful information to the users, <br />
even interfere their thoughts. So you can choose to expand the nodes in a way you see fit. Take Transcription factor CRP as an example. </p><br />
<p>Biopano displays the network dynamically, which makes you able to tease out the relationship among thousands of materials of <br />
E.coli K-12, satisfies your curiosity and helps you discover unknown biological field.</p></div><br />
</div><br />
<div class="underline-tiny"></div><br />
<br />
<br />
<br />
<h5>2. Link Finder</h5><br />
<div class="row"><br />
<div class="large-6 columns"><p>You can input two nodes that seem irrelevant, such as gene A and Transcription FactorB, and the software will <br />
search the route connecting the two nodes for you. Since some routes are too sinuous for further analysis or does not make sense, <br />
you can set a specific number k, Biopano will search and show the k shortest routes for you.</p></div><br />
<div class="large-6 columns"><img src="https://static.igem.org/mediawiki/2014/7/79/2014ustc-Feature-c.png"></div><br />
</div><br />
<div class="underline-tiny"></div><br />
<br />
<br />
<h5>3. BLAST</h5><br />
<div class="row"><br />
<div class="large-6 columns"><img src="https://static.igem.org/mediawiki/2014/7/71/2014ustc-Feature-e.png"></div><br />
<div class="large-6 columns"><p>By BLAST method, Biopano finds E.coli K-12 gene highly similar to the injected sequence. <br />
These genes are regulated by other parts in E.coli K-12, so can provide information of the host environment’s impact on injected <br />
exogenous sequence. Biopano also offers BioBrick helper, enabling you search all kinds of BioBricks on iGEM’s official website. <br />
By BLAST analysis, it helps you design correct gene route with appropriate BioBricks.</p></div><br />
</div><br />
<div class="underline-tiny"></div><br />
<br />
<br />
<h5>4. Data Sharing</h5><br />
<p>Hence, while offering various functions, Biopano also serves as a cooperative network building platform. When you create a project, you can add new nodes, name new biological parts and link them with respect to your comprehension to build a brand new net gradually. Meanwhile, Biopano provides log in service. You can sign up with Google or Baidu account and upload your network to the main database to make it more plentiful. Biopano also supports data importing in batch. You can even import data of a species and a database.</p><br />
<ul class="small-block-grid-2"><br />
<li><img src="https://static.igem.org/mediawiki/2014/2/2a/2014ustc-Feature-f.png"></li><br />
<li><img src="https://static.igem.org/mediawiki/2014/5/57/2014ustc-Feature-g.png"></li><br />
</ul><br />
<div class="underline-tiny"></div><br />
<br />
<h5>5. Details and Reference</h5><br />
<p>When you have already got the entire view and want to know more about the details, double-click the nodes and arcs and the details will be shown. More surprisingly, Biopano supports literature reading in the network. You can view literature corresponding to every node and arc along any gene route in the network, and you will understand how the nodes in the net are associated with each other in depth. If you cast doubt on the reliability of our database, you can verify your thought with authoritative literature.</p><br />
<br />
</ul><br />
<p></p><br />
<h4 id="demos">Demo</h4><br />
<div class="underline-small"><br />
</div><br />
<div><br />
<h4>Next we will demonstrate some common modules of E.coli k-12:</h4><br />
<br />
<h5>1, Lac Operon: When you input LacZYA, a Transcription Unit(TU) of Lac Operon and Expand the node:</h5><br />
<p>You will see four promoters, acZp1, lacZp2, lacZp3 and lacZp4 as<br />
upstream sequences and three structure genes, lacZ, lacY and lacA as <br />
downstream sequences. Meanwhile, you can see the TU belongs to <br />
the Operon lacZYA.<br />
</p><br />
<p>Above the node lacZYA, you also see three Transcription<br />
Factors, namely, CRP, H-NS and lacl. They suppress the expression of <br />
lazZYA.</p><br />
<p>Expand lacZ, lacY and lacA, and we get BgaL, LacY and ThgA<br />
respectively, of which Bgal and ThgA are Enzymes. They catalyze<br />
corresponding reactions. Expand Lacl and we get the gene lacl which<br />
codes it.</p><br />
<ul class="small-block-grid-2"><br />
<li><img src="https://static.igem.org/mediawiki/2014/4/47/2014ustc-B.png"></li><br />
<li><img src="https://static.igem.org/mediawiki/2014/e/ee/C.png"></li><br />
</ul><br />
<br />
<p>Continue to Expand lacZYA and lacl and we find more materials’<br />
connected with them. You can select and drag the nodes to arrange the <br />
network neatly; you can also click Full Screen and the network will be <br />
displayed in full screen.</p><br />
<ul class="small-block-grid-2"><br />
<li><img src="https://static.igem.org/mediawiki/2014/c/c5/2014ustc-D.png"></li><br />
<li><img src="https://static.igem.org/mediawiki/2014/3/3a/2014ustc-E.png"></li><br />
</ul><br />
<br />
<h5>2, Following the same steps, we can also get the regulation network of<br />
the Operon Trp.</h5><br />
<img src="https://static.igem.org/mediawiki/2014/9/9d/2014ustc-F.png"><br />
<iframe width="1280" height="720" src="//www.youtube.com/embed/79uuj5hXsOg" frameborder="0" allowfullscreen></iframe><br />
</div><br />
<br />
<br />
<h4 id="why">Why choose BioPano?</h4><br />
<div class="underline-small"></div><br />
<div><br />
<p> Biopano, do the experiment as you do in the lab.</p><br />
<p>In experiment, synthetic biologists always find gene circuits formed by BioBricks are incompatible with the host cell, thus cannot work as expected. However, Biopano uses sequence alignment to analyze the possible reasons of the failure and design more acute gene circuit for your consideration.</p><br />
<p>Our Blast algorism derives from NCBI. However, the original version only offers sequence alignment and fails to analyze what impact the host environment might have on the injected gene circuit, let along predicts whether it will work.</p><br />
<p>Firstly, Biopano offers BioBrick searching to make it convenient for you to study all standardized biological parts on the official website of iGEM. Secondly, you can input a BioBrick and even construct a brand new sequence. Biopano will find the gene nodes of E.coli K-12 sharing the deepest homology with it based on authoritative Blast algorithm. Then you can Expand these nodes to find out the possible regulation on them. In this way, Biopano helps you analyze whether the injected gene circuit will actually work.</p><br />
<p>Biopano abstracts biological parts and the regulation among them into nodes and arcs to realize data visualization, and displays gene regulation and metabolism network of E.coli K-12 dynamically by continually Expanding nodes. Single database cannot make an entire material network, so our back end combines Regulon DB, KEGG, Uniprot and abundant data. You can ceaselessly Expand the nodes in the network to comb the relationship among them and satisfy your curiosity.</p><br />
<br />
<p>Compared with Biopano, Cytoscape and Netscience mainly support file importing and network displaying without powerful database from the back end. Hence you cannot search for biological parts online and view the certain part of the biological network you need with them.</p><br />
<br />
<p>Now that there is enormous astonishing material relationship in biological body, more and more biologists hope to find the specific function route between two biological parts or even two biological blocks that seem not related to each other, such as c-di-GMP signalling and Quorum Sensing. Unfortunately, the interactions of the biological parts are saved in database as records and it is almost impossible to find the route in thousands of records. There haven’t been any software to offer any help before. Luckily, Biopano brings hope to this.</p><br />
<br />
<p>You can input two biological parts and set several shortest routes, then you will find their relationship. We used this powerful function to find the specific relationship betweem c-di-GMP signalling and Quorum Sensing, which was corroborated by corresponding literature. How amazing!</p><br />
<br />
<p>We have to admit that Biopano may show you wrong gene route. However, it provides you with direction of studying the relationship of two fields. It not only makes your goal for experiment designing clearer, but enables you to understand the connection inside body is so close as well.</p><br />
<br />
<p>While offering function services, Biopano serves as a platform for collaborative network building. You can define new nodes and arcs yourself and sign in with your Google or Baidu account to upload the network you build to our database. You can also invite several companions to complete a project together. Common biological software, such as Cytoscape and Netscience, doesn’t provide a good platform for communication, while Biopano enhances the communication of biological areas by data sharing.</p><br />
<br />
<p>Biopano, your right hand for biological research. Get it now!</p><br />
</div><br />
<br />
<h4 id="futurework">Future Work</h4><br />
<div class="underline-small"></div><br />
<div><br />
<h4>It is undeniable that we still have a lot to do to improve Biopano in many aspects in order to make it even better. We need to think more and develop it as we can. In the future, we hope to:<br />
</h4><br />
<br />
<p>1. Integrate more data in it. Currently, Biopano only integrates data of E.coli k-12 from Regulon DB, KEGG and Uniprot, and our data in regulatory interaction lack accurate numerical data to indicate its strength. etc. Therefore, not only will we update the existing data in the original species, we will also make complement of high-throughput data through other databases and papers, as well as expand information of other species, so that more biological researchers can benefit from our software.</p><br />
<br />
<p>2. Normalize users' rights, improve quality of data. With the increase of the number of users, the data synchronized every day become not only massive, but also in many different forms, and some of them have nevitable errors or redundant information, or there may be different kinds of comprehension of certain regulatory relations. So we want the machine to automatically recognize the validity of the data submitted by the user, and establish a evaluation criteria of credibility. Thus, only those reliable users will be selected, and only their data can be synchronized to the main database, and the redundancy or errors will be eliminated, and they also continue to enhance the credibility and value of the main database.</p><br />
<br />
<p>3. Enhance network analysis functions. When we add the high-throughput kinetic data for biological networks, we can build a variety of mathematical models on the network and carry out quantitative simulation analysis. For example, we can put the nodes that are closely related to one another together in a group. We can make out software automatically arrange the modules for different functions in the organism. We can even do things that are analogic to those in an electric circult. The network provides the entrance and the exit of the signals, and all you need to do is to enter the target product and we will help you find the substance needed for synthesizing it. </p><br />
<br />
<p>4. Supports more file formats. Currently, the file formats we provide to the users are only XML and SBOL. In the future we will make our software support more file formats, such as sif, EMBL, etc., and we will develop its ability to be capable with other biological softwares such as cytoscape and Netscience, seamlessly. You can import and export any file that are constantly used. From this aspect, we will greatly broadens the scope of the functions of the software.</p><br />
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<h5 style="color:#fff;font-weight:bold;margin-bottom: 25px;">Innovation Experiment Centre of Life Science (IEC)</h5><br />
<p>Building of Life Sciences, Room 363</p><br />
<p>University of Science and Technology of China</p><br />
<p>96, Jinzhai Rd, Shushan, Hefei</p><br />
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Hlx1996
http://2014.igem.org/Team:USTC-Software/biopano.php
Team:USTC-Software/biopano.php
2014-10-18T03:48:34Z
<p>Hlx1996: </p>
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<p style="font-size:64px;height:100%;line-height:100%;color:rgb(144,144,144)">Meet Biopano</p><br />
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<div class="row"><br />
<div class="large-12 columns large-centered"><br />
<br />
<p></p><br />
<h4 id="overview">Overview</h4><br />
<div class="underline-small"></div><br />
<p>Designed specifically for biological research, BioPano is a software platform targeted for visualisation of biological relationships as well as cooperative net-building. You can set up your own network of biological relationship by adding information about genetic regulation and metabolic system to the network we already provided for you. Also, the software allows you to explore the links among the substances by just several clicks, and you can even look into the details of the interaction between the exogenous gene and the host. What is even more exciting is that our software will end your loneliness and frustration in research, since it is providing you with cloud cooperating system so that you can view massive amounts of resources in databases, together with build up groups to share information and set up mutual network with others.<br />
</p><br />
<br />
<h4 id="motivation">Motivation</h4><br />
<div class="underline-small"></div><br />
<p><br />
In recent years, people has made a lot of remarkable achievements <br />
in synthetic biology. However, scientists are often faced with <br />
many unpredictable problems when carrying out experiments. <br />
Each kind of biological substance is inextricably linked to the <br />
biological environment to which it belongs, so we have to consider <br />
a question: Can we attain the desired goal, if we simply follow the traditional ideas of synthetic biology and avoid the problem merely by engineering?<br />
</p><br />
<p><br />
A synthetic biologist, Chris Voigt, has successfully transferred a<br />
Toggle Switch, which usually works in the Bacillus <br />
subtilis, into E. coli. Unfortunately, it did not function properly. In <br />
fact, in experiments, due to the unexpected interactions between <br />
BioBrick and the host, it is very common that the designed path do <br />
not work as anticipated.<br />
</p><br />
<p><br />
In fact, the life system is so complex that there are many sorts of <br />
biological substance to support it with complex interations in it. <br />
In order to understand a phenomenon, we keep using new and <br />
sophisticated methods to refine our research and to explore every <br />
detail of life. However, if we widen our perspective, by looking at <br />
our research objectives from a more comprehensive perspective, <br />
we may have some unexpected discoveries.<br />
</p><br />
<br />
<h4 id="features">Features</h4><br />
<div class="underline-small"><br />
</div><br />
<p>Our software has many marvelous features, with which your biology research will become extremely easy and joyful.</p><br />
<ul><br />
<br />
<h5>1. Expansion of single node</h5><br />
<div class="row"><br />
<div class="large-6 columns"><p>In Biopano, every biology part of E.coli K-12 will be displayed as a node of different types and regulation relationship <br />
will be displayed as arc of different types. They are displayed in the biological network in a visualizational way. <br />
You just need to select a node and click “Expand”, and the nodes associated with it will be “expanded”. <br />
Nodes are connected to each other by all kinds of relationship, so users can see how biological parts are connected clearly, <br />
such as LacI Operon. </p></div><br />
<div class="large-6 columns"><img src="https://static.igem.org/mediawiki/2014/4/46/2014ustc-Feature-a.png"></div><br />
</div><br />
<br />
<div class="row"><br />
<div class="large-6 columns"><img src="https://static.igem.org/mediawiki/2014/9/9e/2014ustc-Feature-b.png"></div><br />
<div class="large-6 columns"><p>However, since there are so many biological parts connected to each other in various convoluted, <br />
the expansion of all nodes will give rise to extremely involved nets, which will fail to convey useful information to the users, <br />
even interfere their thoughts. So you can choose to expand the nodes in a way you see fit. Take Transcription factor CRP as an example. </p><br />
<p>Biopano displays the network dynamically, which makes you able to tease out the relationship among thousands of materials of <br />
E.coli K-12, satisfies your curiosity and helps you discover unknown biological field.</p></div><br />
</div><br />
<div class="underline-tiny"></div><br />
<br />
<br />
<br />
<h5>2. Link Finder</h5><br />
<div class="row"><br />
<div class="large-6 columns"><p>You can input two nodes that seem irrelevant, such as gene A and Transcription FactorB, and the software will <br />
search the route connecting the two nodes for you. Since some routes are too sinuous for further analysis or does not make sense, <br />
you can set a specific number k, Biopano will search and show the k shortest routes for you.</p></div><br />
<div class="large-6 columns"><img src="https://static.igem.org/mediawiki/2014/7/79/2014ustc-Feature-c.png"></div><br />
</div><br />
<div class="underline-tiny"></div><br />
<br />
<br />
<h5>3. BLAST</h5><br />
<div class="row"><br />
<div class="large-6 columns"><img src="https://static.igem.org/mediawiki/2014/7/71/2014ustc-Feature-e.png"></div><br />
<div class="large-6 columns"><p>By BLAST method, Biopano finds E.coli K-12 gene highly similar to the injected sequence. <br />
These genes are regulated by other parts in E.coli K-12, so can provide information of the host environment’s impact on injected <br />
exogenous sequence. Biopano also offers BioBrick helper, enabling you search all kinds of BioBricks on iGEM’s official website. <br />
By BLAST analysis, it helps you design correct gene route with appropriate BioBricks.</p></div><br />
</div><br />
<div class="underline-tiny"></div><br />
<br />
<br />
<h5>4. Data Sharing</h5><br />
<p>Hence, while offering various functions, Biopano also serves as a cooperative network building platform. When you create a project, you can add new nodes, name new biological parts and link them with respect to your comprehension to build a brand new net gradually. Meanwhile, Biopano provides log in service. You can sign up with Google or Baidu account and upload your network to the main database to make it more plentiful. Biopano also supports data importing in batch. You can even import data of a species and a database.</p><br />
<ul class="small-block-grid-2"><br />
<li><img src="https://static.igem.org/mediawiki/2014/2/2a/2014ustc-Feature-f.png"></li><br />
<li><img src="https://static.igem.org/mediawiki/2014/5/57/2014ustc-Feature-g.png"></li><br />
</ul><br />
<div class="underline-tiny"></div><br />
<br />
<h5>5. Details and Reference</h5><br />
<p>When you have already got the entire view and want to know more about the details, double-click the nodes and arcs and the details will be shown. More surprisingly, Biopano supports literature reading in the network. You can view literature corresponding to every node and arc along any gene route in the network, and you will understand how the nodes in the net are associated with each other in depth. If you cast doubt on the reliability of our database, you can verify your thought with authoritative literature.</p><br />
<br />
</ul><br />
<p></p><br />
<h4 id="demos">Demo</h4><br />
<div class="underline-small"><br />
</div><br />
<div><br />
<h4>Next we will demonstrate some common modules of E.coli k-12:</h4><br />
<br />
<h5>1, Lac Operon: When you input LacZYA, a Transcription Unit(TU) of Lac Operon and Expand the node:</h5><br />
<p>You will see four promoters, acZp1, lacZp2, lacZp3 and lacZp4 as<br />
upstream sequences and three structure genes, lacZ, lacY and lacA as <br />
downstream sequences. Meanwhile, you can see the TU belongs to <br />
the Operon lacZYA.<br />
</p><br />
<p>Above the node lacZYA, you also see three Transcription<br />
Factors, namely, CRP, H-NS and lacl. They suppress the expression of <br />
lazZYA.</p><br />
<p>Expand lacZ, lacY and lacA, and we get BgaL, LacY and ThgA<br />
respectively, of which Bgal and ThgA are Enzymes. They catalyze<br />
corresponding reactions. Expand Lacl and we get the gene lacl which<br />
codes it.</p><br />
<ul class="small-block-grid-2"><br />
<li><img src="https://static.igem.org/mediawiki/2014/4/47/2014ustc-B.png"></li><br />
<li><img src="https://static.igem.org/mediawiki/2014/e/ee/C.png"></li><br />
</ul><br />
<br />
<p>Continue to Expand lacZYA and lacl and we find more materials’<br />
connected with them. You can select and drag the nodes to arrange the <br />
network neatly; you can also click Full Screen and the network will be <br />
displayed in full screen.</p><br />
<ul class="small-block-grid-2"><br />
<li><img src="https://static.igem.org/mediawiki/2014/c/c5/2014ustc-D.png"></li><br />
<li><img src="https://static.igem.org/mediawiki/2014/3/3a/2014ustc-E.png"></li><br />
</ul><br />
<br />
<h5>2, Following the same steps, we can also get the regulation network of<br />
the Operon Trp.</h5><br />
<img src="https://static.igem.org/mediawiki/2014/9/9d/2014ustc-F.png"><br />
</div><br />
<br />
<br />
<h4 id="why">Why choose BioPano?</h4><br />
<div class="underline-small"></div><br />
<div><br />
<p> Biopano, do the experiment as you do in the lab.</p><br />
<p>In experiment, synthetic biologists always find gene circuits formed by BioBricks are incompatible with the host cell, thus cannot work as expected. However, Biopano uses sequence alignment to analyze the possible reasons of the failure and design more acute gene circuit for your consideration.</p><br />
<p>Our Blast algorism derives from NCBI. However, the original version only offers sequence alignment and fails to analyze what impact the host environment might have on the injected gene circuit, let along predicts whether it will work.</p><br />
<p>Firstly, Biopano offers BioBrick searching to make it convenient for you to study all standardized biological parts on the official website of iGEM. Secondly, you can input a BioBrick and even construct a brand new sequence. Biopano will find the gene nodes of E.coli K-12 sharing the deepest homology with it based on authoritative Blast algorithm. Then you can Expand these nodes to find out the possible regulation on them. In this way, Biopano helps you analyze whether the injected gene circuit will actually work.</p><br />
<p>Biopano abstracts biological parts and the regulation among them into nodes and arcs to realize data visualization, and displays gene regulation and metabolism network of E.coli K-12 dynamically by continually Expanding nodes. Single database cannot make an entire material network, so our back end combines Regulon DB, KEGG, Uniprot and abundant data. You can ceaselessly Expand the nodes in the network to comb the relationship among them and satisfy your curiosity.</p><br />
<br />
<p>Compared with Biopano, Cytoscape and Netscience mainly support file importing and network displaying without powerful database from the back end. Hence you cannot search for biological parts online and view the certain part of the biological network you need with them.</p><br />
<br />
<p>Now that there is enormous astonishing material relationship in biological body, more and more biologists hope to find the specific function route between two biological parts or even two biological blocks that seem not related to each other, such as c-di-GMP signalling and Quorum Sensing. Unfortunately, the interactions of the biological parts are saved in database as records and it is almost impossible to find the route in thousands of records. There haven’t been any software to offer any help before. Luckily, Biopano brings hope to this.</p><br />
<br />
<p>You can input two biological parts and set several shortest routes, then you will find their relationship. We used this powerful function to find the specific relationship betweem c-di-GMP signalling and Quorum Sensing, which was corroborated by corresponding literature. How amazing!</p><br />
<br />
<p>We have to admit that Biopano may show you wrong gene route. However, it provides you with direction of studying the relationship of two fields. It not only makes your goal for experiment designing clearer, but enables you to understand the connection inside body is so close as well.</p><br />
<br />
<p>While offering function services, Biopano serves as a platform for collaborative network building. You can define new nodes and arcs yourself and sign in with your Google or Baidu account to upload the network you build to our database. You can also invite several companions to complete a project together. Common biological software, such as Cytoscape and Netscience, doesn’t provide a good platform for communication, while Biopano enhances the communication of biological areas by data sharing.</p><br />
<br />
<p>Biopano, your right hand for biological research. Get it now!</p><br />
</div><br />
<br />
<h4 id="futurework">Future Work</h4><br />
<div class="underline-small"></div><br />
<div><br />
<h4>It is undeniable that we still have a lot to do to improve Biopano in many aspects in order to make it even better. We need to think more and develop it as we can. In the future, we hope to:<br />
</h4><br />
<br />
<p>1. Integrate more data in it. Currently, Biopano only integrates data of E.coli k-12 from Regulon DB, KEGG and Uniprot, and our data in regulatory interaction lack accurate numerical data to indicate its strength. etc. Therefore, not only will we update the existing data in the original species, we will also make complement of high-throughput data through other databases and papers, as well as expand information of other species, so that more biological researchers can benefit from our software.</p><br />
<br />
<p>2. Normalize users' rights, improve quality of data. With the increase of the number of users, the data synchronized every day become not only massive, but also in many different forms, and some of them have nevitable errors or redundant information, or there may be different kinds of comprehension of certain regulatory relations. So we want the machine to automatically recognize the validity of the data submitted by the user, and establish a evaluation criteria of credibility. Thus, only those reliable users will be selected, and only their data can be synchronized to the main database, and the redundancy or errors will be eliminated, and they also continue to enhance the credibility and value of the main database.</p><br />
<br />
<p>3. Enhance network analysis functions. When we add the high-throughput kinetic data for biological networks, we can build a variety of mathematical models on the network and carry out quantitative simulation analysis. For example, we can put the nodes that are closely related to one another together in a group. We can make out software automatically arrange the modules for different functions in the organism. We can even do things that are analogic to those in an electric circult. The network provides the entrance and the exit of the signals, and all you need to do is to enter the target product and we will help you find the substance needed for synthesizing it. </p><br />
<br />
<p>4. Supports more file formats. Currently, the file formats we provide to the users are only XML and SBOL. In the future we will make our software support more file formats, such as sif, EMBL, etc., and we will develop its ability to be capable with other biological softwares such as cytoscape and Netscience, seamlessly. You can import and export any file that are constantly used. From this aspect, we will greatly broadens the scope of the functions of the software.</p><br />
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<h5 style="color:#fff;font-weight:bold;margin-bottom: 25px;">Innovation Experiment Centre of Life Science (IEC)</h5><br />
<p>Building of Life Sciences, Room 363</p><br />
<p>University of Science and Technology of China</p><br />
<p>96, Jinzhai Rd, Shushan, Hefei</p><br />
<p>230026, Anhui, China</p><br />
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Hlx1996
http://2014.igem.org/Team:USTC-Software/biopano.php
Team:USTC-Software/biopano.php
2014-10-18T03:47:36Z
<p>Hlx1996: </p>
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<p style="font-size:64px;height:100%;line-height:100%;color:rgb(144,144,144)">Meet Biopano</p><br />
<br />
</div><br />
<div class="row"><br />
<div class="large-12 columns large-centered"><br />
<br />
<p></p><br />
<h4 id="overview">Overview</h4><br />
<div class="underline-small"></div><br />
<p>Designed specifically for biological research, BioPano is a software platform targeted for visualisation of biological relationships as well as cooperative net-building. You can set up your own network of biological relationship by adding information about genetic regulation and metabolic system to the network we already provided for you. Also, the software allows you to explore the links among the substances by just several clicks, and you can even look into the details of the interaction between the exogenous gene and the host. What is even more exciting is that our software will end your loneliness and frustration in research, since it is providing you with cloud cooperating system so that you can view massive amounts of resources in databases, together with build up groups to share information and set up mutual network with others.<br />
</p><br />
<br />
<h4 id="motivation">Motivation</h4><br />
<div class="underline-small"></div><br />
<p><br />
In recent years, people has made a lot of remarkable achievements <br />
in synthetic biology. However, scientists are often faced with <br />
many unpredictable problems when carrying out experiments. <br />
Each kind of biological substance is inextricably linked to the <br />
biological environment to which it belongs, so we have to consider <br />
a question: Can we attain the desired goal, if we simply follow the traditional ideas of synthetic biology and avoid the problem merely by engineering?<br />
</p><br />
<p><br />
A synthetic biologist, Chris Voigt, has successfully transferred a<br />
Toggle Switch, which usually works in the Bacillus <br />
subtilis, into E. coli. Unfortunately, it did not function properly. In <br />
fact, in experiments, due to the unexpected interactions between <br />
BioBrick and the host, it is very common that the designed path do <br />
not work as anticipated.<br />
</p><br />
<p><br />
In fact, the life system is so complex that there are many sorts of <br />
biological substance to support it with complex interations in it. <br />
In order to understand a phenomenon, we keep using new and <br />
sophisticated methods to refine our research and to explore every <br />
detail of life. However, if we widen our perspective, by looking at <br />
our research objectives from a more comprehensive perspective, <br />
we may have some unexpected discoveries.<br />
</p><br />
<br />
<h4 id="features">Features</h4><br />
<div class="underline-small"><br />
</div><br />
<p>Our software has many marvelous features, with which your biology research will become extremely easy and joyful.</p><br />
<ul><br />
<br />
<h5>1. Expansion of single node</h5><br />
<div class="row"><br />
<div class="large-6 columns"><p>In Biopano, every biology part of E.coli K-12 will be displayed as a node of different types and regulation relationship <br />
will be displayed as arc of different types. They are displayed in the biological network in a visualizational way. <br />
You just need to select a node and click “Expand”, and the nodes associated with it will be “expanded”. <br />
Nodes are connected to each other by all kinds of relationship, so users can see how biological parts are connected clearly, <br />
such as LacI Operon. </p></div><br />
<div class="large-6 columns"><img src="https://static.igem.org/mediawiki/2014/4/46/2014ustc-Feature-a.png"></div><br />
</div><br />
<br />
<div class="row"><br />
<div class="large-6 columns"><img src="https://static.igem.org/mediawiki/2014/9/9e/2014ustc-Feature-b.png"></div><br />
<div class="large-6 columns"><p>However, since there are so many biological parts connected to each other in various convoluted, <br />
the expansion of all nodes will give rise to extremely involved nets, which will fail to convey useful information to the users, <br />
even interfere their thoughts. So you can choose to expand the nodes in a way you see fit. Take Transcription factor CRP as an example. </p><br />
<p>Biopano displays the network dynamically, which makes you able to tease out the relationship among thousands of materials of <br />
E.coli K-12, satisfies your curiosity and helps you discover unknown biological field.</p></div><br />
</div><br />
<div class="underline-tiny"></div><br />
<br />
<br />
<br />
<h5>2. Link Finder</h5><br />
<div class="row"><br />
<div class="large-6 columns"><p>You can input two nodes that seem irrelevant, such as gene A and Transcription FactorB, and the software will <br />
search the route connecting the two nodes for you. Since some routes are too sinuous for further analysis or does not make sense, <br />
you can set a specific number k, Biopano will search and show the k shortest routes for you.</p></div><br />
<div class="large-6 columns"><img src="https://static.igem.org/mediawiki/2014/7/79/2014ustc-Feature-c.png"></div><br />
</div><br />
<div class="underline-tiny"></div><br />
<br />
<br />
<h5>3. BLAST</h5><br />
<div class="row"><br />
<div class="large-6 columns"><img src="https://static.igem.org/mediawiki/2014/7/71/2014ustc-Feature-e.png"></div><br />
<div class="large-6 columns"><p>By BLAST method, Biopano finds E.coli K-12 gene highly similar to the injected sequence. <br />
These genes are regulated by other parts in E.coli K-12, so can provide information of the host environment’s impact on injected <br />
exogenous sequence. Biopano also offers BioBrick helper, enabling you search all kinds of BioBricks on iGEM’s official website. <br />
By BLAST analysis, it helps you design correct gene route with appropriate BioBricks.</p></div><br />
</div><br />
<div class="underline-tiny"></div><br />
<br />
<br />
<h5>4. Data Sharing</h5><br />
<p>Hence, while offering various functions, Biopano also serves as a cooperative network building platform. When you create a project, you can add new nodes, name new biological parts and link them with respect to your comprehension to build a brand new net gradually. Meanwhile, Biopano provides log in service. You can sign up with Google or Baidu account and upload your network to the main database to make it more plentiful. Biopano also supports data importing in batch. You can even import data of a species and a database.</p><br />
<ul class="small-block-grid-2"><br />
<li><img src="https://static.igem.org/mediawiki/2014/2/2a/2014ustc-Feature-f.png"></li><br />
<li><img src="https://static.igem.org/mediawiki/2014/5/57/2014ustc-Feature-g.png"></li><br />
</ul><br />
<div class="underline-tiny"></div><br />
<br />
<h5>5. Details and Reference</h5><br />
<p>When you have already got the entire view and want to know more about the details, double-click the nodes and arcs and the details will be shown. More surprisingly, Biopano supports literature reading in the network. You can view literature corresponding to every node and arc along any gene route in the network, and you will understand how the nodes in the net are associated with each other in depth. If you cast doubt on the reliability of our database, you can verify your thought with authoritative literature.</p><br />
<br />
</ul><br />
<p></p><br />
<h4 id="demos">Demo</h4><br />
<div class="underline-small"><br />
</div><br />
<div><br />
<h4>Next we will demonstrate some common modules of E.coli k-12:</h4><br />
<br />
<h5>1, Lac Operon: When you input LacZYA, a Transcription Unit(TU) of Lac Operon and Expand the node:</h5><br />
<p>You will see four promoters, acZp1, lacZp2, lacZp3 and lacZp4 as<br />
upstream sequences and three structure genes, lacZ, lacY and lacA as <br />
downstream sequences. Meanwhile, you can see the TU belongs to <br />
the Operon lacZYA.<br />
</p><br />
<p>Above the node lacZYA, you also see three Transcription<br />
Factors, namely, CRP, H-NS and lacl. They suppress the expression of <br />
lazZYA.</p><br />
<p>Expand lacZ, lacY and lacA, and we get BgaL, LacY and ThgA<br />
respectively, of which Bgal and ThgA are Enzymes. They catalyze<br />
corresponding reactions. Expand Lacl and we get the gene lacl which<br />
codes it.</p><br />
<ul class="small-block-grid-2"><br />
<li><img src="https://static.igem.org/mediawiki/2014/4/47/2014ustc-B.png"></li><br />
<li><img src="https://static.igem.org/mediawiki/2014/e/ee/C.png"></li><br />
</ul><br />
<br />
<p>Continue to Expand lacZYA and lacl and we find more materials’<br />
connected with them. You can select and drag the nodes to arrange the <br />
network neatly; you can also click Full Screen and the network will be <br />
displayed in full screen.</p><br />
<ul class="small-block-grid-2"><br />
<li><img src="https://static.igem.org/mediawiki/2014/c/c5/2014ustc-D.png"></li><br />
<li><img src="https://static.igem.org/mediawiki/2014/3/3a/2014ustc-E.png"></li><br />
</ul><br />
<br />
<h5>2, Following the same steps, we can also get the regulation network of<br />
the Operon Trp.</h5><br />
<img src="https://static.igem.org/mediawiki/2014/9/9d/2014ustc-F.png"><br />
<iframe width="560" height="315" src="//www.youtube.com/embed/79uuj5hXsOg" frameborder="0" allowfullscreen></iframe><br />
<iframe width="560" height="315" src="//www.youtube.com/embed/79uuj5hXsOg" frameborder="0" allowfullscreen></iframe><br />
</div><br />
<br />
<br />
<h4 id="why">Why choose BioPano?</h4><br />
<div class="underline-small"></div><br />
<div><br />
<p> Biopano, do the experiment as you do in the lab.</p><br />
<p>In experiment, synthetic biologists always find gene circuits formed by BioBricks are incompatible with the host cell, thus cannot work as expected. However, Biopano uses sequence alignment to analyze the possible reasons of the failure and design more acute gene circuit for your consideration.</p><br />
<p>Our Blast algorism derives from NCBI. However, the original version only offers sequence alignment and fails to analyze what impact the host environment might have on the injected gene circuit, let along predicts whether it will work.</p><br />
<p>Firstly, Biopano offers BioBrick searching to make it convenient for you to study all standardized biological parts on the official website of iGEM. Secondly, you can input a BioBrick and even construct a brand new sequence. Biopano will find the gene nodes of E.coli K-12 sharing the deepest homology with it based on authoritative Blast algorithm. Then you can Expand these nodes to find out the possible regulation on them. In this way, Biopano helps you analyze whether the injected gene circuit will actually work.</p><br />
<p>Biopano abstracts biological parts and the regulation among them into nodes and arcs to realize data visualization, and displays gene regulation and metabolism network of E.coli K-12 dynamically by continually Expanding nodes. Single database cannot make an entire material network, so our back end combines Regulon DB, KEGG, Uniprot and abundant data. You can ceaselessly Expand the nodes in the network to comb the relationship among them and satisfy your curiosity.</p><br />
<br />
<p>Compared with Biopano, Cytoscape and Netscience mainly support file importing and network displaying without powerful database from the back end. Hence you cannot search for biological parts online and view the certain part of the biological network you need with them.</p><br />
<br />
<p>Now that there is enormous astonishing material relationship in biological body, more and more biologists hope to find the specific function route between two biological parts or even two biological blocks that seem not related to each other, such as c-di-GMP signalling and Quorum Sensing. Unfortunately, the interactions of the biological parts are saved in database as records and it is almost impossible to find the route in thousands of records. There haven’t been any software to offer any help before. Luckily, Biopano brings hope to this.</p><br />
<br />
<p>You can input two biological parts and set several shortest routes, then you will find their relationship. We used this powerful function to find the specific relationship betweem c-di-GMP signalling and Quorum Sensing, which was corroborated by corresponding literature. How amazing!</p><br />
<br />
<p>We have to admit that Biopano may show you wrong gene route. However, it provides you with direction of studying the relationship of two fields. It not only makes your goal for experiment designing clearer, but enables you to understand the connection inside body is so close as well.</p><br />
<br />
<p>While offering function services, Biopano serves as a platform for collaborative network building. You can define new nodes and arcs yourself and sign in with your Google or Baidu account to upload the network you build to our database. You can also invite several companions to complete a project together. Common biological software, such as Cytoscape and Netscience, doesn’t provide a good platform for communication, while Biopano enhances the communication of biological areas by data sharing.</p><br />
<br />
<p>Biopano, your right hand for biological research. Get it now!</p><br />
</div><br />
<br />
<h4 id="futurework">Future Work</h4><br />
<div class="underline-small"></div><br />
<div><br />
<h4>It is undeniable that we still have a lot to do to improve Biopano in many aspects in order to make it even better. We need to think more and develop it as we can. In the future, we hope to:<br />
</h4><br />
<br />
<p>1. Integrate more data in it. Currently, Biopano only integrates data of E.coli k-12 from Regulon DB, KEGG and Uniprot, and our data in regulatory interaction lack accurate numerical data to indicate its strength. etc. Therefore, not only will we update the existing data in the original species, we will also make complement of high-throughput data through other databases and papers, as well as expand information of other species, so that more biological researchers can benefit from our software.</p><br />
<br />
<p>2. Normalize users' rights, improve quality of data. With the increase of the number of users, the data synchronized every day become not only massive, but also in many different forms, and some of them have nevitable errors or redundant information, or there may be different kinds of comprehension of certain regulatory relations. So we want the machine to automatically recognize the validity of the data submitted by the user, and establish a evaluation criteria of credibility. Thus, only those reliable users will be selected, and only their data can be synchronized to the main database, and the redundancy or errors will be eliminated, and they also continue to enhance the credibility and value of the main database.</p><br />
<br />
<p>3. Enhance network analysis functions. When we add the high-throughput kinetic data for biological networks, we can build a variety of mathematical models on the network and carry out quantitative simulation analysis. For example, we can put the nodes that are closely related to one another together in a group. We can make out software automatically arrange the modules for different functions in the organism. We can even do things that are analogic to those in an electric circult. The network provides the entrance and the exit of the signals, and all you need to do is to enter the target product and we will help you find the substance needed for synthesizing it. </p><br />
<br />
<p>4. Supports more file formats. Currently, the file formats we provide to the users are only XML and SBOL. In the future we will make our software support more file formats, such as sif, EMBL, etc., and we will develop its ability to be capable with other biological softwares such as cytoscape and Netscience, seamlessly. You can import and export any file that are constantly used. From this aspect, we will greatly broadens the scope of the functions of the software.</p><br />
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<h5 style="color:#fff;font-weight:bold;margin-bottom: 25px;">Innovation Experiment Centre of Life Science (IEC)</h5><br />
<p>Building of Life Sciences, Room 363</p><br />
<p>University of Science and Technology of China</p><br />
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Hlx1996
http://2014.igem.org/Team:USTC-Software/biopano.php
Team:USTC-Software/biopano.php
2014-10-18T03:42:32Z
<p>Hlx1996: </p>
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<p style="font-size:64px;height:100%;line-height:100%;color:rgb(144,144,144)">Meet Biopano</p><br />
<br />
</div><br />
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<div class="large-12 columns large-centered"><br />
<br />
<p></p><br />
<h4 id="overview">Overview</h4><br />
<div class="underline-small"></div><br />
<p>Designed specifically for biological research, BioPano is a software platform targeted for visualisation of biological relationships as well as cooperative net-building. You can set up your own network of biological relationship by adding information about genetic regulation and metabolic system to the network we already provided for you. Also, the software allows you to explore the links among the substances by just several clicks, and you can even look into the details of the interaction between the exogenous gene and the host. What is even more exciting is that our software will end your loneliness and frustration in research, since it is providing you with cloud cooperating system so that you can view massive amounts of resources in databases, together with build up groups to share information and set up mutual network with others.<br />
</p><br />
<br />
<h4 id="motivation">Motivation</h4><br />
<div class="underline-small"></div><br />
<p><br />
In recent years, people has made a lot of remarkable achievements <br />
in synthetic biology. However, scientists are often faced with <br />
many unpredictable problems when carrying out experiments. <br />
Each kind of biological substance is inextricably linked to the <br />
biological environment to which it belongs, so we have to consider <br />
a question: Can we attain the desired goal, if we simply follow the traditional ideas of synthetic biology and avoid the problem merely by engineering?<br />
</p><br />
<p><br />
A synthetic biologist, Chris Voigt, has successfully transferred a<br />
Toggle Switch, which usually works in the Bacillus <br />
subtilis, into E. coli. Unfortunately, it did not function properly. In <br />
fact, in experiments, due to the unexpected interactions between <br />
BioBrick and the host, it is very common that the designed path do <br />
not work as anticipated.<br />
</p><br />
<p><br />
In fact, the life system is so complex that there are many sorts of <br />
biological substance to support it with complex interations in it. <br />
In order to understand a phenomenon, we keep using new and <br />
sophisticated methods to refine our research and to explore every <br />
detail of life. However, if we widen our perspective, by looking at <br />
our research objectives from a more comprehensive perspective, <br />
we may have some unexpected discoveries.<br />
</p><br />
<br />
<h4 id="features">Features</h4><br />
<div class="underline-small"><br />
</div><br />
<p>Our software has many marvelous features, with which your biology research will become extremely easy and joyful.</p><br />
<ul><br />
<br />
<h5>1. Expansion of single node</h5><br />
<div class="row"><br />
<div class="large-6 columns"><p>In Biopano, every biology part of E.coli K-12 will be displayed as a node of different types and regulation relationship <br />
will be displayed as arc of different types. They are displayed in the biological network in a visualizational way. <br />
You just need to select a node and click “Expand”, and the nodes associated with it will be “expanded”. <br />
Nodes are connected to each other by all kinds of relationship, so users can see how biological parts are connected clearly, <br />
such as LacI Operon. </p></div><br />
<div class="large-6 columns"><img src="https://static.igem.org/mediawiki/2014/4/46/2014ustc-Feature-a.png"></div><br />
</div><br />
<br />
<div class="row"><br />
<div class="large-6 columns"><img src="https://static.igem.org/mediawiki/2014/9/9e/2014ustc-Feature-b.png"></div><br />
<div class="large-6 columns"><p>However, since there are so many biological parts connected to each other in various convoluted, <br />
the expansion of all nodes will give rise to extremely involved nets, which will fail to convey useful information to the users, <br />
even interfere their thoughts. So you can choose to expand the nodes in a way you see fit. Take Transcription factor CRP as an example. </p><br />
<p>Biopano displays the network dynamically, which makes you able to tease out the relationship among thousands of materials of <br />
E.coli K-12, satisfies your curiosity and helps you discover unknown biological field.</p></div><br />
</div><br />
<div class="underline-tiny"></div><br />
<br />
<br />
<br />
<h5>2. Link Finder</h5><br />
<div class="row"><br />
<div class="large-6 columns"><p>You can input two nodes that seem irrelevant, such as gene A and Transcription FactorB, and the software will <br />
search the route connecting the two nodes for you. Since some routes are too sinuous for further analysis or does not make sense, <br />
you can set a specific number k, Biopano will search and show the k shortest routes for you.</p></div><br />
<div class="large-6 columns"><img src="https://static.igem.org/mediawiki/2014/7/79/2014ustc-Feature-c.png"></div><br />
</div><br />
<div class="underline-tiny"></div><br />
<br />
<br />
<h5>3. BLAST</h5><br />
<div class="row"><br />
<div class="large-6 columns"><img src="https://static.igem.org/mediawiki/2014/7/71/2014ustc-Feature-e.png"></div><br />
<div class="large-6 columns"><p>By BLAST method, Biopano finds E.coli K-12 gene highly similar to the injected sequence. <br />
These genes are regulated by other parts in E.coli K-12, so can provide information of the host environment’s impact on injected <br />
exogenous sequence. Biopano also offers BioBrick helper, enabling you search all kinds of BioBricks on iGEM’s official website. <br />
By BLAST analysis, it helps you design correct gene route with appropriate BioBricks.</p></div><br />
</div><br />
<div class="underline-tiny"></div><br />
<br />
<br />
<h5>4. Data Sharing</h5><br />
<p>Hence, while offering various functions, Biopano also serves as a cooperative network building platform. When you create a project, you can add new nodes, name new biological parts and link them with respect to your comprehension to build a brand new net gradually. Meanwhile, Biopano provides log in service. You can sign up with Google or Baidu account and upload your network to the main database to make it more plentiful. Biopano also supports data importing in batch. You can even import data of a species and a database.</p><br />
<ul class="small-block-grid-2"><br />
<li><img src="https://static.igem.org/mediawiki/2014/2/2a/2014ustc-Feature-f.png"></li><br />
<li><img src="https://static.igem.org/mediawiki/2014/5/57/2014ustc-Feature-g.png"></li><br />
</ul><br />
<div class="underline-tiny"></div><br />
<br />
<h5>5. Details and Reference</h5><br />
<p>When you have already got the entire view and want to know more about the details, double-click the nodes and arcs and the details will be shown. More surprisingly, Biopano supports literature reading in the network. You can view literature corresponding to every node and arc along any gene route in the network, and you will understand how the nodes in the net are associated with each other in depth. If you cast doubt on the reliability of our database, you can verify your thought with authoritative literature.</p><br />
<br />
</ul><br />
<p></p><br />
<h4 id="demos">Demo</h4><br />
<div class="underline-small"><br />
</div><br />
<div><br />
<h4>Next we will demonstrate some common modules of E.coli k-12:</h4><br />
<br />
<h5>1, Lac Operon: When you input LacZYA, a Transcription Unit(TU) of Lac Operon and Expand the node:</h5><br />
<p>You will see four promoters, acZp1, lacZp2, lacZp3 and lacZp4 as<br />
upstream sequences and three structure genes, lacZ, lacY and lacA as <br />
downstream sequences. Meanwhile, you can see the TU belongs to <br />
the Operon lacZYA.<br />
</p><br />
<p>Above the node lacZYA, you also see three Transcription<br />
Factors, namely, CRP, H-NS and lacl. They suppress the expression of <br />
lazZYA.</p><br />
<p>Expand lacZ, lacY and lacA, and we get BgaL, LacY and ThgA<br />
respectively, of which Bgal and ThgA are Enzymes. They catalyze<br />
corresponding reactions. Expand Lacl and we get the gene lacl which<br />
codes it.</p><br />
<ul class="small-block-grid-2"><br />
<li><img src="https://static.igem.org/mediawiki/2014/4/47/2014ustc-B.png"></li><br />
<li><img src="https://static.igem.org/mediawiki/2014/e/ee/C.png"></li><br />
</ul><br />
<br />
<p>Continue to Expand lacZYA and lacl and we find more materials’<br />
connected with them. You can select and drag the nodes to arrange the <br />
network neatly; you can also click Full Screen and the network will be <br />
displayed in full screen.</p><br />
<ul class="small-block-grid-2"><br />
<li><img src="https://static.igem.org/mediawiki/2014/c/c5/2014ustc-D.png"></li><br />
<li><img src="https://static.igem.org/mediawiki/2014/3/3a/2014ustc-E.png"></li><br />
</ul><br />
<br />
<h5>2, Following the same steps, we can also get the regulation network of<br />
the Operon Trp.</h5><br />
<img src="https://static.igem.org/mediawiki/2014/9/9d/2014ustc-F.png"><br />
<br />
</div><br />
<br />
<br />
<h4 id="why">Why choose BioPano?</h4><br />
<div class="underline-small"></div><br />
<div><br />
<p> Biopano, do the experiment as you do in the lab.</p><br />
<p>In experiment, synthetic biologists always find gene circuits formed by BioBricks are incompatible with the host cell, thus cannot work as expected. However, Biopano uses sequence alignment to analyze the possible reasons of the failure and design more acute gene circuit for your consideration.</p><br />
<p>Our Blast algorism derives from NCBI. However, the original version only offers sequence alignment and fails to analyze what impact the host environment might have on the injected gene circuit, let along predicts whether it will work.</p><br />
<p>Firstly, Biopano offers BioBrick searching to make it convenient for you to study all standardized biological parts on the official website of iGEM. Secondly, you can input a BioBrick and even construct a brand new sequence. Biopano will find the gene nodes of E.coli K-12 sharing the deepest homology with it based on authoritative Blast algorithm. Then you can Expand these nodes to find out the possible regulation on them. In this way, Biopano helps you analyze whether the injected gene circuit will actually work.</p><br />
<p>Biopano abstracts biological parts and the regulation among them into nodes and arcs to realize data visualization, and displays gene regulation and metabolism network of E.coli K-12 dynamically by continually Expanding nodes. Single database cannot make an entire material network, so our back end combines Regulon DB, KEGG, Uniprot and abundant data. You can ceaselessly Expand the nodes in the network to comb the relationship among them and satisfy your curiosity.</p><br />
<br />
<p>Compared with Biopano, Cytoscape and Netscience mainly support file importing and network displaying without powerful database from the back end. Hence you cannot search for biological parts online and view the certain part of the biological network you need with them.</p><br />
<br />
<p>Now that there is enormous astonishing material relationship in biological body, more and more biologists hope to find the specific function route between two biological parts or even two biological blocks that seem not related to each other, such as c-di-GMP signalling and Quorum Sensing. Unfortunately, the interactions of the biological parts are saved in database as records and it is almost impossible to find the route in thousands of records. There haven’t been any software to offer any help before. Luckily, Biopano brings hope to this.</p><br />
<br />
<p>You can input two biological parts and set several shortest routes, then you will find their relationship. We used this powerful function to find the specific relationship betweem c-di-GMP signalling and Quorum Sensing, which was corroborated by corresponding literature. How amazing!</p><br />
<br />
<p>We have to admit that Biopano may show you wrong gene route. However, it provides you with direction of studying the relationship of two fields. It not only makes your goal for experiment designing clearer, but enables you to understand the connection inside body is so close as well.</p><br />
<br />
<p>While offering function services, Biopano serves as a platform for collaborative network building. You can define new nodes and arcs yourself and sign in with your Google or Baidu account to upload the network you build to our database. You can also invite several companions to complete a project together. Common biological software, such as Cytoscape and Netscience, doesn’t provide a good platform for communication, while Biopano enhances the communication of biological areas by data sharing.</p><br />
<br />
<p>Biopano, your right hand for biological research. Get it now!</p><br />
</div><br />
<br />
<h4 id="futurework">Future Work</h4><br />
<div class="underline-small"></div><br />
<div><br />
<h4>It is undeniable that we still have a lot to do to improve Biopano in many aspects in order to make it even better. We need to think more and develop it as we can. In the future, we hope to:<br />
</h4><br />
<br />
<p>1. Integrate more data in it. Currently, Biopano only integrates data of E.coli k-12 from Regulon DB, KEGG and Uniprot, and our data in regulatory interaction lack accurate numerical data to indicate its strength. etc. Therefore, not only will we update the existing data in the original species, we will also make complement of high-throughput data through other databases and papers, as well as expand information of other species, so that more biological researchers can benefit from our software.</p><br />
<br />
<p>2. Normalize users' rights, improve quality of data. With the increase of the number of users, the data synchronized every day become not only massive, but also in many different forms, and some of them have nevitable errors or redundant information, or there may be different kinds of comprehension of certain regulatory relations. So we want the machine to automatically recognize the validity of the data submitted by the user, and establish a evaluation criteria of credibility. Thus, only those reliable users will be selected, and only their data can be synchronized to the main database, and the redundancy or errors will be eliminated, and they also continue to enhance the credibility and value of the main database.</p><br />
<br />
<p>3. Enhance network analysis functions. When we add the high-throughput kinetic data for biological networks, we can build a variety of mathematical models on the network and carry out quantitative simulation analysis. For example, we can put the nodes that are closely related to one another together in a group. We can make out software automatically arrange the modules for different functions in the organism. We can even do things that are analogic to those in an electric circult. The network provides the entrance and the exit of the signals, and all you need to do is to enter the target product and we will help you find the substance needed for synthesizing it. </p><br />
<br />
<p>4. Supports more file formats. Currently, the file formats we provide to the users are only XML and SBOL. In the future we will make our software support more file formats, such as sif, EMBL, etc., and we will develop its ability to be capable with other biological softwares such as cytoscape and Netscience, seamlessly. You can import and export any file that are constantly used. From this aspect, we will greatly broadens the scope of the functions of the software.</p><br />
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<h5 style="color:#fff;font-weight:bold;margin-bottom: 25px;">Innovation Experiment Centre of Life Science (IEC)</h5><br />
<p>Building of Life Sciences, Room 363</p><br />
<p>University of Science and Technology of China</p><br />
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Hlx1996
http://2014.igem.org/Team:USTC-Software/biopano.php
Team:USTC-Software/biopano.php
2014-10-18T03:37:20Z
<p>Hlx1996: </p>
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<p style="font-size:64px;height:100%;line-height:100%;color:rgb(144,144,144)">Meet Biopano</p><br />
<br />
</div><br />
<div class="row"><br />
<div class="large-12 columns large-centered"><br />
<br />
<p></p><br />
<h4 id="overview">Overview</h4><br />
<div class="underline-small"></div><br />
<p>Designed specifically for biological research, BioPano is a software platform targeted for visualisation of biological relationships as well as cooperative net-building. You can set up your own network of biological relationship by adding information about genetic regulation and metabolic system to the network we already provided for you. Also, the software allows you to explore the links among the substances by just several clicks, and you can even look into the details of the interaction between the exogenous gene and the host. What is even more exciting is that our software will end your loneliness and frustration in research, since it is providing you with cloud cooperating system so that you can view massive amounts of resources in databases, together with build up groups to share information and set up mutual network with others.<br />
</p><br />
<br />
<h4 id="motivation">Motivation</h4><br />
<div class="underline-small"></div><br />
<p><br />
In recent years, people has made a lot of remarkable achievements <br />
in synthetic biology. However, scientists are often faced with <br />
many unpredictable problems when carrying out experiments. <br />
Each kind of biological substance is inextricably linked to the <br />
biological environment to which it belongs, so we have to consider <br />
a question: Can we attain the desired goal, if we simply follow the traditional ideas of synthetic biology and avoid the problem merely by engineering?<br />
</p><br />
<p><br />
A synthetic biologist, Chris Voigt, has successfully transferred a<br />
Toggle Switch, which usually works in the Bacillus <br />
subtilis, into E. coli. Unfortunately, it did not function properly. In <br />
fact, in experiments, due to the unexpected interactions between <br />
BioBrick and the host, it is very common that the designed path do <br />
not work as anticipated.<br />
</p><br />
<p><br />
In fact, the life system is so complex that there are many sorts of <br />
biological substance to support it with complex interations in it. <br />
In order to understand a phenomenon, we keep using new and <br />
sophisticated methods to refine our research and to explore every <br />
detail of life. However, if we widen our perspective, by looking at <br />
our research objectives from a more comprehensive perspective, <br />
we may have some unexpected discoveries.<br />
</p><br />
<br />
<h4 id="features">Features</h4><br />
<div class="underline-small"><br />
</div><br />
<p>Our software has many marvelous features, with which your biology research will become extremely easy and joyful.</p><br />
<ul><br />
<br />
<h5>1. Expansion of single node</h5><br />
<div class="row"><br />
<div class="large-6 columns"><p>In Biopano, every biology part of E.coli K-12 will be displayed as a node of different types and regulation relationship <br />
will be displayed as arc of different types. They are displayed in the biological network in a visualizational way. <br />
You just need to select a node and click “Expand”, and the nodes associated with it will be “expanded”. <br />
Nodes are connected to each other by all kinds of relationship, so users can see how biological parts are connected clearly, <br />
such as LacI Operon. </p></div><br />
<div class="large-6 columns"><img src="https://static.igem.org/mediawiki/2014/4/46/2014ustc-Feature-a.png"></div><br />
</div><br />
<br />
<div class="row"><br />
<div class="large-6 columns"><img src="https://static.igem.org/mediawiki/2014/9/9e/2014ustc-Feature-b.png"></div><br />
<div class="large-6 columns"><p>However, since there are so many biological parts connected to each other in various convoluted, <br />
the expansion of all nodes will give rise to extremely involved nets, which will fail to convey useful information to the users, <br />
even interfere their thoughts. So you can choose to expand the nodes in a way you see fit. Take Transcription factor CRP as an example. </p><br />
<p>Biopano displays the network dynamically, which makes you able to tease out the relationship among thousands of materials of <br />
E.coli K-12, satisfies your curiosity and helps you discover unknown biological field.</p></div><br />
</div><br />
<div class="underline-tiny"></div><br />
<br />
<br />
<br />
<h5>2. Link Finder</h5><br />
<div class="row"><br />
<div class="large-6 columns"><p>You can input two nodes that seem irrelevant, such as gene A and Transcription FactorB, and the software will <br />
search the route connecting the two nodes for you. Since some routes are too sinuous for further analysis or does not make sense, <br />
you can set a specific number k, Biopano will search and show the k shortest routes for you.</p></div><br />
<div class="large-6 columns"><img src="https://static.igem.org/mediawiki/2014/7/79/2014ustc-Feature-c.png"></div><br />
</div><br />
<div class="underline-tiny"></div><br />
<br />
<br />
<h5>3. BLAST</h5><br />
<div class="row"><br />
<div class="large-6 columns"><img src="https://static.igem.org/mediawiki/2014/7/71/2014ustc-Feature-e.png"></div><br />
<div class="large-6 columns"><p>By BLAST method, Biopano finds E.coli K-12 gene highly similar to the injected sequence. <br />
These genes are regulated by other parts in E.coli K-12, so can provide information of the host environment’s impact on injected <br />
exogenous sequence. Biopano also offers BioBrick helper, enabling you search all kinds of BioBricks on iGEM’s official website. <br />
By BLAST analysis, it helps you design correct gene route with appropriate BioBricks.</p></div><br />
</div><br />
<div class="underline-tiny"></div><br />
<br />
<br />
<h5>4. Data Sharing</h5><br />
<p>Hence, while offering various functions, Biopano also serves as a cooperative network building platform. When you create a project, you can add new nodes, name new biological parts and link them with respect to your comprehension to build a brand new net gradually. Meanwhile, Biopano provides log in service. You can sign up with Google or Baidu account and upload your network to the main database to make it more plentiful. Biopano also supports data importing in batch. You can even import data of a species and a database.</p><br />
<ul class="small-block-grid-2"><br />
<li><img src="https://static.igem.org/mediawiki/2014/2/2a/2014ustc-Feature-f.png"></li><br />
<li><img src="https://static.igem.org/mediawiki/2014/5/57/2014ustc-Feature-g.png"></li><br />
</ul><br />
<div class="underline-tiny"></div><br />
<br />
<h5>5. Details and Reference</h5><br />
<p>When you have already got the entire view and want to know more about the details, double-click the nodes and arcs and the details will be shown. More surprisingly, Biopano supports literature reading in the network. You can view literature corresponding to every node and arc along any gene route in the network, and you will understand how the nodes in the net are associated with each other in depth. If you cast doubt on the reliability of our database, you can verify your thought with authoritative literature.</p><br />
<br />
</ul><br />
<p></p><br />
<h4 id="demos">Demo</h4><br />
<div class="underline-small"><br />
</div><br />
<div><br />
<h4>Next we will demonstrate some common modules of E.coli k-12:</h4><br />
<br />
<h5>1, Lac Operon: When you input LacZYA, a Transcription Unit(TU) of Lac Operon and Expand the node:</h5><br />
<p>You will see four promoters, acZp1, lacZp2, lacZp3 and lacZp4 as<br />
upstream sequences and three structure genes, lacZ, lacY and lacA as <br />
downstream sequences. Meanwhile, you can see the TU belongs to <br />
the Operon lacZYA.<br />
</p><br />
<p>Above the node lacZYA, you also see three Transcription<br />
Factors, namely, CRP, H-NS and lacl. They suppress the expression of <br />
lazZYA.</p><br />
<p>Expand lacZ, lacY and lacA, and we get BgaL, LacY and ThgA<br />
respectively, of which Bgal and ThgA are Enzymes. They catalyze<br />
corresponding reactions. Expand Lacl and we get the gene lacl which<br />
codes it.</p><br />
<ul class="small-block-grid-2"><br />
<li><img src="https://static.igem.org/mediawiki/2014/4/47/2014ustc-B.png"></li><br />
<li><img src="https://static.igem.org/mediawiki/2014/e/ee/C.png"></li><br />
</ul><br />
<br />
<p>Continue to Expand lacZYA and lacl and we find more materials’<br />
connected with them. You can select and drag the nodes to arrange the <br />
network neatly; you can also click Full Screen and the network will be <br />
displayed in full screen.</p><br />
<ul class="small-block-grid-2"><br />
<li><img src="https://static.igem.org/mediawiki/2014/c/c5/2014ustc-D.png"></li><br />
<li><img src="https://static.igem.org/mediawiki/2014/3/3a/2014ustc-E.png"></li><br />
</ul><br />
<br />
<h5>2, Following the same steps, we can also get the regulation network of<br />
the Operon Trp.</h5><br />
<img src="https://static.igem.org/mediawiki/2014/9/9d/2014ustc-F.png"><br />
<iframe width="560" height="315" src="//www.youtube.com/embed/79uuj5hXsOg" frameborder="0" allowfullscreen></iframe><br />
<br />
</div><br />
<br />
<br />
<h4 id="why">Why choose BioPano?</h4><br />
<div class="underline-small"></div><br />
<div><br />
<p> Biopano, do the experiment as you do in the lab.</p><br />
<p>In experiment, synthetic biologists always find gene circuits formed by BioBricks are incompatible with the host cell, thus cannot work as expected. However, Biopano uses sequence alignment to analyze the possible reasons of the failure and design more acute gene circuit for your consideration.</p><br />
<p>Our Blast algorism derives from NCBI. However, the original version only offers sequence alignment and fails to analyze what impact the host environment might have on the injected gene circuit, let along predicts whether it will work.</p><br />
<p>Firstly, Biopano offers BioBrick searching to make it convenient for you to study all standardized biological parts on the official website of iGEM. Secondly, you can input a BioBrick and even construct a brand new sequence. Biopano will find the gene nodes of E.coli K-12 sharing the deepest homology with it based on authoritative Blast algorithm. Then you can Expand these nodes to find out the possible regulation on them. In this way, Biopano helps you analyze whether the injected gene circuit will actually work.</p><br />
<p>Biopano abstracts biological parts and the regulation among them into nodes and arcs to realize data visualization, and displays gene regulation and metabolism network of E.coli K-12 dynamically by continually Expanding nodes. Single database cannot make an entire material network, so our back end combines Regulon DB, KEGG, Uniprot and abundant data. You can ceaselessly Expand the nodes in the network to comb the relationship among them and satisfy your curiosity.</p><br />
<br />
<p>Compared with Biopano, Cytoscape and Netscience mainly support file importing and network displaying without powerful database from the back end. Hence you cannot search for biological parts online and view the certain part of the biological network you need with them.</p><br />
<br />
<p>Now that there is enormous astonishing material relationship in biological body, more and more biologists hope to find the specific function route between two biological parts or even two biological blocks that seem not related to each other, such as c-di-GMP signalling and Quorum Sensing. Unfortunately, the interactions of the biological parts are saved in database as records and it is almost impossible to find the route in thousands of records. There haven’t been any software to offer any help before. Luckily, Biopano brings hope to this.</p><br />
<br />
<p>You can input two biological parts and set several shortest routes, then you will find their relationship. We used this powerful function to find the specific relationship betweem c-di-GMP signalling and Quorum Sensing, which was corroborated by corresponding literature. How amazing!</p><br />
<br />
<p>We have to admit that Biopano may show you wrong gene route. However, it provides you with direction of studying the relationship of two fields. It not only makes your goal for experiment designing clearer, but enables you to understand the connection inside body is so close as well.</p><br />
<br />
<p>While offering function services, Biopano serves as a platform for collaborative network building. You can define new nodes and arcs yourself and sign in with your Google or Baidu account to upload the network you build to our database. You can also invite several companions to complete a project together. Common biological software, such as Cytoscape and Netscience, doesn’t provide a good platform for communication, while Biopano enhances the communication of biological areas by data sharing.</p><br />
<br />
<p>Biopano, your right hand for biological research. Get it now!</p><br />
</div><br />
<br />
<h4 id="futurework">Future Work</h4><br />
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<h4>It is undeniable that we still have a lot to do to improve Biopano in many aspects in order to make it even better. We need to think more and develop it as we can. In the future, we hope to:<br />
</h4><br />
<br />
<p>1. Integrate more data in it. Currently, Biopano only integrates data of E.coli k-12 from Regulon DB, KEGG and Uniprot, and our data in regulatory interaction lack accurate numerical data to indicate its strength. etc. Therefore, not only will we update the existing data in the original species, we will also make complement of high-throughput data through other databases and papers, as well as expand information of other species, so that more biological researchers can benefit from our software.</p><br />
<br />
<p>2. Normalize users' rights, improve quality of data. With the increase of the number of users, the data synchronized every day become not only massive, but also in many different forms, and some of them have nevitable errors or redundant information, or there may be different kinds of comprehension of certain regulatory relations. So we want the machine to automatically recognize the validity of the data submitted by the user, and establish a evaluation criteria of credibility. Thus, only those reliable users will be selected, and only their data can be synchronized to the main database, and the redundancy or errors will be eliminated, and they also continue to enhance the credibility and value of the main database.</p><br />
<br />
<p>3. Enhance network analysis functions. When we add the high-throughput kinetic data for biological networks, we can build a variety of mathematical models on the network and carry out quantitative simulation analysis. For example, we can put the nodes that are closely related to one another together in a group. We can make out software automatically arrange the modules for different functions in the organism. We can even do things that are analogic to those in an electric circult. The network provides the entrance and the exit of the signals, and all you need to do is to enter the target product and we will help you find the substance needed for synthesizing it. </p><br />
<br />
<p>4. Supports more file formats. Currently, the file formats we provide to the users are only XML and SBOL. In the future we will make our software support more file formats, such as sif, EMBL, etc., and we will develop its ability to be capable with other biological softwares such as cytoscape and Netscience, seamlessly. You can import and export any file that are constantly used. From this aspect, we will greatly broadens the scope of the functions of the software.</p><br />
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<p>University of Science and Technology of China</p><br />
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Hlx1996
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2014-10-18T03:34:29Z
<p>Hlx1996: </p>
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<div class = "details"><img src="https://static.igem.org/mediawiki/2014/6/62/2014ustc-Xyc.jpg" alt="Xue Yuechuan" align="left"><p>Team Leader<br>Junior of physical electronics major<br>His work: team leading and art design.</p><br />
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<div class = "details"><img src="https://static.igem.org/mediawiki/2014/6/6e/2014ustc-Glz.jpg" alt="Gan Longzhi" align="left"><p>Team Manager<br>Sophomore from School of Earth and Space Science<br>His work: team managing web editing and document writing<br>His words: Try hard, have fun.</p><br />
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<div class = "details"><img src="https://static.igem.org/mediawiki/2014/d/d0/2014ustc-Zzy.jpg" alt="Zhang Zhiyuan" align="left"><p>Member<br>Senior of Hua Loo-Keng Talent Program in Mathematics, majoring in fundamental mathematics<br>translation and document writing<br>Her words: To see, to ask, to search, to believe.</p><br />
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<div class = "details"><img src="https://static.igem.org/mediawiki/2014/7/7d/2014ustc-Gyf.jpg" alt="Yifan Gao" align="left"><p>Member<br>Junior of optics major<br>His work: back end work<br>His words: Perfection is achieved not when there is nothing more to add, but rather when there is nothing more to take away.</p><br />
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<div class = "details"><img src="https://static.igem.org/mediawiki/2014/4/4b/2014ustc-Dcx.jpg" alt="Dong Chenxiao" align="left"><p>Member<br>Sophomore from School of Physics Science<br>His work: data hunting and organizing, software design and document writing<br>His words: All the time, try retorting any idea from team.</p><br />
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<div class = "details"><img src="https://static.igem.org/mediawiki/2014/2/28/2014ustc-Jzy.jpg" alt="Haiyan Liu" align="left"><p>Member<br>Sophomore from School of Earth and Space Science<br>His work: data hunting and organizing, software design and document writing<br>His words: Not most powerful, but highly responsible!</p><br />
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<img src="https://static.igem.org/mediawiki/2014/9/97/2014ustc-Zl.jpg" alt="Haiyan Liu"><br />
<div class ="nameplate"><a href="#">Zhou Long</a></div><br />
<div class = "details"><img src="https://static.igem.org/mediawiki/2014/9/97/2014ustc-Zl.jpg" alt="Haiyan Liu" align="left"><p>Member<br>Junior of nuclear physics major<br>His work: front end work<br>His words: Simply Enjoy.</p><br />
</div><br />
</li><br />
<br />
<li class ="profilewrap"><br />
<img src="https://static.igem.org/mediawiki/2014/a/a1/2014ustc-Hlx.jpg" alt="Han Luxin"><br />
<div class ="nameplate"><a href="#">Han Luxin</a></div><br />
<div class = "details"><img src="https://static.igem.org/mediawiki/2014/a/a1/2014ustc-Hlx.jpg" alt="Han Luxin" align="left"><p>Member who is <b>MOST HANDSOME</b><br>Sophomore from School for the Gifted Young, majoring in computer science<br>His work: algorithm design and writing and web editing<br>His words: Where there is a will, there is a way.</p><br />
</div><br />
</li><br />
<br />
<li class ="profilewrap"><br />
<img src="https://static.igem.org/mediawiki/2014/8/8d/2014ustc-Ycp.jpg" alt="Yu Chuanping"><br />
<div class ="nameplate"><a href="#">Yu Chuanping</a></div><br />
<div class = "details"><img src="https://static.igem.org/mediawiki/2014/8/8d/2014ustc-Ycp.jpg" alt="Yu Chuanping" align="left"><p>Member<br>Senior of statistics major<br>Her work: translation<br>Her words: Do one thing at a time, and do well.</p><br />
</div><br />
</li><br />
<br />
<li class ="profilewrap"><br />
<img src="https://static.igem.org/mediawiki/2014/4/44/2014ustc-Zhy.jpg" alt="Zhang Huayu"><br />
<div class ="nameplate"><a href="#">Zhang Huayu</a></div><br />
<div class = "details"><img src="https://static.igem.org/mediawiki/2014/4/44/2014ustc-Zhy.jpg" alt="Zhang Huayu" align="left"><p>Member<br>Sophomore from School of Physics Science<br>His work: front end work<br>His words: Be the best yourself, to be No.1. </p><br />
</div><br />
</li><br />
<br />
</li><br />
<br />
<li class ="profilewrap"><br />
<img src="https://static.igem.org/mediawiki/2014/9/96/2014ustc-Fyc.jpg" alt="Haiyan Liu"><br />
<div class ="nameplate"><a href="#">Fei Yicheng</a></div><br />
<div class = "details"><img src="https://static.igem.org/mediawiki/2014/9/96/2014ustc-Fyc.jpg" alt="Haiyan Liu" align="left"><p>Member<br>Sophomore from School of Physics Science<br>His work: back end work<br>His words: Be the best yourself, to be No.1. </p><br />
</div><br />
</li><br />
<br />
<li class ="profilewrap"><br />
<img src="https://static.igem.org/mediawiki/2014/b/bc/2014ustc-Ctl.jpg" alt="Chen Tianlong"><br />
<div class ="nameplate"><a href="#">Chen Tianlong</a></div><br />
<div class = "details"><img src="https://static.igem.org/mediawiki/2014/b/bc/2014ustc-Ctl.jpg" alt="Chen Tianlong" align="left"><p>Member<br>Sophomore of mathematics major<br>His work: web design<br>His words: Be the best yourself, to be No.1. </p><br />
</div><br />
</li><br />
<br />
<li class ="profilewrap"><br />
<img src="https://static.igem.org/mediawiki/2014/3/36/2014ustc-Clf.jpg" alt="Chen Lingfan"><br />
<div class ="nameplate"><a href="#">Chen Lingfan</a></div><br />
<div class = "details"><img src="https://static.igem.org/mediawiki/2014/3/36/2014ustc-Clf.jpg" alt="Chen Lingfan" align="left"><p>Member<br>Junior of computational mathematics major<br>His work: algorithm design<br>His words: Study in USTC, work in USTC, and make friends in USTC.</p><br />
</div><br />
</li><br />
<br />
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<h4 id="I_A">Instructors & Advisors</h4><br />
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<img src="https://static.igem.org/mediawiki/2014/d/de/2014ustc-G.png" alt="Haiyan Liu"><br />
<div class ="nameplate"><a href="#">Haiyan Liu</a></div><br />
<div class = "details"><img src="https://static.igem.org/mediawiki/2014/d/de/2014ustc-G.png" alt="Haiyan Liu" ><br />
<p><b>Email:</b>hyliu@ustc.edu.cn</p><br />
<p><b>Brief Intro:</b>Haiyan Liu was born in Sichuan Province, China. He received his BS degree in Biology in 1990 and PhD degree in Biochemistry and Molecular Biology in 1996, both from USTC. Between 1993 and 1995 he was a visiting graduate student in Laboratory of Physical Chemistry of ETH, Zurich (Switzerland). From 1998 to 2000 he was post-doctoral research associate at Department of Chemistry, Duke University (USA) and Department of Biochemistry and Biophysics UNC-Chapel Hill (USA). Since 2001, he has been a professor of computational biology at School of Life Sciences, USTC.</p><br />
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</li><br />
<br />
<br />
<li class ="profilewrap"><br />
<img src="https://static.igem.org/mediawiki/2014/a/af/2014ustc-H.png" alt="Zhi Liang"><br />
<div class ="nameplate"><a href="#">Zhi Liang</a></div><br />
<div class = "details"><img src="https://static.igem.org/mediawiki/2014/a/af/2014ustc-H.png" alt="Zhi Liang" ><br />
<p><b>Email:</b>liangzhi@ustc.edu.cn</p><br />
<p><b>Brief Intro:</b>Liang Zhi, Ph.D., Associate Professor Extraordinary . 2000 graduated from the school of Life Sciences in the University of Science and Technology of China, received bachelor's degree in biology and electronics and information engineering dual degree. 2006 graduated from the school of Life Sciences in the University of Science and Technology of China protein crystallography laboratory , PhD. From 2007 to 2012 in the school of Life Sciences in the University of Science and Technology of China Systems Biology Laboratory in systems biology postdoctoral research. Postdoctoral period has won China Postdoctoral Science Foundation funded second and Natural Science Foundation funding. 2012 University of Science and Technology of China Extraordinary Life Sciences Research Associate . Research results published on Nucleic Acids Res, Bioinformatics, Bioinformatics, J Biol Chem.</p><br />
</div><br />
</li><br />
<br />
<li class ="profilewrap"><br />
<img src="https://static.igem.org/mediawiki/2014/9/93/2014ustc-I.png"><br />
<div class ="nameplate"><a href="#">Jiong Hong</a></div><br />
<div class = "details"><img src="https://static.igem.org/mediawiki/2014/9/93/2014ustc-I.png" alt="Jiong Hong" ><br />
<p>Professor, School of Life Sciences University of Science & Technology of China</p><br />
<p><br />
<b>Email:</b> hjiong@ustc.edu.cn<br /><br /><br />
<b>Brief Intro:</b>Jiong Hong was born in Anhui Province, China. He received his BS degree in 1993 from Anhui Normal University, MSc degree in 1996 from Beijing Normal University, and Ph.D degree in 2003 from Kyoto University, all in Life Sciences. From 2006 to 2008, he did post-doctoral research in Virginia Tech University, USA. Since 2008, he has been introduced to the USTC as talented.<br />
</p><br />
</div><br />
</li><br />
<br />
<br />
<li class ="profilewrap"><br />
<img src="https://static.igem.org/mediawiki/2014/9/92/2014ustc-J.png" alt="Fan Jin"><br />
<div class ="nameplate"><a href="#">Fan Jin</a></div><br />
<div class = "details"><img src="https://static.igem.org/mediawiki/2014/9/92/2014ustc-J.png" alt="Fan Jin" ><br />
<br />
<br /><br /><br />
<p>1997.07-2002.07 B.S., Student, Department of Applied Chemistry, University of Science & Technology of China, P. R. China.<br />
Degree awarded: B.S. in chemistry, 07/2002</p><br />
<br />
<p>2003.08-2007.06 Ph.D. Candidate, Department of Chemistry, The Chinese University of Hong Kong.<br />
Degree awarded: Ph.D in chemistry, 06/2007</p><br />
<br />
<p>2002.07-2003.07 R.A., The Hefei National Laboratory of Physical Science at Microscale, Department of Chemical Physics, University of Science & Technology of China, P. R. China.</p><br />
<br />
<p>2007.06-2009.01 Postdoctoral Associate, Department of Chemistry, The Chinese University of Hong Kong.</p><br />
<br />
<p>2009.01-2009.11 Postdoctoral Associate, Department of Materials Science and Engineering, University of Illinois at Urbana Champaign.</p><br />
<br />
<p>2009.11-2011.8 Postdoctoral Associate, Department of Bioengineering, California Nanosystems Institute, University of California, Los Angeles. </p><br />
<br />
<p>2011.8-present Professor, Department of Polymer Materials Science and Engineering, University of Science and Technology of China, CAS Key Lab of Soft Matter Chemistry. </p><br />
<br />
<h4>Research Interests</h4><br />
<p>Polyelectrolyte and colloidal particles in the oil-water interface. </p><br />
<p>Interaction between Antibiotic peptides and lipids membrane. </p><br />
<p>Living cell image and living cell micro-manipulation.</p><br />
<p>Biological macromolecules, characterization of supramolecular assembly and its applications in drug delivery and gene transfection. </p><br />
<p>Bacterial communities. (Ex: signaling, motility, social organization in biofilms)</p><br />
<br />
<br />
<br />
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</ul><br />
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<br />
<br />
<h4 id="Additional_thanks">Additional Thanks</h4><br />
<div class="underline-small"><br />
<br />
</div><br />
<div style="line-height:200%"><br />
<li><br />
Thanks for financial assistance from Deutsche Bank, USTCIF and USTC Teaching Affair Office. Only with their help could we finish the competition;<br />
</li><br />
<li><br />
Thank data from RegulonDB, KEGG, Uniprot and NCBI. Only with their data and apis could we refine our database; <br />
</li><br />
<li><br />
Thank project guidance from Haiyan Liu, Zhi Liang, Fan Jin and Jiong Hong. Only with their guidance could our project be improved and deepened; <br />
</li><br />
<li><br />
Thank Chen Liao for participating in the use, evaluation and popularization of Biopano.He pointed out many deficiencies and bugs of our software.<br />
</li><br />
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Hlx1996
http://2014.igem.org/Team:USTC-Software/requirements.php
Team:USTC-Software/requirements.php
2014-10-18T03:27:54Z
<p>Hlx1996: </p>
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<p style="font-size:32px">Requirements</p><br />
<br />
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<h4 id="medals">Medals</h4><br />
<div class="underline-small"><br />
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<h4><img src="https://static.igem.org/mediawiki/2014/4/4c/2014ustc-Bronze.png" width="60" height="60" alt="Bronze" >Bronze</h4><br />
<p> The following 4 goals must be achieved:</p><br />
<br />
<br />
<br />
<h5><img src="https://static.igem.org/mediawiki/2014/c/c1/Hfut-A.png" width="30" height="30" alt="Complete" ><br />
Register the team, have a great summer, and have fun attending the Jamboree in Boston.<br />
</h5><br />
<br />
<br />
<br />
<br />
<h5><img src="https://static.igem.org/mediawiki/2014/c/c1/Hfut-A.png" width="30" height="30" alt="Complete" ><br />
Create and share a description of the team's project via the iGEM wiki.<br />
</h5><br />
<br />
<br />
<br />
<br />
<h5><img src="https://static.igem.org/mediawiki/2014/c/c1/Hfut-A.png" width="30" height="30" alt="Complete" ><br />
Present a Poster and Talk at the Regional Jamboree and World Championship Jamboree.<br />
</h5><br />
<br />
<br />
<br />
<br />
<h5><img src="https://static.igem.org/mediawiki/2014/c/c1/Hfut-A.png" width="30" height="30" alt="Complete" ><br />
Develop and make available via The Registry of Software Tools, an open source software tool that supports Synthetic Biology based on Standard Parts.<br />
</h5><br />
You can directly enter the precise number of Standard Part, you can get its all types in BioBrick Assistant Windows.<br />
<div class="large-12 columns text-center"><br />
<img style="margin:1em" src="https://static.igem.org/mediawiki/2014/c/ce/2014ustc-medal1.png"><br />
</div> <br />
<p>&nbsp;</p><br />
<br />
<div class="underline-tiny"></div> <br />
<br />
<h4><img src="https://static.igem.org/mediawiki/2014/c/c6/2014ustc-Silver.png" width="60" height="60" alt="Sliver" >Silver</h4><br />
<p> In addition to the Bronze Medal requirements, the following 4 goals must be achieved:</p><br />
<br />
<br />
<br />
<br />
<h5><img src="https://static.igem.org/mediawiki/2014/c/c1/Hfut-A.png" width="30" height="30" alt="Complete" ><br />
Demonstrate the relevance of your development for Synthetic Biology based on standard Parts.<br />
</h5><br />
<p>You can directly enter the precise number of Standard Part, you can get its types in BioBrick Assistant Windows .then you can use blast tool with the sequence from BioBrick Assistant.By comparing the homology between the sequence of the part and in our database, we could predict its impact on the target body when injected to some extent.</p><br />
<div class="large-12 columns text-center"><br />
<img style="margin:1em" src="https://static.igem.org/mediawiki/2014/e/ee/2014ustc-medal2.png"><br />
</div><br />
<br />
<br />
<br />
<br />
<br />
<h5><img src="https://static.igem.org/mediawiki/2014/c/c1/Hfut-A.png" width="30" height="30" alt="Complete" ><br />
Provide a comprehensive and well-designed User Guide. (Be creative! An instructional video may work as well.)<br />
</h5><br />
<p>We have a complete user manual <a href="http://www.biopano.org/biopanohelp.pdf">here!</a></p><br />
<br />
<br />
<br />
<br />
<h5><img src="https://static.igem.org/mediawiki/2014/c/c1/Hfut-A.png" width="30" height="30" alt="Complete" ><br />
Provide detailed API documentation, preferably, automatically built from source code documentation (use tools like doxygen, yard, rdoc, naturaldocs, etc).<br />
</h5><br />
<p>We use toc to automatically produce api document. <a href="http://www.biopano.org/api.html">Here!</a></p><br />
<br />
<br />
<br />
<br />
<h5><img src="https://static.igem.org/mediawiki/2014/c/c1/Hfut-A.png" width="30" height="30" alt="Complete" ><br />
Demonstrate that you followed best practises in software development so that other developers can modify, use and reuse your code. Provide more than one realistic test case. Examples of best practices are automated unit testing and documentation of test coverage , bug tracking facilities, documentation of releases and changes between releases.<br />
</h5><br />
<p><b><a href="http://bug.biopano.org">Problem feedback and bug tracking</a>:</b> You can cast inquiry on us by GitHub, GitLab and YouTrack. Meanwhile, YouTrack is also used for bug tracking, ensuring your feedback goes to the developer as soon as possible. <br />
<br /><br /><br />
<b><a href="http://ci.biopano.org"> Automated Deployment</a>:</b> Our server has automated deployment capabilities. Server-side applications are bound with the Product branch of Git. All codes pushed to the Product branch will be deployed to many servers over the world in ten seconds. In order to prevent fault codes from being deployed to the servers by mistake, all the testing branches will be deployed to the testing server real-timely to be tested by developers.<br />
<br /><br /><br />
<b>Unit Testing:</b> Our server applies automated unit testing to dealing with uploaded back end codes. It will test the basic legitimacy and function of the codes, including robustness testing with respect to illegitimate uploaded parameters, legitimacy testing on data legitimacy, status testing of the database and testing of function realizaton, etc.</p><br />
<br />
<p>&nbsp;</p><br />
<div class="underline-tiny"></div><br />
<h4><img src="https://static.igem.org/mediawiki/2014/8/88/2014ustc-Gold.png" width="60" height="60" alt="Gold" >Gold</h4><br />
<p> In addition to the Bronze and Silver Medal requirements, two additional goals must be achieved:</p><br />
<br />
<br />
<br />
<br />
<h5><img src="https://static.igem.org/mediawiki/2014/c/c1/Hfut-A.png" width="30" height="30" alt="Complete" ><br />
Provide a convincing validation, testing the performance of the development -- experimentally (can be outsourced) or by other teams and users. Note, even if the algorithm or tool turns out not to work that well, the Gold requirement is fulfilled if the test is good and the analysis convincing. Validation may include: preferably experiments, informatics analysis (complexity, run time) of an algorithm, or user studies.<br />
</h5><br />
<p><b>Analysis of pathway finder (k-shortest pathway search):</b><br /><br />
We use a specail heuristic algorithm , <a href="http://en.wikipedia.org/wiki/A*_search_algorithm">A* search algorithm</a>, to find more than one path connected two nodes in a given network.The run time of A* depends on structure of the given network. The space complexity is the number of edges plus the number of nodes. In our back end, we test this algorithm. The average of time which database reading costs is 1"40, the average of time which Vars initialization costs is 0"70, the average of time which <a href="http://en.wikipedia.org/wiki/Shortest_Path_Faster_Algorithm">SPFA(abbreviation for Shortest Path Faster Algorithm)</a> costs is 0"37, and the average of time which Serialize costs is 0"21.</p> <br />
<br />
<br />
<h4><br />
And the second goal can be any one of the following:<br />
</h4><br />
<br />
<br />
<br />
<br />
<h5><img src="https://static.igem.org/mediawiki/2014/c/c1/Hfut-A.png" width="30" height="30" alt="Complete" ><br />
Make your software interact / interface with the Registry.<br />
</h5><p>You can directly enter the precise number of Standard Part, you can get its types in BioBrick Assistant Windows .then you can use blast tool with the sequence from BioBrick Assistant.By comparing the homology between the sequence of the part and in our database, we could predict its impact on the target body when injected to some extent.</p><br />
<br />
<div class="large-12 columns text-center"><br />
<img style="margin:1em" src="https://static.igem.org/mediawiki/2014/c/ce/2014ustc-medal1.png"><br />
</div><br />
<br />
<br />
<br />
<br />
<h5><img src="https://static.igem.org/mediawiki/2014/c/c1/Hfut-A.png" width="30" height="30" alt="Complete" ><br />
Re-use and further develop previous iGEM software projects (or parts thereof) or use and/or improvement of existing synthetic biology tools or frameworks.<br />
</h5><br />
<p>We use blast code from <a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi">ncbi </a>to comparing the homology.</p><br />
<br />
<br />
<br />
<br />
<br />
<h5><img src="https://static.igem.org/mediawiki/2014/c/c1/Hfut-A.png" width="30" height="30" alt="Complete" ><br />
Develop a well documented library or API for other developers (rather than “only” a stand-alone app for end users.)<br />
</h5><br />
<p>We use toc to automatically produce api document. <a href="http://www.biopano.org/docs/">Here!</a></p><br />
<br />
<br />
<br />
<br />
<h5><img src="https://static.igem.org/mediawiki/2014/c/c1/Hfut-A.png" width="30" height="30" alt="Complete" ><br />
Support and use the SBOL and / or SBOLv standard.<br />
</h5><br />
<p>Biopano supports file format conversion to sbol perfectly.</p><br />
<div class="large-12 columns text-center"><br />
<img style="margin:1em" src="https://static.igem.org/mediawiki/2014/d/dd/2014ustc-medal3.png"><br />
</div><br />
<br />
<p></p><br />
<h4 id="safety">Safety</h4><br />
<div class="underline-small"> </div><br />
<h5>1. Are you using the iGEM Software repository at github.com/igemsoftware? If you have instead stored your code elsewhere, please explain where and why you have put it there. If your code is not in the iGEM repository, a re you using any version control system such as Git, CVS, or SVN?<br />
</h5><br />
<p>Yes, we use the iGEM Software repository at github.com/igemsoftware.<br />
</p><br />
<h5> 2. Does your software store any private data supplied by the user? (For example: the user's name and email address, passwords, DNA sequences, circuit designs, etc.) If yes, please describe what kind of data is stored. If no, skip the rest of this question and move on to question 3.<br />
</h5><br />
<p>We store the user's name, the email address (if he/she logs in using Gmail account) or the username (if logged in using Baidu account), and the user's all data designed with our software.<br />
Especially, we DO NOT store the user's password because we only allow users to log in with their Gmail account or Baidu account using OAuth2.0 ,<br />
which is a very secure protocol describing a third-party login pattern.<br />
</p><br />
<h5>3. Does your software include any other security features? Please describe them here. </h5><br />
<p><br />
We use OAuth technology in user system. So users can log in with their GOOGLE account or BAIDU account without telling us their passwords.<br />
</p> <br />
<h5> 4. Does your software let the user create a design by choosing parts/genes from a list/database, such as the Registry? If so, which lists/databases are included? Is there any restriction on which parts/ genes the user can choose?</h5><br />
<p> <br />
Yes, users can use database built by our team to assist themself to create a design. The database we build is the result of merging and reforming parts of KEGG, RegulonDB, Uniport.<br />
</p><br />
<h5>5. Does your software allow users to write new data into any public lists or databases? If so, do you check the new data for errors before allowing it to be written?</h5><br />
<p><br />
Yes, users can upload their data to our database anytime.<br /><br />Yes, we will check validation and format of data before it is written in the back end.<br />
</p><br />
<h5>6. Does your software include any other features that encourage the user to create safe designs? Please describe them. </h5><br />
<p>No.</p><br />
<br />
<h5>7. Is your team also doing biological work in a wet lab ? </h5><br />
<p>No.</p><br />
<p></p><br />
<h4 id="collaboration">Collaboration</h4><br />
<div class="underline-small"><br />
<br />
</div><br />
<p>While preparing for iGEM, we always hope we can accomplish more and more people can join this great project. Luckily, by cooperation with others, all these hopes come ture.</p><br />
<li>Collaboration with professors</li> <br />
<p></p><br />
<p>While completing our project, we encountered all kinds of problems, of which some could hardly solve by ourselves. We solved them by discussing and cooperating with many professors of USTC. At the same time, we knew more about the original thoughts of synthetic biological researchers. So we tried to combine their needs and our project, hoping we could also help them. Now, we believe that we realized our original intention.</p><br />
<li>Collaboration with Chinese iGEMers</li><br />
<p></p><br />
<p>One reason why iGEM competition is unforgettable is that it makes us know more like-minded people. This year, we hoped iGEM teams could communicate more with each other, so we organized iGEM meetup this summer. Teams from China got familiar through the meetup, and we kept in touch after it. We not only got to know each other by frequent communication, but helped each other with their problems to bring about good results for us all as well.</p><br />
<li>Collaboration with HFUT_CHINA</li><br />
<p></p><br />
<p>While enjoying iGEM, we hoped more people could join us. This year, HFUT_CHINA sent a team for iGEM for the first time. As a team new to iGEM, it would surely encounter more problems. As their neighbor, we kept in touch with them and did everything we could to help them with their project. Through the course, we got to know a lot of people enthusiastic about iGEM of our age. We are glad that they also join iGEM.</p><br />
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</div><br />
<div class="large-6 medium-6 columns" style="color:#fff"><br />
<h5 style="color:#fff;font-weight:bold;margin-bottom: 25px;">Innovation Experiment Centre of Life Science (IEC)</h5><br />
<p>Building of Life Sciences, Room 363</p><br />
<p>University of Science and Technology of China</p><br />
<p>96, Jinzhai Rd, Shushan, Hefei</p><br />
<p>230026, Anhui, China</p><br />
<p>support@biopano.org</p><br />
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Hlx1996
http://2014.igem.org/Team:USTC-Software/api.html
Team:USTC-Software/api.html
2014-10-18T03:23:17Z
<p>Hlx1996: </p>
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<title>API document</title><br />
<script type="text/x-mathjax-config">MathJax.Hub.Config({tex2jax:{inlineMath:[['$$$','$$$']]}});</script><script src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><br />
</head><br />
<body><br />
<h1>API document</h1><br />
<br />
<h2>Instruction</h2><br />
<br />
<p>All the following API(expect OAUTH) must have Authorization parameter in Http Header.</p><br />
<br />
<pre><code> Authorization: Token 13sdfs32fsadf <br />
</code></pre><br />
<br />
<blockquote><p>The default response is in json, if you want the response in other format, please add parameter "format=XML", "format=YAML", etc.</p></blockquote><br />
<br />
<p>If anything goes south, you will get a error response:</p><br />
<br />
<pre><code>{<br />
'status': 'error',<br />
'reason': '&lt;err_reason&gt;',<br />
}<br />
</code></pre><br />
<br />
<h2>DIRECTORY</h2><br />
<br />
<pre><code>POST /auth/oauth/(baidu|google)/login<br />
GET /auth/oauth/(baidu|google)/complete&amp;...<br />
#GET /user/&lt;uid&gt;<br />
<br />
<br />
GET /project/project # list my project<br />
POST /project/project # add<br />
<br />
GET /project/&lt;pid&gt; # login<br />
PUT /project&lt;pid&gt; # modify<br />
DELETE /project&lt;pid&gt; # delete<br />
<br />
POST /project/&lt;pid&gt;/collaborator/&lt;uid&gt; <br />
DELETE /project/&lt;pid&gt;/collaborator/&lt;uid&gt;<br />
<br />
<br />
GET /data/(node|link)/&lt;id&gt;<br />
POST /data/(node|link)<br />
DELETE /data/(node|link)/&lt;ref_id&gt;<br />
PATCH /data/node/&lt;ref_id&gt;<br />
PUT /data/(node|link)/&lt;id&gt;<br />
<br />
GET /data/project/&lt;pid&gt;<br />
</code></pre><br />
<br />
<blockquote><p>GET /data/(node|link)/&lt;ref_id>/link<br />
@zhaosensen</p></blockquote><br />
<br />
<pre><code>POST /search/(node|link)<br />
POST /search/user<br />
POST /search/project<br />
<br />
POST /algorithm/shortestpath<br />
POST /algorithm/blastn<br />
</code></pre><br />
<br />
<h2>OAUTH LOGIN:</h2><br />
<br />
<p>request:</p><br />
<br />
<pre><code>POST /auth/oauth/(baidu|google)/login<br />
</code></pre><br />
<br />
<p>When the user login in sucessfully, the pages will redict to the /auth/oauth/&lt;baidu|google>/complete</p><br />
<br />
<h2>OAUTH COMPLETE</h2><br />
<br />
<p>request(automaticlly):</p><br />
<br />
<pre><code>GET /auth/oauth/(baidu|google)/complete&amp;....<br />
</code></pre><br />
<br />
<p>success :</p><br />
<br />
<pre><code>{<br />
"status": "success",<br />
"token": "16517d0809f225b7b65a79ef1dc8c552441bf58a", <br />
"uid": 8,<br />
"googleid": "zhoulong6@gmail.com",<br />
[或者"baiduid": "347238434"]<br />
} <br />
</code></pre><br />
<br />
<h2>LIST PROJECT</h2><br />
<br />
<p>request:</p><br />
<br />
<pre><code>GET .org/project/project (**没有s**)<br />
</code></pre><br />
<br />
<p>response:</p><br />
<br />
<pre><code>{ <br />
'status':'success',<br />
'resultes': <br />
[<br />
...<br />
]<br />
}<br />
</code></pre><br />
<br />
<h2>ADD PROJECT</h2><br />
<br />
<p>request:</p><br />
<br />
<pre><code>POST .org/project/project<br />
<br />
prj_name:&lt;string&gt;<br />
[species:&lt;string&gt;]<br />
[description:&lt;string&gt;]<br />
</code></pre><br />
<br />
<p>response:</p><br />
<br />
<pre><code>{<br />
'status':'success',<br />
'pid':...<br />
}<br />
</code></pre><br />
<br />
<h2>PROJECT INFO</h2><br />
<br />
<p>request:</p><br />
<br />
<pre><code>GET .org/project/&lt;pid&gt;<br />
</code></pre><br />
<br />
<p>success response:</p><br />
<br />
<pre><code>{<br />
'status': 'success',<br />
'result':<br />
{<br />
'pid':....,<br />
'prj_name':...,<br />
'author':...,<br />
'authorid':...,<br />
'species':...,<br />
'description':...,<br />
'collaborators':<br />
[1, 5, ...<br />
]<br />
}<br />
}<br />
</code></pre><br />
<br />
<h2>DELETE PROJECT</h2><br />
<br />
<p>request:</p><br />
<br />
<pre><code>DELETE .org/project/&lt;pid&gt;<br />
</code></pre><br />
<br />
<p>response:</p><br />
<br />
<pre><code>{<br />
'status':'success'<br />
}<br />
</code></pre><br />
<br />
<h2>MODIFY PROJECT</h2><br />
<br />
<p>request:</p><br />
<br />
<pre><code>PUT .org/project/&lt;pid&gt;<br />
request体(类似POST):<br />
<br />
name : ...,<br />
species: ...,<br />
description:...<br />
</code></pre><br />
<br />
<h2>ADD COLLABORATOR</h2><br />
<br />
<p>request:</p><br />
<br />
<pre><code>POST .org/project/&lt;pid&gt;/collaborator<br />
uid:&lt;uid&gt;<br />
</code></pre><br />
<br />
<p>response:</p><br />
<br />
<pre><code>{<br />
'status':'success'<br />
}<br />
</code></pre><br />
<br />
<h2>DELETE COLLABORATOR</h2><br />
<br />
<p>request:</p><br />
<br />
<pre><code>DELETE .org/project/&lt;pid&gt;/collaborator/&lt;uid&gt;<br />
</code></pre><br />
<br />
<p>response:</p><br />
<br />
<pre><code>{<br />
'status':'success'<br />
}<br />
</code></pre><br />
<br />
<h2>LOGOUT:</h2><br />
<br />
<p>request:</p><br />
<br />
<pre><code>POST .org/auth/logout<br />
</code></pre><br />
<br />
<p>response:</p><br />
<br />
<pre><code>{<br />
'status': 'success‘,<br />
}<br />
</code></pre><br />
<br />
<h2>DETAIL</h2><br />
<br />
<p>request:</p><br />
<br />
<pre><code>GET /data/(node|link)/&lt;ref_id&gt;<br />
</code></pre><br />
<br />
<p>response:</p><br />
<br />
<pre><code>{<br />
I'm results<br />
}<br />
</code></pre><br />
<br />
<h2>ADD</h2><br />
<br />
<p>request:</p><br />
<br />
<pre><code>POST /data/(node|link)<br />
<br />
info: <br />
{<br />
'TYPE': 'Gene',<br />
'NAME': 'trnL',<br />
...<br />
}<br />
x: 123.123131<br />
y: 321314.324<br />
pid: 12<br />
<br />
----<br />
PS:<br />
x,y(float) is optional<br />
pid,info are required<br />
</code></pre><br />
<br />
<p>response:</p><br />
<br />
<pre><code>{<br />
'ref_id': '&lt;ref_id&gt;' <br />
}<br />
</code></pre><br />
<br />
<h2>REFERENCE</h2><br />
<br />
<p>request:</p><br />
<br />
<pre><code>PUT /data/(node|link)/&lt;node\link_id&gt;/<br />
<br />
pid: 23<br />
x: 123.123<br />
y: -213.231<br />
</code></pre><br />
<br />
<p>response:</p><br />
<br />
<pre><code>{<br />
'ref_id': '&lt;ref_id&gt;' <br />
}<br />
</code></pre><br />
<br />
<h2>PATCH</h2><br />
<br />
<p>request:</p><br />
<br />
<pre><code>PATCH /data/(node|link)/&lt;ref_id<br />
<br />
x: 1231.123<br />
y: 232.234234<br />
</code></pre><br />
<br />
<h2>DELETE</h2><br />
<br />
<p>request:</p><br />
<br />
<pre><code>DELETE /data/(node|link)/&lt;ref_id&gt;<br />
</code></pre><br />
<br />
<p>response:</p><br />
<br />
<pre><code>{<br />
'status': 'success‘,<br />
}<br />
</code></pre><br />
<br />
<h2>LIST ALL DATA IN PROJECT</h2><br />
<br />
<p>request:</p><br />
<br />
<pre><code>GET /data/project/&lt;pid&gt;<br />
</code></pre><br />
<br />
<p>response:</p><br />
<br />
<pre><code>{<br />
'status': 'success',<br />
'node': [<br />
{},{}...<br />
],<br />
'link': [<br />
{},{}..<br />
],<br />
}<br />
</code></pre><br />
<br />
<h2>SEARCH NODE|LINK</h2><br />
<br />
<p>request:</p><br />
<br />
<pre><code>POST /search/(node|link)<br />
<br />
method:query<br />
spec:{}<br />
fields:{}<br />
skip:[INTEGER]<br />
limit:[INTEGER]<br />
</code></pre><br />
<br />
<p>default:</p><br />
<br />
<pre><code>skip:0<br />
limit:infinite<br />
</code></pre><br />
<br />
<p>response:</p><br />
<br />
<pre><code>{<br />
results:<br />
[<br />
{<br />
'_id':'53f455e1af4bd63ddccee4a3',<br />
'NAME':'ehrL',<br />
'TYPE':'Gene',<br />
'....':'...'<br />
<br />
},<br />
{<br />
'_id':'53f455e1af4bd63ddccee4a4'<br />
'NAME':'thrA',<br />
'TYPE':'Gene',<br />
'....':'...'<br />
}<br />
]<br />
}<br />
</code></pre><br />
<br />
<h3>ex1</h3><br />
<br />
<p>request :</p><br />
<br />
<pre><code>POST /search/(node|link)<br />
<br />
'spec':<br />
{<br />
"$and":<br />
[<br />
{"$or":<br />
[<br />
{"key1":"abc"},<br />
{"key2":123},<br />
{"key3":"sfda"}<br />
]},<br />
{"key4":"feiyicheng"}<br />
]<br />
}<br />
</code></pre><br />
<br />
<p>explain:</p><br />
<br />
<pre><code>(key1 || key2 || key3) &amp;&amp; key4<br />
</code></pre><br />
<br />
<h3>ex2</h3><br />
<br />
<p>request:</p><br />
<br />
<pre><code>POST /search/(node|link)<br />
<br />
'spec':<br />
{<br />
"age":<br />
{<br />
"$gt":18<br />
}<br />
}<br />
</code></pre><br />
<br />
<p>explain:</p><br />
<br />
<pre><code>&lt; : "$lt"<br />
&gt; : "$gt"<br />
&lt;= : "$le"<br />
&gt;= : "$ge"<br />
!= : "$ne"<br />
</code></pre><br />
<br />
<h3>ex3</h3><br />
<br />
<p>only return ID, NAME and TYPE fileds</p><br />
<br />
<p>request:</p><br />
<br />
<pre><code>POST /search/(node|link)<br />
<br />
spec:<br />
{<br />
}<br />
field:<br />
{<br />
'NAME':True,<br />
'TYPE':True<br />
}<br />
</code></pre><br />
<br />
<h3>ex4</h3><br />
<br />
<p>return all fileds except NAME</p><br />
<br />
<p>request:</p><br />
<br />
<pre><code>POST /search/(node|link)<br />
<br />
'spec':<br />
{<br />
}<br />
'field':<br />
{<br />
'NAME':False<br />
}<br />
</code></pre><br />
<br />
<h2>SEARCH USER</h2><br />
<br />
<p>request:</p><br />
<br />
<pre><code>POST /search/user<br />
name: &lt;name&gt;<br />
<br />
----<br />
PS: It will be fuzzy search<br />
eg:<br />
POST /search/user<br />
name: zhoulo<br />
</code></pre><br />
<br />
<p>response:</p><br />
<br />
<pre><code>{<br />
'status': 'success', <br />
'results': <br />
[<br />
{<br />
'username': &lt;username&gt;,<br />
'first_name': &lt;first_name&gt;,<br />
'last_name': &lt;last_name&gt;,<br />
'id':&lt;uid&gt;,<br />
},<br />
{}...<br />
]<br />
}<br />
</code></pre><br />
<br />
<h2>SEARCH PROJECT</h2><br />
<br />
<p>request:</p><br />
<br />
<pre><code>POST /search/project<br />
query: &lt;query&gt;<br />
<br />
PS: query must conform the json format, and all the fields are shown as following:<br />
'name','author','authorid',<br />
</code></pre><br />
<br />
<p>response:</p><br />
<br />
<pre><code>{<br />
'status': 'success',<br />
'results': <br />
{<br />
{<br />
'pid':...,<br />
'name':...,<br />
'authorid':...,<br />
'collaborators':<br />
[<br />
2,412,4...<br />
]<br />
},<br />
{}...<br />
}<br />
}<br />
</code></pre><br />
<br />
<h2>SHORTESTPATH</h2><br />
<br />
<p>request:</p><br />
<br />
<pre><code>POST /algorithm/shortestpath<br />
<br />
ID1:&lt;string&gt;<br />
ID2:&lt;string&gt;<br />
global:[boolean]<br />
</code></pre><br />
<br />
<p>default:</p><br />
<br />
<pre><code>global:False<br />
</code></pre><br />
<br />
<p>response:</p><br />
<br />
<pre><code>{<br />
results:<br />
[<br />
{<br />
node:[1,2,3,4,5],<br />
link:[12,23,34,45]<br />
},<br />
{<br />
node:[1,2,7,8,9,10,11],<br />
link:[......]<br />
}<br />
]<br />
}<br />
</code></pre><br />
<br />
<h2>BLASTN</h2><br />
<br />
<p>request:</p><br />
<br />
<pre><code>POST /algorithm/blastn<br />
//TODO<br />
</code></pre><br />
</body><br />
</html></div>
Hlx1996
http://2014.igem.org/Team:USTC-Software/api.html
Team:USTC-Software/api.html
2014-10-18T03:22:59Z
<p>Hlx1996: Created page with "<!doctype html> <html> <head> <meta charset="utf-8"> <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes"> <style> body { font-family: Helve..."</p>
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<title>API document</title><br />
<script type="text/x-mathjax-config">MathJax.Hub.Config({tex2jax:{inlineMath:[['$$$','$$$']]}});</script><script src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><br />
</head><br />
<body><br />
<h1>API document</h1><br />
<br />
<h2>Instruction</h2><br />
<br />
<p>All the following API(expect OAUTH) must have Authorization parameter in Http Header.</p><br />
<br />
<pre><code> Authorization: Token 13sdfs32fsadf <br />
</code></pre><br />
<br />
<blockquote><p>The default response is in json, if you want the response in other format, please add parameter "format=XML", "format=YAML", etc.</p></blockquote><br />
<br />
<p>If anything goes south, you will get a error response:</p><br />
<br />
<pre><code>{<br />
'status': 'error',<br />
'reason': '&lt;err_reason&gt;',<br />
}<br />
</code></pre><br />
<br />
<h2>DIRECTORY</h2><br />
<br />
<pre><code>POST /auth/oauth/(baidu|google)/login<br />
GET /auth/oauth/(baidu|google)/complete&amp;...<br />
#GET /user/&lt;uid&gt;<br />
<br />
<br />
GET /project/project # list my project<br />
POST /project/project # add<br />
<br />
GET /project/&lt;pid&gt; # login<br />
PUT /project&lt;pid&gt; # modify<br />
DELETE /project&lt;pid&gt; # delete<br />
<br />
POST /project/&lt;pid&gt;/collaborator/&lt;uid&gt; <br />
DELETE /project/&lt;pid&gt;/collaborator/&lt;uid&gt;<br />
<br />
<br />
GET /data/(node|link)/&lt;id&gt;<br />
POST /data/(node|link)<br />
DELETE /data/(node|link)/&lt;ref_id&gt;<br />
PATCH /data/node/&lt;ref_id&gt;<br />
PUT /data/(node|link)/&lt;id&gt;<br />
<br />
GET /data/project/&lt;pid&gt;<br />
</code></pre><br />
<br />
<blockquote><p>GET /data/(node|link)/&lt;ref_id>/link<br />
@zhaosensen</p></blockquote><br />
<br />
<pre><code>POST /search/(node|link)<br />
POST /search/user<br />
POST /search/project<br />
<br />
POST /algorithm/shortestpath<br />
POST /algorithm/blastn<br />
</code></pre><br />
<br />
<h2>OAUTH LOGIN:</h2><br />
<br />
<p>request:</p><br />
<br />
<pre><code>POST /auth/oauth/(baidu|google)/login<br />
</code></pre><br />
<br />
<p>When the user login in sucessfully, the pages will redict to the /auth/oauth/&lt;baidu|google>/complete</p><br />
<br />
<h2>OAUTH COMPLETE</h2><br />
<br />
<p>request(automaticlly):</p><br />
<br />
<pre><code>GET /auth/oauth/(baidu|google)/complete&amp;....<br />
</code></pre><br />
<br />
<p>success :</p><br />
<br />
<pre><code>{<br />
"status": "success",<br />
"token": "16517d0809f225b7b65a79ef1dc8c552441bf58a", <br />
"uid": 8,<br />
"googleid": "zhoulong6@gmail.com",<br />
[或者"baiduid": "347238434"]<br />
} <br />
</code></pre><br />
<br />
<h2>LIST PROJECT</h2><br />
<br />
<p>request:</p><br />
<br />
<pre><code>GET .org/project/project (**没有s**)<br />
</code></pre><br />
<br />
<p>response:</p><br />
<br />
<pre><code>{ <br />
'status':'success',<br />
'resultes': <br />
[<br />
...<br />
]<br />
}<br />
</code></pre><br />
<br />
<h2>ADD PROJECT</h2><br />
<br />
<p>request:</p><br />
<br />
<pre><code>POST .org/project/project<br />
<br />
prj_name:&lt;string&gt;<br />
[species:&lt;string&gt;]<br />
[description:&lt;string&gt;]<br />
</code></pre><br />
<br />
<p>response:</p><br />
<br />
<pre><code>{<br />
'status':'success',<br />
'pid':...<br />
}<br />
</code></pre><br />
<br />
<h2>PROJECT INFO</h2><br />
<br />
<p>request:</p><br />
<br />
<pre><code>GET .org/project/&lt;pid&gt;<br />
</code></pre><br />
<br />
<p>success response:</p><br />
<br />
<pre><code>{<br />
'status': 'success',<br />
'result':<br />
{<br />
'pid':....,<br />
'prj_name':...,<br />
'author':...,<br />
'authorid':...,<br />
'species':...,<br />
'description':...,<br />
'collaborators':<br />
[1, 5, ...<br />
]<br />
}<br />
}<br />
</code></pre><br />
<br />
<h2>DELETE PROJECT</h2><br />
<br />
<p>request:</p><br />
<br />
<pre><code>DELETE .org/project/&lt;pid&gt;<br />
</code></pre><br />
<br />
<p>response:</p><br />
<br />
<pre><code>{<br />
'status':'success'<br />
}<br />
</code></pre><br />
<br />
<h2>MODIFY PROJECT</h2><br />
<br />
<p>request:</p><br />
<br />
<pre><code>PUT .org/project/&lt;pid&gt;<br />
request体(类似POST):<br />
<br />
name : ...,<br />
species: ...,<br />
description:...<br />
</code></pre><br />
<br />
<h2>ADD COLLABORATOR</h2><br />
<br />
<p>request:</p><br />
<br />
<pre><code>POST .org/project/&lt;pid&gt;/collaborator<br />
uid:&lt;uid&gt;<br />
</code></pre><br />
<br />
<p>response:</p><br />
<br />
<pre><code>{<br />
'status':'success'<br />
}<br />
</code></pre><br />
<br />
<h2>DELETE COLLABORATOR</h2><br />
<br />
<p>request:</p><br />
<br />
<pre><code>DELETE .org/project/&lt;pid&gt;/collaborator/&lt;uid&gt;<br />
</code></pre><br />
<br />
<p>response:</p><br />
<br />
<pre><code>{<br />
'status':'success'<br />
}<br />
</code></pre><br />
<br />
<h2>LOGOUT:</h2><br />
<br />
<p>request:</p><br />
<br />
<pre><code>POST .org/auth/logout<br />
</code></pre><br />
<br />
<p>response:</p><br />
<br />
<pre><code>{<br />
'status': 'success‘,<br />
}<br />
</code></pre><br />
<br />
<h2>DETAIL</h2><br />
<br />
<p>request:</p><br />
<br />
<pre><code>GET /data/(node|link)/&lt;ref_id&gt;<br />
</code></pre><br />
<br />
<p>response:</p><br />
<br />
<pre><code>{<br />
I'm results<br />
}<br />
</code></pre><br />
<br />
<h2>ADD</h2><br />
<br />
<p>request:</p><br />
<br />
<pre><code>POST /data/(node|link)<br />
<br />
info: <br />
{<br />
'TYPE': 'Gene',<br />
'NAME': 'trnL',<br />
...<br />
}<br />
x: 123.123131<br />
y: 321314.324<br />
pid: 12<br />
<br />
----<br />
PS:<br />
x,y(float) is optional<br />
pid,info are required<br />
</code></pre><br />
<br />
<p>response:</p><br />
<br />
<pre><code>{<br />
'ref_id': '&lt;ref_id&gt;' <br />
}<br />
</code></pre><br />
<br />
<h2>REFERENCE</h2><br />
<br />
<p>request:</p><br />
<br />
<pre><code>PUT /data/(node|link)/&lt;node\link_id&gt;/<br />
<br />
pid: 23<br />
x: 123.123<br />
y: -213.231<br />
</code></pre><br />
<br />
<p>response:</p><br />
<br />
<pre><code>{<br />
'ref_id': '&lt;ref_id&gt;' <br />
}<br />
</code></pre><br />
<br />
<h2>PATCH</h2><br />
<br />
<p>request:</p><br />
<br />
<pre><code>PATCH /data/(node|link)/&lt;ref_id<br />
<br />
x: 1231.123<br />
y: 232.234234<br />
</code></pre><br />
<br />
<h2>DELETE</h2><br />
<br />
<p>request:</p><br />
<br />
<pre><code>DELETE /data/(node|link)/&lt;ref_id&gt;<br />
</code></pre><br />
<br />
<p>response:</p><br />
<br />
<pre><code>{<br />
'status': 'success‘,<br />
}<br />
</code></pre><br />
<br />
<h2>LIST ALL DATA IN PROJECT</h2><br />
<br />
<p>request:</p><br />
<br />
<pre><code>GET /data/project/&lt;pid&gt;<br />
</code></pre><br />
<br />
<p>response:</p><br />
<br />
<pre><code>{<br />
'status': 'success',<br />
'node': [<br />
{},{}...<br />
],<br />
'link': [<br />
{},{}..<br />
],<br />
}<br />
</code></pre><br />
<br />
<h2>SEARCH NODE|LINK</h2><br />
<br />
<p>request:</p><br />
<br />
<pre><code>POST /search/(node|link)<br />
<br />
method:query<br />
spec:{}<br />
fields:{}<br />
skip:[INTEGER]<br />
limit:[INTEGER]<br />
</code></pre><br />
<br />
<p>default:</p><br />
<br />
<pre><code>skip:0<br />
limit:infinite<br />
</code></pre><br />
<br />
<p>response:</p><br />
<br />
<pre><code>{<br />
results:<br />
[<br />
{<br />
'_id':'53f455e1af4bd63ddccee4a3',<br />
'NAME':'ehrL',<br />
'TYPE':'Gene',<br />
'....':'...'<br />
<br />
},<br />
{<br />
'_id':'53f455e1af4bd63ddccee4a4'<br />
'NAME':'thrA',<br />
'TYPE':'Gene',<br />
'....':'...'<br />
}<br />
]<br />
}<br />
</code></pre><br />
<br />
<h3>ex1</h3><br />
<br />
<p>request :</p><br />
<br />
<pre><code>POST /search/(node|link)<br />
<br />
'spec':<br />
{<br />
"$and":<br />
[<br />
{"$or":<br />
[<br />
{"key1":"abc"},<br />
{"key2":123},<br />
{"key3":"sfda"}<br />
]},<br />
{"key4":"feiyicheng"}<br />
]<br />
}<br />
</code></pre><br />
<br />
<p>explain:</p><br />
<br />
<pre><code>(key1 || key2 || key3) &amp;&amp; key4<br />
</code></pre><br />
<br />
<h3>ex2</h3><br />
<br />
<p>request:</p><br />
<br />
<pre><code>POST /search/(node|link)<br />
<br />
'spec':<br />
{<br />
"age":<br />
{<br />
"$gt":18<br />
}<br />
}<br />
</code></pre><br />
<br />
<p>explain:</p><br />
<br />
<pre><code>&lt; : "$lt"<br />
&gt; : "$gt"<br />
&lt;= : "$le"<br />
&gt;= : "$ge"<br />
!= : "$ne"<br />
</code></pre><br />
<br />
<h3>ex3</h3><br />
<br />
<p>only return ID, NAME and TYPE fileds</p><br />
<br />
<p>request:</p><br />
<br />
<pre><code>POST /search/(node|link)<br />
<br />
spec:<br />
{<br />
}<br />
field:<br />
{<br />
'NAME':True,<br />
'TYPE':True<br />
}<br />
</code></pre><br />
<br />
<h3>ex4</h3><br />
<br />
<p>return all fileds except NAME</p><br />
<br />
<p>request:</p><br />
<br />
<pre><code>POST /search/(node|link)<br />
<br />
'spec':<br />
{<br />
}<br />
'field':<br />
{<br />
'NAME':False<br />
}<br />
</code></pre><br />
<br />
<h2>SEARCH USER</h2><br />
<br />
<p>request:</p><br />
<br />
<pre><code>POST /search/user<br />
name: &lt;name&gt;<br />
<br />
----<br />
PS: It will be fuzzy search<br />
eg:<br />
POST /search/user<br />
name: zhoulo<br />
</code></pre><br />
<br />
<p>response:</p><br />
<br />
<pre><code>{<br />
'status': 'success', <br />
'results': <br />
[<br />
{<br />
'username': &lt;username&gt;,<br />
'first_name': &lt;first_name&gt;,<br />
'last_name': &lt;last_name&gt;,<br />
'id':&lt;uid&gt;,<br />
},<br />
{}...<br />
]<br />
}<br />
</code></pre><br />
<br />
<h2>SEARCH PROJECT</h2><br />
<br />
<p>request:</p><br />
<br />
<pre><code>POST /search/project<br />
query: &lt;query&gt;<br />
<br />
PS: query must conform the json format, and all the fields are shown as following:<br />
'name','author','authorid',<br />
</code></pre><br />
<br />
<p>response:</p><br />
<br />
<pre><code>{<br />
'status': 'success',<br />
'results': <br />
{<br />
{<br />
'pid':...,<br />
'name':...,<br />
'authorid':...,<br />
'collaborators':<br />
[<br />
2,412,4...<br />
]<br />
},<br />
{}...<br />
}<br />
}<br />
</code></pre><br />
<br />
<h2>SHORTESTPATH</h2><br />
<br />
<p>request:</p><br />
<br />
<pre><code>POST /algorithm/shortestpath<br />
<br />
ID1:&lt;string&gt;<br />
ID2:&lt;string&gt;<br />
global:[boolean]<br />
</code></pre><br />
<br />
<p>default:</p><br />
<br />
<pre><code>global:False<br />
</code></pre><br />
<br />
<p>response:</p><br />
<br />
<pre><code>{<br />
results:<br />
[<br />
{<br />
node:[1,2,3,4,5],<br />
link:[12,23,34,45]<br />
},<br />
{<br />
node:[1,2,7,8,9,10,11],<br />
link:[......]<br />
}<br />
]<br />
}<br />
</code></pre><br />
<br />
<h2>BLASTN</h2><br />
<br />
<p>request:</p><br />
<br />
<pre><code>POST /algorithm/blastn<br />
//TODO<br />
</code></pre><br />
</body><br />
</html></div>
Hlx1996
http://2014.igem.org/Team:USTC-Software/team.php
Team:USTC-Software/team.php
2014-10-18T03:16:57Z
<p>Hlx1996: </p>
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<li><a href="/Team:USTC-Software/acknowledge.php#dbank">Deutsche Bank</a></li><br />
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}<br />
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#pop_up_display {<br />
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margin: 150px 340px 0px;<br />
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}<br />
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<p style="font-size:32px">Team</p><br />
<br />
</div><br />
<div class="row"><br />
<div class="large-12 columns large-centered"><br />
<h4 id="team_members">Team Members</h4><br />
<div class="underline-small"></div><br />
<ul class="large-block-grid-6 medium-block-grid-4 small-block-grid-2 text-center"><br />
<br />
<li class ="profilewrap"><br />
<img src="https://static.igem.org/mediawiki/2014/6/62/2014ustc-Xyc.jpg" alt="Xue Yuechuan"><br />
<div class ="nameplate"><a href="#">Xue Yuechuan</a></div><br />
<div class = "details"><img src="https://static.igem.org/mediawiki/2014/6/62/2014ustc-Xyc.jpg" alt="Xue Yuechuan" align="left"><p>Team Leader<br>Junior of physical electronics major<br>His work: team leading and art design.</p><br />
</div><br />
</li><br />
<br />
<li class ="profilewrap"><br />
<img src="https://static.igem.org/mediawiki/2014/e/ee/2014ustc-Zss.jpg" alt="Zhao Shensen"><br />
<div class ="nameplate"><a href="#">Zhao Shensen</a></div><br />
<div class = "details"><img src="https://static.igem.org/mediawiki/2014/e/ee/2014ustc-Zss.jpg" alt="Zhao Shensen" align="left"><p>Vice Team Leader<br>Senior of physical electronics major<br>His work: team managing assistance and back end work</br>His words: Work which make idea true make me happy.</p><br />
</div><br />
</li><br />
<li class ="profilewrap"><br />
<img src="https://static.igem.org/mediawiki/2014/6/6e/2014ustc-Glz.jpg" alt="Gan Longzhi"><br />
<div class ="nameplate"><a href="#">Gan Longzhi</a></div><br />
<div class = "details"><img src="https://static.igem.org/mediawiki/2014/6/6e/2014ustc-Glz.jpg" alt="Gan Longzhi" align="left"><p>Team Manager<br>Sophomore from School of Earth and Space Science<br>His work: team managing web editing and document writing<br>His words: Try hard, have fun.</p><br />
</div><br />
</li><br />
<li class ="profilewrap"><br />
<img src="https://static.igem.org/mediawiki/2014/6/6c/2014ustc-Ltx.jpg" alt="Lin Taixing"><br />
<div class ="nameplate"><a href="#">Lin Taixing</a></div><br />
<div class = "details"><img style="width:200px" src="https://static.igem.org/mediawiki/2014/6/6c/2014ustc-Ltx.jpg" alt="Lin Taixing" align="left"><p>Member<br>Junior of atomic and molecular physics major<br>His work: web designing<br>His words: Dream what you want to dream; go where you want to go; be what you want to be, because you have only one life and one chance to do all the things you want to do.</p><br />
</div><br />
</li><br />
<li class ="profilewrap"><br />
<img src="https://static.igem.org/mediawiki/2014/1/1e/2014ustc-Wws.jpg" alt="Wang Wenshuo"><br />
<div class ="nameplate"><a href="#">Wang Wenshuo</a></div><br />
<div class = "details"><img src="https://static.igem.org/mediawiki/2014/1/1e/2014ustc-Wws.jpg" alt="Wang Wenshuo" align="left"><p>Member<br>Junior of the Special Class for the Gifted Young, majoring in Statistics<br>His work: translation and document writing<br>His words: There is no fate but what we make.</p><br />
</div><br />
</li><br />
<li class ="profilewrap"><br />
<img src="https://static.igem.org/mediawiki/2014/d/d0/2014ustc-Zzy.jpg" alt="Zhang Zhiyuan"><br />
<div class ="nameplate"><a href="#">Zhang Zhiyuan</a></div><br />
<div class = "details"><img src="https://static.igem.org/mediawiki/2014/d/d0/2014ustc-Zzy.jpg" alt="Zhang Zhiyuan" align="left"><p>Member<br>Senior of Hua Loo-Keng Talent Program in Mathematics, majoring in fundamental mathematics<br>translation and document writing<br>Her words: To see, to ask, to search, to believe.</p><br />
</div><br />
</li><br />
<br />
<li class ="profilewrap"><br />
<img src="https://static.igem.org/mediawiki/2014/7/7d/2014ustc-Gyf.jpg" alt="Gao Yifan"><br />
<div class ="nameplate"><a href="#">Gao Yifan</a></div><br />
<div class = "details"><img src="https://static.igem.org/mediawiki/2014/7/7d/2014ustc-Gyf.jpg" alt="Yifan Gao" align="left"><p>Member<br>Junior of optics major<br>His work: back end work<br>His words: Perfection is achieved not when there is nothing more to add, but rather when there is nothing more to take away.</p><br />
</div><br />
</li><br />
<li class ="profilewrap"><br />
<img src="https://static.igem.org/mediawiki/2014/4/4b/2014ustc-Dcx.jpg" alt="Dong Chenxiao"><br />
<div class ="nameplate"><a href="#">Dong Chenxiao</a></div><br />
<div class = "details"><img src="https://static.igem.org/mediawiki/2014/4/4b/2014ustc-Dcx.jpg" alt="Dong Chenxiao" align="left"><p>Member<br>Sophomore from School of Physics Science<br>His work: data hunting and organizing, software design and document writing<br>His words: All the time, try retorting any idea from team.</p><br />
</div><br />
</li><br />
<br />
<li class ="profilewrap"><br />
<img src="https://static.igem.org/mediawiki/2014/2/28/2014ustc-Jzy.jpg" alt="Haiyan Liu"><br />
<div class ="nameplate"><a href="#">Jin Zeyu</a></div><br />
<div class = "details"><img src="https://static.igem.org/mediawiki/2014/2/28/2014ustc-Jzy.jpg" alt="Haiyan Liu" align="left"><p>Member<br>Sophomore from School of Earth and Space Science<br>His work: data hunting and organizing, software design and document writing<br>His words: Not most powerful, but highly responsible!</p><br />
</div><br />
</li><br />
<br />
<li class ="profilewrap"><br />
<img src="https://static.igem.org/mediawiki/2014/9/97/2014ustc-Zl.jpg" alt="Haiyan Liu"><br />
<div class ="nameplate"><a href="#">Zhou Long</a></div><br />
<div class = "details"><img src="https://static.igem.org/mediawiki/2014/9/97/2014ustc-Zl.jpg" alt="Haiyan Liu" align="left"><p>Member<br>Junior of nuclear physics major<br>His work: front end work<br>His words: Simply Enjoy.</p><br />
</div><br />
</li><br />
<br />
<li class ="profilewrap"><br />
<img src="https://static.igem.org/mediawiki/2014/a/a1/2014ustc-Hlx.jpg" alt="Han Luxin"><br />
<div class ="nameplate"><a href="#">Han Luxin</a></div><br />
<div class = "details"><img src="https://static.igem.org/mediawiki/2014/a/a1/2014ustc-Hlx.jpg" alt="Han Luxin" align="left"><p>Member who is <b>MOST HANDSOME</b><br>Sophomore from School for the Gifted Young, majoring in computer science<br>His work: algorithm design and writing and web editing<br>His words: Where there is a will, there is a way.</p><br />
</div><br />
</li><br />
<br />
<li class ="profilewrap"><br />
<img src="https://static.igem.org/mediawiki/2014/8/8d/2014ustc-Ycp.jpg" alt="Yu Chuanping"><br />
<div class ="nameplate"><a href="#">Yu Chuanping</a></div><br />
<div class = "details"><img src="https://static.igem.org/mediawiki/2014/8/8d/2014ustc-Ycp.jpg" alt="Yu Chuanping" align="left"><p>Member<br>Senior of statistics major<br>Her work: translation<br>Her words: Do one thing at a time, and do well.</p><br />
</div><br />
</li><br />
<br />
<li class ="profilewrap"><br />
<img src="https://static.igem.org/mediawiki/2014/4/44/2014ustc-Zhy.jpg" alt="Zhang Huayu"><br />
<div class ="nameplate"><a href="#">Zhang Huayu</a></div><br />
<div class = "details"><img src="https://static.igem.org/mediawiki/2014/4/44/2014ustc-Zhy.jpg" alt="Zhang Huayu" align="left"><p>Member<br>Sophomore from School of Physics Science<br>His work: front end work<br>His words: Be the best yourself, to be No.1. </p><br />
</div><br />
</li><br />
<br />
</li><br />
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<li class ="profilewrap"><br />
<img src="https://static.igem.org/mediawiki/2014/9/96/2014ustc-Fyc.jpg" alt="Haiyan Liu"><br />
<div class ="nameplate"><a href="#">Fei Yicheng</a></div><br />
<div class = "details"><img src="https://static.igem.org/mediawiki/2014/9/96/2014ustc-Fyc.jpg" alt="Haiyan Liu" align="left"><p>Member<br>Sophomore from School of Physics Science<br>His work: back end work<br>His words: Be the best yourself, to be No.1. </p><br />
</div><br />
</li><br />
<br />
<li class ="profilewrap"><br />
<img src="https://static.igem.org/mediawiki/2014/b/bc/2014ustc-Ctl.jpg" alt="Chen Tianlong"><br />
<div class ="nameplate"><a href="#">Chen Tianlong</a></div><br />
<div class = "details"><img src="https://static.igem.org/mediawiki/2014/b/bc/2014ustc-Ctl.jpg" alt="Chen Tianlong" align="left"><p>Member<br>Sophomore of mathematics major<br>His work: web design<br>His words: Be the best yourself, to be No.1. </p><br />
</div><br />
</li><br />
<br />
<li class ="profilewrap"><br />
<img src="https://static.igem.org/mediawiki/2014/e/e8/Clf.jpg" alt="Chen Lingfan"><br />
<div class ="nameplate"><a href="#">Chen Lingfan</a></div><br />
<div class = "details"><img src="https://static.igem.org/mediawiki/2014/e/e8/Clf.jpg" alt="Chen Lingfan" align="left"><p>Member<br>Junior of computational mathematics major<br>His work: algorithm design<br>His words: Study in USTC, work in USTC, and make friends in USTC.</p><br />
</div><br />
</li><br />
<br />
</ul><br />
<h4 id="I_A">Instructors & Advisors</h4><br />
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<img src="https://static.igem.org/mediawiki/2014/d/de/2014ustc-G.png" alt="Haiyan Liu"><br />
<div class ="nameplate"><a href="#">Haiyan Liu</a></div><br />
<div class = "details"><img src="https://static.igem.org/mediawiki/2014/d/de/2014ustc-G.png" alt="Haiyan Liu" ><br />
<p><b>Email:</b>hyliu@ustc.edu.cn</p><br />
<p><b>Brief Intro:</b>Haiyan Liu was born in Sichuan Province, China. He received his BS degree in Biology in 1990 and PhD degree in Biochemistry and Molecular Biology in 1996, both from USTC. Between 1993 and 1995 he was a visiting graduate student in Laboratory of Physical Chemistry of ETH, Zurich (Switzerland). From 1998 to 2000 he was post-doctoral research associate at Department of Chemistry, Duke University (USA) and Department of Biochemistry and Biophysics UNC-Chapel Hill (USA). Since 2001, he has been a professor of computational biology at School of Life Sciences, USTC.</p><br />
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<li class ="profilewrap"><br />
<img src="https://static.igem.org/mediawiki/2014/a/af/2014ustc-H.png" alt="Zhi Liang"><br />
<div class ="nameplate"><a href="#">Zhi Liang</a></div><br />
<div class = "details"><img src="https://static.igem.org/mediawiki/2014/a/af/2014ustc-H.png" alt="Zhi Liang" ><br />
<p><b>Email:</b>liangzhi@ustc.edu.cn</p><br />
<p><b>Brief Intro:</b>Liang Zhi, Ph.D., Associate Professor Extraordinary . 2000 graduated from the school of Life Sciences in the University of Science and Technology of China, received bachelor's degree in biology and electronics and information engineering dual degree. 2006 graduated from the school of Life Sciences in the University of Science and Technology of China protein crystallography laboratory , PhD. From 2007 to 2012 in the school of Life Sciences in the University of Science and Technology of China Systems Biology Laboratory in systems biology postdoctoral research. Postdoctoral period has won China Postdoctoral Science Foundation funded second and Natural Science Foundation funding. 2012 University of Science and Technology of China Extraordinary Life Sciences Research Associate . Research results published on Nucleic Acids Res, Bioinformatics, Bioinformatics, J Biol Chem.</p><br />
</div><br />
</li><br />
<br />
<li class ="profilewrap"><br />
<img src="https://static.igem.org/mediawiki/2014/9/93/2014ustc-I.png"><br />
<div class ="nameplate"><a href="#">Jiong Hong</a></div><br />
<div class = "details"><img src="https://static.igem.org/mediawiki/2014/9/93/2014ustc-I.png" alt="Jiong Hong" ><br />
<p>Professor, School of Life Sciences University of Science & Technology of China</p><br />
<p><br />
<b>Email:</b> hjiong@ustc.edu.cn<br /><br /><br />
<b>Brief Intro:</b>Jiong Hong was born in Anhui Province, China. He received his BS degree in 1993 from Anhui Normal University, MSc degree in 1996 from Beijing Normal University, and Ph.D degree in 2003 from Kyoto University, all in Life Sciences. From 2006 to 2008, he did post-doctoral research in Virginia Tech University, USA. Since 2008, he has been introduced to the USTC as talented.<br />
</p><br />
</div><br />
</li><br />
<br />
<br />
<li class ="profilewrap"><br />
<img src="https://static.igem.org/mediawiki/2014/9/92/2014ustc-J.png" alt="Fan Jin"><br />
<div class ="nameplate"><a href="#">Fan Jin</a></div><br />
<div class = "details"><img src="https://static.igem.org/mediawiki/2014/9/92/2014ustc-J.png" alt="Fan Jin" ><br />
<br />
<br /><br /><br />
<p>1997.07-2002.07 B.S., Student, Department of Applied Chemistry, University of Science & Technology of China, P. R. China.<br />
Degree awarded: B.S. in chemistry, 07/2002</p><br />
<br />
<p>2003.08-2007.06 Ph.D. Candidate, Department of Chemistry, The Chinese University of Hong Kong.<br />
Degree awarded: Ph.D in chemistry, 06/2007</p><br />
<br />
<p>2002.07-2003.07 R.A., The Hefei National Laboratory of Physical Science at Microscale, Department of Chemical Physics, University of Science & Technology of China, P. R. China.</p><br />
<br />
<p>2007.06-2009.01 Postdoctoral Associate, Department of Chemistry, The Chinese University of Hong Kong.</p><br />
<br />
<p>2009.01-2009.11 Postdoctoral Associate, Department of Materials Science and Engineering, University of Illinois at Urbana Champaign.</p><br />
<br />
<p>2009.11-2011.8 Postdoctoral Associate, Department of Bioengineering, California Nanosystems Institute, University of California, Los Angeles. </p><br />
<br />
<p>2011.8-present Professor, Department of Polymer Materials Science and Engineering, University of Science and Technology of China, CAS Key Lab of Soft Matter Chemistry. </p><br />
<br />
<h4>Research Interests</h4><br />
<p>Polyelectrolyte and colloidal particles in the oil-water interface. </p><br />
<p>Interaction between Antibiotic peptides and lipids membrane. </p><br />
<p>Living cell image and living cell micro-manipulation.</p><br />
<p>Biological macromolecules, characterization of supramolecular assembly and its applications in drug delivery and gene transfection. </p><br />
<p>Bacterial communities. (Ex: signaling, motility, social organization in biofilms)</p><br />
<br />
<br />
<br />
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</li><br />
</ul><br />
<br />
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<br />
<br />
<h4 id="Additional_thanks">Additional Thanks</h4><br />
<div class="underline-small"><br />
<br />
</div><br />
<div style="line-height:200%"><br />
<li><br />
Thanks for financial assistance from Deutsche Bank, USTCIF and USTC Teaching Affair Office. Only with their help could we finish the competition;<br />
</li><br />
<li><br />
Thank data from RegulonDB, KEGG, Uniprot and NCBI. Only with their data and apis could we refine our database; <br />
</li><br />
<li><br />
Thank project guidance from Haiyan Liu, Zhi Liang, Fan Jin and Jiong Hong. Only with their guidance could our project be improved and deepened; <br />
</li><br />
<li><br />
Thank Chen Liao for participating in the use, evaluation and popularization of Biopano.He pointed out many deficiencies and bugs of our software.<br />
</li><br />
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Hlx1996
http://2014.igem.org/Team:USTC-Software/acknowledge.php
Team:USTC-Software/acknowledge.php
2014-10-18T03:13:12Z
<p>Hlx1996: </p>
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<h4 id="dbank">Deutsche Bank</h4><br />
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<p><br />
Deutsche Bank is a German global banking and financial services company with its<br />
headquarters in the Deutsche Bank Twin Towers in Frankfurt. It has more than 100,000<br />
employees in over 70 countries, and has a large presence in Europe, the Americas, Asia-<br />
Pacific and the emerging markets. In 2009, Deutsche Bank was the largest foreign exchange<br />
dealer in the world with a market share of 21 percent.<br />
Deutsche Bank has offices in major financial centres including London, New York City,<br />
Singapore, Hong Kong, Tokyo, Paris, Moscow, Sydney, Toronto, Jakarta, Istanbul, Madrid,<br />
Dublin, Amsterdam, Warsaw, Mumbai, Kuala Lumpur, São Paulo, Dubai, Riyadh, Bangkok,<br />
Karachi, Belgrade, Manila and George Town (Cayman Islands).<br />
The bank offers financial products and services for corporate and institutional clients along<br />
with private and business clients. Services include sales, trading, research and origination of<br />
debt and equity; mergers and acquisitions (M&A); risk management products, such as<br />
derivatives, corporate finance, wealth management, retail banking, fund management, and<br />
transaction banking<br />
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<h4 id="ustcif">USTCIF</h4><br />
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USTCIF, The University of Science and Technology of China Initiative Foundation, is a educational NGO serves to help with the development of USTC. As one of USTC's alumni foundations, its purpose is to enhence the alumni foundations to make USTC better. USTIF is the first college alumni foundation indepentant from the university.<br />
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<h4 id="utao">USTC Teaching Affair Office</h4><br />
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http://www.teach.ustc.edu.cn/<br />
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<img src="https://static.igem.org/mediawiki/2014/c/ca/2014ustc-Kegg.jpg" style="height:100px"></a></li><br />
<li><a href="http://www.ncbi.nlm.nih.gov/"><br />
<img src="https://static.igem.org/mediawiki/2014/5/55/2014ustc-NCBI.jpg" style="height:100px"></a></li><br />
<li><a href=" http://www.uniprot.org/"><br />
<img src="https://static.igem.org/mediawiki/2014/4/47/2014ustc-Uniprot.png" style="height:100px"></a></li><br />
</ul><br />
<p>We would like to thank RegulonDB, Kegg, NCBI and uniprot for their data, without which Biopano can never be finished. Thanks again for their work and effort.</p><br />
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<h5 style="color:#fff;font-weight:bold;margin-bottom: 25px;">Innovation Experiment Centre of Life Science (IEC)</h5><br />
<p>Building of Life Sciences, Room 363</p><br />
<p>University of Science and Technology of China</p><br />
<p>96, Jinzhai Rd, Shushan, Hefei</p><br />
<p>230026, Anhui, China</p><br />
<p>support@biopano.org</p><br />
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Hlx1996
http://2014.igem.org/Team:USTC-Software/human_practice.php
Team:USTC-Software/human practice.php
2014-10-18T03:12:47Z
<p>Hlx1996: </p>
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<p style="font-size:32px">Human Practice</p><br />
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<div class="row large-12 columns large-centered"><br />
<h4 id="management">Management</h4><br />
<div class="underline-small"><br />
<br />
</div><br />
<h5> iGEM, Efficiency, Environment and Enjoyment</h5><br />
<p>During the entire iGEM project, we adhered to the four elements,<br />
iGEM, efficiency, environment and enjoyment. When the project is drawing to a close,<br />
we tease out our project management experience according<br />
to them and put it online as reference for more people.</p><br />
<div class="underline-tiny"></div><br />
<h5>iGEM</h5><br />
<br />
<p>Since our project is for participating in iGEM,<br />
we always emphasized the leading position of iGEM in our project.<br />
We set up study group specifically for iGEM project. Independent of the working group,<br />
they worked on synthetic biology. Although some of their results turned out to be useless,<br />
they played a critical role in every phase of our project, such as the decision of our final project,<br />
the optimization of functions of the software and teaching other team members<br />
not majoring in biology some biological knowledge. A group focusing on the subject guarantees<br />
that the whole project runs smoothly on track. The experience above applies to project of any subject.<br />
Just replace “iGEM” with your own word.</p><br />
<div class="underline-tiny"></div><br />
<h5>Efficiency</h5><br />
<br />
<p>In any project, efficiency is always a significant factor.<br />
During our project, we took regular and necessary methods,<br />
such as wholesome team management system (team leader, team manager,<br />
group supervisor) and explicit regulations. In addition,<br />
we managed our team in an innovative way—electronic platform.<br />
All work plans are put on electronic notebook shared by all team members.<br />
We also built a platform for team members to report their working achievements periodically.<br />
Last but not least, we established a GitLab ourselves accessible to all team members,<br />
which avoided the detriment of environment caused by paper-based platform <br />
(this will be mentioned again later).</p><br />
<div class="underline-tiny"></div><br />
<h5>Environment</h5><br />
<br />
<p><br />
Environmental protection is one of the most compelling problems nowadays.<br />
We kept thinking about this while proceeding the project. As mentioned above,<br />
we built a paperless office, except for necessary invoices. Compared with previous iGEM teams of USTC,<br />
we saved a lot of paper. Meanwhile, we paid attention to keeping our working environment neat and clean.<br />
The workplace was cleaned by our team members every day.<br />
Garbage was classified and dropped in the garbage bin. We believe that<br />
appropriate regulation can ensure that working group of any project can <br />
do their work comfortably and protect the earth at the same time.<br />
</p><br />
<div class="underline-tiny"></div><br />
<h5>Enjoyment</h5><br />
<p><br />
Although there were a lot of work to do, our project experience was joyful.<br />
At the beginning of the project, team members with experience in software <br />
development prepared courses for other members. Well-prepared courses made us accomplish <br />
the assignments successfully and gain new knowledge. We also organized various kinds of <br />
activities to relax our team members. In the summer vacation, we had group activities <br />
after a whole day’s hard work, including having dinner outside, playing sports and even<br />
computer game competition. We also recommend these activities to every team. They not only<br />
relax team members, but also improve the relationship among team members, making the whole<br />
working experience enjoyable and unforgettable.<br />
<br />
</p><br />
<br />
<br />
<h3 id="hlxisveryhandsome">Software & Platforms We Used</h3><br />
<div class="underline-small"><br />
<br />
</div><br />
<br />
<h5>Google group</h5><br />
<br />
<p>At the formation of USTC-Software of 2014, the team leader of 2013 recommended Google group as an online platform for communication and team management. Although every team member was highly enthusiastic about iGEM, they had their own school work to worry about. Meanwhile, our team members lived in different areas of the campus. Hence it became a serious problem that how team members could receive notifications in time to accomplish the work separately while co-working time could not be guaranteed. Google group solved this problem. Google group offers open online platform to users and users can build their own platform for sharing. Messages on the platform are accessible to all users joining the group. Emails can also be pushed to users. We built a platform of our team, and all messages on the platform could be pushed to team members in time. By Google group, we were able to:</p><br />
<ul><br />
<li>1. send notifications and arrangements to all team members in time;</li><br />
<li>2. make team members share their thoughts and innovation conveniently;</li><br />
<li>3. make regulations, assessments and financal issues transparent by sharing work logs.</li><br />
</ul><br />
<p>We recommend Google group for project management based on our experience. It can enhance communication among team members by breaking through the limitations of time and space. It can also make team work transparent and increase management efficiency.</p><br />
<div class="underline-tiny"></div><br />
<h5>Wunderlist</h5><br />
<p>Conversation sharing of Google group became inconvenient as the project proceeded and our work became more and more complicated. So we chose to use Wunderlist at the same time.<br /><br />Wunderlist is specifically designed for work arrangement. People in charge can create lists for their part of work and invite other users to help them with the work. Specifically, they can assign different members for different tasks and set deadlines. Other members can give feedbacks to the list after the corresponding work is done, and people in charge can delete the work from the list. Another advantage of Wunderlist is that it is available for all platforms, including PC and mobile phone. This way, all team members could receive the latest work notices.<br /><br />During the project, we created lists based on our work, including iGEM-backend, iGEM-frontend, iGEM-wiki and iGEM-finance, etc. Complicated assignments were distributed to different people. We also used the feedback service of Wunderlist to monitor the work progress. The use of Wunderlist enabled us to assign tasks in a scientific way and keep us informed of the progress of our project all the time to make sure that everything goes according to the plan.<br />
<br />
</p><br />
<div class="underline-tiny"></div><br />
<h5>OneNote</h5><br />
<br />
<p><br />
For every team, the financial problem is a big one. Of course, you may think of separating money and account easily, but how do you keep two or more financial managers in the same stage? We chose to solve the problem by OneNote.<br /><br />OneNote is originally designed for instant creation and notes sharing, and so it can be applied to financial management smoothly. We could create notebooks according to different items and mark the accounts that have been cleared or have not yet been cleared. By inviting others, the team leader can supervise the manager about he financial situation timely and make sure about the accuracy of this.<br />
</p><br />
<div class="underline-tiny"></div><br />
<h5>Omni outliner & Mindmap</h5><br />
<br />
<p><br />
No matter you are in what stage of what project, when you need new thoughts, it is always quite a hard time to get a satisfying result. Brainstorm might be a really nice idea, but in most of the time you have to stare at a whiteboard full of messy ideas on it without action. To solve the problem, you need some kind of software for thought assistance, such as Omni Outliner and Mingmap.<br /><br />Software like Omni Outliner can help you sort out all the necessary points and arrange your thoughts when you are writing articles, and software like Mindmap can enable you to draw a succinct "map" of your ideas to clarify your thoughts and summarize the viewpoints. Therefore you can quickly extract a wonderful idea from the numerous viewpoints raised in the brainstorm.<br />
<br />
</p><br />
<div class="underline-tiny"></div><br />
<h5>Dropbox</h5><br />
<br />
<p><br />
During the project, all kinds of files were created unremittingly. To be specific, articles to read, work log to be displayed, finished program codes, relevant materials, photos of us, etc. How will you store the files? You don’t store all of them in only one person’s computer, for they are too many and other people may also need them. We have a great solution—Dropbox.<br /><br />Dropbox is a cloud storage platform. It allows users to store files in the cloud, and thus any team member, knowing the password of the account, has access to these files no matter when and where. In the meantime, cloud storage is also very secure. Even if you accidentally spill coffee on your computer or the manuscripts, you can still keep your files safe.<br />
</p><br />
<br />
<h3>Biological Cooperation</h3><br />
<div class="underline-small"><br />
<br />
</div><br />
<br />
<p>Fine communication in any field enhances the development of the field, especially when it comes to biological field. Nowadays, there are already some ways of communication in biology. They are traditional ways, however. Communication by literature publishing, meeting attending and emailing is relatively slow and hard to be used in global range. What’s more important is that communication in these ways will restrict a biologist’s research field. This suppresses the cross-field communication of biology. As we all know, communication of different fields will bring about amazing breakthroughs. Therefore, if the restriction can be broken, it will benefit the development of biology astonishingly.<br /><br />BioPano is based on an online server, so it supports communication and cooperation perfectly. Users can release their research results on our software platform. BioPano will record the information and all biologists using the software all over the world can see the modifications. What’s better, we add group function usually in social software into BioPano. Biologists from different fields can form a group with BioPano. They can communicate more conveniently in the group. Meanwhile, BioPano offers other project co-management services to help biologists from different fields complete the research together.<br /><br />Popularization of BioPano will surely improve the connection among biologists greatly and enhance the progress of biology. Furthermore, BioPano will change the frequency and pattern of research results updating of biology, and even show every single change of biology real-timely like Wikipedia. Every researcher can share the progress of biology, and biological research will stride into the information age.<br /><br />We have already reccomended BioPano to many biological researchers, and received great feedbacks.</p><br />
<br />
<h3>Summer Vacation Meetup</h3><br />
<div class="underline-small"><br />
<br />
</div><br />
<br />
<p>Since local competitions are not held this year, iGEM foundation encourages every district to organize communication activity themselves. We responded to the call and organized summer vacation meetup at University of Science and Technology of China.<br /><br />This summer, we invited several iGEM teams from China to USTC from August 15th to August 17th for project showing and ideas interchanging. SJTU-Software, SJTU-BioX-China, SYSU-Software, XMU-China, HFUT_China, USTC_Software and USTC-China paticipated in this activity.<br /><br />The meetup was successful. Firstly, iGEM teams from China got to know each other, and developed profound friendship. Secondly, we understood each other’s project, which would benefit the improvements of our projects. Thirdly, the meetup simulated the real competition segments. We felt the atmosphere of the competition and found the deficiency of our presentations. During the meetup, we also discussed a lot about iGEM, hoping that iGEM could get better and better.<br /><br />All teams attending the meetup make positive evaluations to the activity.</p><br />
<br />
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<h5 style="color:#fff;font-weight:bold;margin-bottom: 25px;">Innovation Experiment Centre of Life Science (IEC)</h5><br />
<p>Building of Life Sciences, Room 363</p><br />
<p>University of Science and Technology of China</p><br />
<p>96, Jinzhai Rd, Shushan, Hefei</p><br />
<p>230026, Anhui, China</p><br />
<p>support@biopano.org</p><br />
</div><br />
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<a href="http://en.ustc.edu.cn"><h4 style="color:antiquewhite">University of Science and Technology of China</h4></a><br />
<p class="copyright">© 2014 USTC-Software,University of Science and Technology of China. All rights reserved.</p><br />
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Hlx1996
http://2014.igem.org/Team:USTC-Software/requirements.php
Team:USTC-Software/requirements.php
2014-10-18T03:11:36Z
<p>Hlx1996: </p>
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<p style="font-size:32px">Requirements</p><br />
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<h4 id="medals">Medals</h4><br />
<div class="underline-small"><br />
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<br />
<br />
<h4><img src="https://static.igem.org/mediawiki/2014/4/4c/2014ustc-Bronze.png" width="60" height="60" alt="Bronze" >Bronze</h4><br />
<p> The following 4 goals must be achieved:</p><br />
<br />
<br />
<br />
<h5><img src="https://static.igem.org/mediawiki/2014/c/c1/Hfut-A.png" width="30" height="30" alt="Complete" ><br />
Register the team, have a great summer, and have fun attending the Jamboree in Boston.<br />
</h5><br />
<br />
<br />
<br />
<br />
<h5><img src="https://static.igem.org/mediawiki/2014/c/c1/Hfut-A.png" width="30" height="30" alt="Complete" ><br />
Create and share a description of the team's project via the iGEM wiki.<br />
</h5><br />
<br />
<br />
<br />
<br />
<h5><img src="https://static.igem.org/mediawiki/2014/c/c1/Hfut-A.png" width="30" height="30" alt="Complete" ><br />
Present a Poster and Talk at the Regional Jamboree and World Championship Jamboree.<br />
</h5><br />
<br />
<br />
<br />
<br />
<h5><img src="https://static.igem.org/mediawiki/2014/c/c1/Hfut-A.png" width="30" height="30" alt="Complete" ><br />
Develop and make available via The Registry of Software Tools, an open source software tool that supports Synthetic Biology based on Standard Parts.<br />
</h5><br />
You can directly enter the precise number of Standard Part, you can get its all types in BioBrick Assistant Windows.<br />
<div class="large-12 columns text-center"><br />
<img style="margin:1em" src="https://static.igem.org/mediawiki/2014/c/ce/2014ustc-medal1.png"><br />
</div> <br />
<p>&nbsp;</p><br />
<br />
<div class="underline-tiny"></div> <br />
<br />
<h4><img src="https://static.igem.org/mediawiki/2014/c/c6/2014ustc-Silver.png" width="60" height="60" alt="Sliver" >Silver</h4><br />
<p> In addition to the Bronze Medal requirements, the following 4 goals must be achieved:</p><br />
<br />
<br />
<br />
<br />
<h5><img src="https://static.igem.org/mediawiki/2014/c/c1/Hfut-A.png" width="30" height="30" alt="Complete" ><br />
Demonstrate the relevance of your development for Synthetic Biology based on standard Parts.<br />
</h5><br />
<p>You can directly enter the precise number of Standard Part, you can get its types in BioBrick Assistant Windows .then you can use blast tool with the sequence from BioBrick Assistant.By comparing the homology between the sequence of the part and in our database, we could predict its impact on the target body when injected to some extent.</p><br />
<div class="large-12 columns text-center"><br />
<img style="margin:1em" src="https://static.igem.org/mediawiki/2014/e/ee/2014ustc-medal2.png"><br />
</div><br />
<br />
<br />
<br />
<br />
<br />
<h5><img src="https://static.igem.org/mediawiki/2014/c/c1/Hfut-A.png" width="30" height="30" alt="Complete" ><br />
Provide a comprehensive and well-designed User Guide. (Be creative! An instructional video may work as well.)<br />
</h5><br />
<p>We have a complete user manual <a href="biopanohelp.pdf">here!</a></p><br />
<br />
<br />
<br />
<br />
<h5><img src="https://static.igem.org/mediawiki/2014/c/c1/Hfut-A.png" width="30" height="30" alt="Complete" ><br />
Provide detailed API documentation, preferably, automatically built from source code documentation (use tools like doxygen, yard, rdoc, naturaldocs, etc).<br />
</h5><br />
<p>We use toc to automatically produce api document. <a href="./api.html">Here!</a></p><br />
<br />
<br />
<br />
<br />
<h5><img src="https://static.igem.org/mediawiki/2014/c/c1/Hfut-A.png" width="30" height="30" alt="Complete" ><br />
Demonstrate that you followed best practises in software development so that other developers can modify, use and reuse your code. Provide more than one realistic test case. Examples of best practices are automated unit testing and documentation of test coverage , bug tracking facilities, documentation of releases and changes between releases.<br />
</h5><br />
<p><b><a href="http://bug.biopano.org">Problem feedback and bug tracking</a>:</b> You can cast inquiry on us by GitHub, GitLab and YouTrack. Meanwhile, YouTrack is also used for bug tracking, ensuring your feedback goes to the developer as soon as possible. <br />
<br /><br /><br />
<b><a href="http://ci.biopano.org"> Automated Deployment</a>:</b> Our server has automated deployment capabilities. Server-side applications are bound with the Product branch of Git. All codes pushed to the Product branch will be deployed to many servers over the world in ten seconds. In order to prevent fault codes from being deployed to the servers by mistake, all the testing branches will be deployed to the testing server real-timely to be tested by developers.<br />
<br /><br /><br />
<b>Unit Testing:</b> Our server applies automated unit testing to dealing with uploaded back end codes. It will test the basic legitimacy and function of the codes, including robustness testing with respect to illegitimate uploaded parameters, legitimacy testing on data legitimacy, status testing of the database and testing of function realizaton, etc.</p><br />
<br />
<p>&nbsp;</p><br />
<div class="underline-tiny"></div><br />
<h4><img src="https://static.igem.org/mediawiki/2014/8/88/2014ustc-Gold.png" width="60" height="60" alt="Gold" >Gold</h4><br />
<p> In addition to the Bronze and Silver Medal requirements, two additional goals must be achieved:</p><br />
<br />
<br />
<br />
<br />
<h5><img src="https://static.igem.org/mediawiki/2014/c/c1/Hfut-A.png" width="30" height="30" alt="Complete" ><br />
Provide a convincing validation, testing the performance of the development -- experimentally (can be outsourced) or by other teams and users. Note, even if the algorithm or tool turns out not to work that well, the Gold requirement is fulfilled if the test is good and the analysis convincing. Validation may include: preferably experiments, informatics analysis (complexity, run time) of an algorithm, or user studies.<br />
</h5><br />
<p><b>Analysis of pathway finder (k-shortest pathway search):</b><br /><br />
We use a specail heuristic algorithm , <a href="http://en.wikipedia.org/wiki/A*_search_algorithm">A* search algorithm</a>, to find more than one path connected two nodes in a given network.The run time of A* depends on structure of the given network. The space complexity is the number of edges plus the number of nodes. In our back end, we test this algorithm. The average of time which database reading costs is 1"40, the average of time which Vars initialization costs is 0"70, the average of time which <a href="http://en.wikipedia.org/wiki/Shortest_Path_Faster_Algorithm">SPFA(abbreviation for Shortest Path Faster Algorithm)</a> costs is 0"37, and the average of time which Serialize costs is 0"21.</p> <br />
<br />
<br />
<h4><br />
And the second goal can be any one of the following:<br />
</h4><br />
<br />
<br />
<br />
<br />
<h5><img src="https://static.igem.org/mediawiki/2014/c/c1/Hfut-A.png" width="30" height="30" alt="Complete" ><br />
Make your software interact / interface with the Registry.<br />
</h5><p>You can directly enter the precise number of Standard Part, you can get its types in BioBrick Assistant Windows .then you can use blast tool with the sequence from BioBrick Assistant.By comparing the homology between the sequence of the part and in our database, we could predict its impact on the target body when injected to some extent.</p><br />
<br />
<div class="large-12 columns text-center"><br />
<img style="margin:1em" src="https://static.igem.org/mediawiki/2014/c/ce/2014ustc-medal1.png"><br />
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<br />
<br />
<br />
<br />
<h5><img src="https://static.igem.org/mediawiki/2014/c/c1/Hfut-A.png" width="30" height="30" alt="Complete" ><br />
Re-use and further develop previous iGEM software projects (or parts thereof) or use and/or improvement of existing synthetic biology tools or frameworks.<br />
</h5><br />
<p>We use blast code from <a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi">ncbi </a>to comparing the homology.</p><br />
<br />
<br />
<br />
<br />
<br />
<h5><img src="https://static.igem.org/mediawiki/2014/c/c1/Hfut-A.png" width="30" height="30" alt="Complete" ><br />
Develop a well documented library or API for other developers (rather than “only” a stand-alone app for end users.)<br />
</h5><br />
<p>We use toc to automatically produce api document. <a href="./docs/">Here!</a></p><br />
<br />
<br />
<br />
<br />
<h5><img src="https://static.igem.org/mediawiki/2014/c/c1/Hfut-A.png" width="30" height="30" alt="Complete" ><br />
Support and use the SBOL and / or SBOLv standard.<br />
</h5><br />
<p>Biopano supports file format conversion to sbol perfectly.</p><br />
<div class="large-12 columns text-center"><br />
<img style="margin:1em" src="https://static.igem.org/mediawiki/2014/d/dd/2014ustc-medal3.png"><br />
</div><br />
<br />
<p></p><br />
<h4 id="safety">Safety</h4><br />
<div class="underline-small"> </div><br />
<h5>1. Are you using the iGEM Software repository at github.com/igemsoftware? If you have instead stored your code elsewhere, please explain where and why you have put it there. If your code is not in the iGEM repository, a re you using any version control system such as Git, CVS, or SVN?<br />
</h5><br />
<p>Yes, we use the iGEM Software repository at github.com/igemsoftware.<br />
</p><br />
<h5> 2. Does your software store any private data supplied by the user? (For example: the user's name and email address, passwords, DNA sequences, circuit designs, etc.) If yes, please describe what kind of data is stored. If no, skip the rest of this question and move on to question 3.<br />
</h5><br />
<p>We store the user's name, the email address (if he/she logs in using Gmail account) or the username (if logged in using Baidu account), and the user's all data designed with our software.<br />
Especially, we DO NOT store the user's password because we only allow users to log in with their Gmail account or Baidu account using OAuth2.0 ,<br />
which is a very secure protocol describing a third-party login pattern.<br />
</p><br />
<h5>3. Does your software include any other security features? Please describe them here. </h5><br />
<p><br />
We use OAuth technology in user system. So users can log in with their GOOGLE account or BAIDU account without telling us their passwords.<br />
</p> <br />
<h5> 4. Does your software let the user create a design by choosing parts/genes from a list/database, such as the Registry? If so, which lists/databases are included? Is there any restriction on which parts/ genes the user can choose?</h5><br />
<p> <br />
Yes, users can use database built by our team to assist themself to create a design. The database we build is the result of merging and reforming parts of KEGG, RegulonDB, Uniport.<br />
</p><br />
<h5>5. Does your software allow users to write new data into any public lists or databases? If so, do you check the new data for errors before allowing it to be written?</h5><br />
<p><br />
Yes, users can upload their data to our database anytime.<br /><br />Yes, we will check validation and format of data before it is written in the back end.<br />
</p><br />
<h5>6. Does your software include any other features that encourage the user to create safe designs? Please describe them. </h5><br />
<p>No.</p><br />
<br />
<h5>7. Is your team also doing biological work in a wet lab ? </h5><br />
<p>No.</p><br />
<p></p><br />
<h4 id="collaboration">Collaboration</h4><br />
<div class="underline-small"><br />
<br />
</div><br />
<p>While preparing for iGEM, we always hope we can accomplish more and more people can join this great project. Luckily, by cooperation with others, all these hopes come ture.</p><br />
<li>Collaboration with professors</li> <br />
<p></p><br />
<p>While completing our project, we encountered all kinds of problems, of which some could hardly solve by ourselves. We solved them by discussing and cooperating with many professors of USTC. At the same time, we knew more about the original thoughts of synthetic biological researchers. So we tried to combine their needs and our project, hoping we could also help them. Now, we believe that we realized our original intention.</p><br />
<li>Collaboration with Chinese iGEMers</li><br />
<p></p><br />
<p>One reason why iGEM competition is unforgettable is that it makes us know more like-minded people. This year, we hoped iGEM teams could communicate more with each other, so we organized iGEM meetup this summer. Teams from China got familiar through the meetup, and we kept in touch after it. We not only got to know each other by frequent communication, but helped each other with their problems to bring about good results for us all as well.</p><br />
<li>Collaboration with HFUT_CHINA</li><br />
<p></p><br />
<p>While enjoying iGEM, we hoped more people could join us. This year, HFUT_CHINA sent a team for iGEM for the first time. As a team new to iGEM, it would surely encounter more problems. As their neighbor, we kept in touch with them and did everything we could to help them with their project. Through the course, we got to know a lot of people enthusiastic about iGEM of our age. We are glad that they also join iGEM.</p><br />
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<h5 style="color:#fff;font-weight:bold;margin-bottom: 25px;">Innovation Experiment Centre of Life Science (IEC)</h5><br />
<p>Building of Life Sciences, Room 363</p><br />
<p>University of Science and Technology of China</p><br />
<p>96, Jinzhai Rd, Shushan, Hefei</p><br />
<p>230026, Anhui, China</p><br />
<p>support@biopano.org</p><br />
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<div class="medium-8 medium-8 pull-5 columns"><br />
<a href="http://en.ustc.edu.cn"><h4 style="color:antiquewhite">University of Science and Technology of China</h4></a><br />
<p class="copyright">© 2014 USTC-Software,University of Science and Technology of China. All rights reserved.</p><br />
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Hlx1996
http://2014.igem.org/Team:USTC-Software/server.php
Team:USTC-Software/server.php
2014-10-18T03:11:18Z
<p>Hlx1996: </p>
<hr />
<div><html class="no-js" lang="en"><br />
<head><br />
<meta charset="utf-8" /><br />
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<li><a href="/Team:USTC-Software/biopano.php#features">Features</a></li><br />
<li><a href="/Team:USTC-Software/biopano.php#demos">Demos</a></li><br />
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<a href="server.php" class="">Server</a><br />
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<li><a href="/Team:USTC-Software/acknowledge.php#utao">USTC Teaching Affair Office</a></li><br />
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str = str + img + status[s].name+"<br /><br />";<br />
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$("#server_status").html(str);<br />
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title: { <br />
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xAxis: { //X轴 <br />
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<div class="main-content"><br />
<div class="row large-12 columns large-centered"><br />
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<div class="large-6 medium-6 columns" style="color:#fff"><br />
<h5 style="color:#fff;font-weight:bold;margin-bottom: 25px;">Innovation Experiment Centre of Life Science (IEC)</h5><br />
<p>Building of Life Sciences, Room 363</p><br />
<p>University of Science and Technology of China</p><br />
<p>96, Jinzhai Rd, Shushan, Hefei</p><br />
<p>230026, Anhui, China</p><br />
<p>support@biopano.org</p><br />
</div><br />
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</div><br />
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<div class="row" ><br />
<div class="medium-4 medium-4 push-9 columns"><br />
<ul class="home-social"><br />
<li><a href="http://www.twitter.com/USTC_Software" class="twitter"></a></li><br />
<li><a href="http://www.facebook.com/USTCSoftware" class="facebook"></a></li><br />
<li><a href="#contactus" class="mail"></a></li><br />
</ul><br />
</div><br />
<div class="medium-8 medium-8 pull-5 columns"><br />
<a href="http://en.ustc.edu.cn"><h4 style="color:antiquewhite">University of Science and Technology of China</h4></a><br />
<p class="copyright">© 2014 USTC-Software,University of Science and Technology of China. All rights reserved.</p><br />
</div><br />
</div><br />
</div><br />
<br />
<script><br />
$(function(){<br />
$('.row .nameplate').click(function(){<br />
var description = $(this).parent().find('.details').html();<br />
var titleText = $(this).text();//text();<br />
$('#pop_up_content').html('<h2>' + titleText + '</h2>' + description);<br />
$('#pop_up').fadeIn();<br />
$(document.body).css("overflow","hidden");//禁止body 滚动条<br />
$("html").css("overflow","hidden");<br />
return false;<br />
});<br />
$('.row .profilewrap').click(function(){<br />
var description = $(this).find('.details').html();<br />
var titleText = $(this).find('.nameplate').text();//text();<br />
$('#pop_up_content').html('<h2>' + titleText + '</h2>' + description);<br />
$('#pop_up').fadeIn();<br />
$(document.body).css("overflow","hidden");//禁止body 滚动条<br />
$("html").css("overflow","hidden");<br />
return false;<br />
}); <br />
$('#pop_up #pop_up_close').click(function(){<br />
$('#pop_up').fadeOut();<br />
$(document.body).css("overflow","auto");<br />
$("html").css("overflow","auto");<br />
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$('#pop_up #pop_up_underlay').click(function(){<br />
$('#pop_up').fadeOut();<br />
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<style type="text/css"><br />
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-webkit-transition: opacity .4s ease-in-out;<br />
-moz-transition: opacity .4s ease-in-out;<br />
-o-transition: opacity .4s ease-in-out;<br />
opacity: 1;<br />
z-index: 100000000;<br />
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#totop {<br />
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background: url(https://static.igem.org/mediawiki/2014/3/31/2014ustc-Totop.png) center center no-repeat;<br />
background-color: #444;<br />
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Hlx1996
http://2014.igem.org/Team:USTC-Software/develop.php
Team:USTC-Software/develop.php
2014-10-18T03:10:57Z
<p>Hlx1996: </p>
<hr />
<div><html class="no-js" lang="en"><br />
<head><br />
<meta charset="utf-8" /><br />
<meta name="viewport" content="width=device-width, initial-scale=1.0" /><br />
<title>USTC-Software | Welcome</title><br />
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<meta name="description" content="iGEM"><br />
<meta name="author" content="Taixing Lin"><br />
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<li><a href="/Team:USTC-Software/biopano.php#features">Features</a></li><br />
<li><a href="/Team:USTC-Software/biopano.php#demos">Demos</a></li><br />
<li><a href="/Team:USTC-Software/biopano.php#why">Why choose BioPano?</a></li><br />
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<div class="row"><br />
<div class="large-12 columns large-centered"><br />
<h3 id="front_end">Front End</h3><br />
<div class="underline-small"></div><br />
<p>The work of front end is various and complicated. We generally divided it into 4 large parts as below:</p><br />
<ul><br />
<li>UI Framework</li><br />
<li>Canvas System</li><br />
<li>Project & Cloud System</li><br />
<li>Functional Units</li><br />
</ul><br />
<p></p><br />
<p>In concise, users can create a biological network on the Canvas, save or browse their work as Projects, get or share biological information by Cloud, and analyze biological data with Functional Units, all of which happen in the friendly environment provided by the UI Framework.</p><br />
<p></p><br />
<p>We based our program on Adobe Air 15.0 platform, with programming language Action Script 3.0 (AS 3.0). AS 3.0 is powerful in vector illustration processing, and provides rich interactions and responsiveness, these two features meet the demand of our project exactly.</p><br />
<p></p><br />
<p>The major techniques we used are as following: Smart Canvas, Operation Track, Multi-Threading and Heterogeneous computing.</p><br />
<p></p><br />
<div class="underline-tiny"> </div><br />
<h5>UI Framework</h5><br />
<p>In order to provide a better user experience, we designed a completely new UI Framework, in which most of the operations can be directly performed while the interface keeps simple and tidy. Meanwhile, this new framework aims for demonstrating information clearly, so there are fewer containers but richer contents. We also added guiding animation responding to most operations so that all the processes are smooth and easy to understand.</p><br />
<p></p><br />
<div class="underline-tiny"> </div><br />
<h5>Canvas System (Smart Canvas)</h5><br />
<p>The canvas to display the biological network is the most important part of this software, so this receives the most concern. A simple canvas with all objects sticking on could not meet the demand of a boundless and highly complicated visual network. So we need to design the structure of both data and displaying object to guarantee the capability of performing mass information while consuming limited system resources. After several trials and analyses, we build our canvas in two major layers and five sub layers:</p><br />
<p></p><br />
<ul><br />
<li>1. Node Layer<br />
<ul><br />
<li>a) Float layer</li><br />
<li>b) Compressed partitioned layer</li><br />
</ul><br />
</li><br />
<li>2. Link Layer<br />
<ul><br />
<li>a) Fast redraw layer</li><br />
<li>b) Float layer</li><br />
<li>c) Compressed layer</li><br />
</ul><br />
</li><br />
</ul><br />
<p>For float layer, objects exist independently, which means they have their own RAM and Graphic. These independent objects have many event listeners that can interact with users easily. Specifically, users can simply move, double-click and edit them. Though a few dozens of objects working in this way together will be quite well, more (thousands of) objects exist in the float layer at the same time will consume a great amount of resources with an unacceptable low speed.</p><br />
<p></p><br />
<p>A biological network can be huge and highly convoluted. To meet the requirement of higher efficiency, we use compressed layer, on which objects are drawn together as one or several (partitioned) bitmaps, to solve this problem. These bitmaps draw fast with GPU acceleration and cost much fewer resources, but they are not interactive. So a significant task we have done is to translate an operation towards an object drawn in compressed layer to the real object by calculating its geometry characteristic. Once a focus intension is traced, the object will emerge to the float layer to interact with the user, and when it loses focus, it will submerge into the compressed layer again and the RAM space will be cleared.</p><br />
<p></p><br />
<p>In most of time, objects stay in compressed layers. But there is still another problem: the graph may be too large to draw at one time while most part of the graph is out of screen. So we use partitioned bitmap blocks (for nodes) and fast drawing layer (for links) in place of one huge bitmap, and redrawing only happens to the blocks (for nodes) or the range (for lines) shown on the screen.</p><br />
<p></p><br />
<p>With all these methods, we could save over 90% costs of system resources while providing an enjoyable user experience.</p><br />
<div class="underline-tiny"> </div><br />
<h5>Project System</h5><br />
<p>Project is the basic unit to manage a biological network. Three kinds of information are saved in a project:</p><br />
<ul><br />
<li>1. Node information</li><br />
<li>2. Link information</li><br />
<li>3. Project information</li><br />
</ul><br />
<p>You can import nodes and links to the project from cloud database or add yours; both can be saved into one project. Meanwhile, two ways are provided to store a project, storing locally and on cloud.</p><br />
<p></p><br />
<p>For a local project, information saved as an XML file, so you can open, save or copy it like any other kind of document.</p><br />
<p></p><br />
<p>Building projects on cloud is strongly recommended, for not only these projects can be open and edit on any computer with your account, but the existence of the nodes and links in the project are recorded in the global biological network database, in which all the nodes and links exist together as well. With more projects uploaded to the cloud, the global database will be extended, thus more information will be provided to users and an ultimate biological network will be built up someday.</p><br />
<p></p><br />
<p>With projects on cloud, researchers worldwide will be able to share and quote the findings of each other or directly build one project together by registering as colleagues. For more information about project management, see documentation of the Back End.</p><br />
<div class="underline-tiny"> </div><br />
<h5>Functional Units</h5><br />
<p><b>BioBrick Assistant:</b><br />BioBrick Assistant will get the BioPart in the form of XML from the official website when the user inputs keywords. Then we extract the important information by using Actionscript XML processing functions in the form of a table.</p><br />
<p></p><br />
<p><b>Google API:</b><br />When the user inputs the keyword, it will be searched on Google. Then we parse the returned HTML, and save the title, author, abstract, and URL of the literature, which is convenient for the user.</p><br />
<p></p><br />
<p><b>Layout Algorithm:</b></p><br />
<p></p><br />
<p>1. Even Layout: First we calculate the border region which the user selected, namely the minimum and maximum of X and Y. So that we can get the height and width of the area. During the process, the number of nodes is gotten. Then we select the value of m and n as below: m, n are integers, m / n is closest to the width / height and m*n is no smaller than the number of the nodes. After m and n are set, the nodes will be arranged that the horizontal interval between horizontally adjacent nodes is width / m, and the vertical interval between vertically adjacent nodes is height / n.</p><br />
<p>2. Plasmid Arrangement: the arrangement of the radius of the circle size is in proportion to the number of nodes selected. Node will be sorted according to the type and arranged on the circle.</p><br />
<p>3. Force-directed Arrangement: Imagine that we assign each node with a positive charge, those nodes are mutually exclusive, and the repulsive force is inversely proportional to the square of the distance. Imagine that every edge is a spring, the force it applies on the nodes at its ends is proportional to the length of the spring. By calculating the force applied to each node, we can determine the direction and magnitude of its displacement. This process is called an iteration. After fifty times of iteration, all the nodes will be in steady state. We make their positions now their final positions for arrangement. The parameters of gravitation and repulsion are determined by experiments. The advantage of the algorithm is that it can arrange the graph like a tree and reduce the cross of edges greatly to show the relationships among the nodes more lucidly.<br />
<br />Force-directed algorithm and GPU acceleration: the time complexity of the arrangement algorithm is O(n^2), so it will take a long time if the number of the nodes is large. So we spill the algorithm among several threads (users can still operate while the back end is calculating) and use the powerful ability for floating-point computation and parallel computation of GPU to accelerate the calculation. Taken multi-platform support into consideration, we use opencl as our programming language. The acceleration uses socket communication for data transfer. The front end send the amount of the nodes, the number and position of each node, the amount of the links and the number of nodes each edge connects to the calculation end. The calculation end spill the computation that the computation of each node is done in a single thread. Visit all the nodes and edges only once and we can get the acceleration of each node. When the computation is done, the calculation end sends every node’s position to the front end.</p><br />
<p></p><br />
<h3 id="back_end">Back End</h3><br />
<div class="underline-small"><br />
</div><br />
<h5>Framework</h5><br />
<p>Our server uses Linux as operating system, MongoDB to manage abundant biological data, including information of millions of nodes, and MySQL database to store data of users and information of projects and species. Our server-side program is based on Django development, and is optimized for multi-node and remote-controlling circumstances, ensuring that your request will be answered wherever you are. When a node breaks down, our server will separate the node from the group and realize automatic failover.</p> <br />
<br />
<br />
<br />
<br />
<div class="underline-tiny"> </div><br />
<h5>Account System:</h5><br />
<p>Oauth is used as login credential. You just need to provide your Google or Baidu account and use Biopano conveniently without signing up. Meanwhile, Oauth is decoupled with local account system, providing convenience for developers to offer more ways for authentication.</p><br />
<br />
<div class="underline-tiny"> </div><br />
<h5>Rapid Server Deployment:</h5> <br />
<P>We do not recommend users to build at local Biopano server, for one of the main advantages of Biopano is data sharing. However, for special cases such as intranet, you could use the docker repository we provide to deploy a Biopano server rapidly. We encapsulate basic databases to offer powerful basic biological data support for your intranet server.</P><br />
<br />
<div class="underline-tiny"> </div><br />
<h5>Interface Design:</h5><br />
<p>The server communicate with front end based on HTTP protocol. It uses interfaces of RESTful style. It is a kind of completely public and universal interface and offers detailed documentation. You can develop your own applications based on these interfaces. These interfaces have been optimized a lot for Biopano-client, so the communication efficiency has been enhanced significantly.</p><br />
<br />
<div class="underline-tiny"> </div><br />
<h5>Automated Deployment:</h5><br />
<p>Our server has automated deployment capabilities. Server-side applications are bound with the Product branch of Git. All codes pushed to the Product branch will be deployed to many servers over the world in ten seconds. In order to prevent fault codes from being deployed to the servers by mistake, all the testing branches will be deployed to the testing server real-timely to be tested by developers.</p><br />
<br />
<div class="underline-tiny"> </div><br />
<h5>Unit Testing:</h5><br />
<p>Our server applies automated unit testing to dealing with uploaded back end codes. It will test the basic legitimacy and function of the codes, including robustness testing with respect to illegitimate uploaded parameters, legitimacy testing on data legitimacy, status testing of the database and testing of function realizaton, etc.</p><br />
<br />
<h3 id="alogrithm">Alogrithm</h3><br />
<div class = "underline-small"></div> <br />
<h5>Pathway Finder Alogrithm:</h5><br />
<p>The software can search for paths between two selected nodes. We used a-stark short-path algorithm to achieve the function of discovering potential relationship in the biological network.<br />
A* algorithm is a search algorithm based on greedy, which can always visit fewer nodes and get a better solution at the same time.<br />
In this way, however, we get the shortest path in graph theory. By giving different and appopraite weights to different edges, the algorithm can find the shortest path in the sense of biology.</p><br />
<br />
<div class="underline-tiny"> </div><br />
<h5>BLAST:</h5><br />
<p><br />
We use two packages, namely, NCBI_Blast and the Python package called for NCBI_Blast. Different from NCBI, our alignment database combines RegulonDB and user-define databases. When the user inputs a sequence (such as a BioBrick sequence), Biopano will the node that shares the deepest homology with it in the server database, and show other nodes connected with it. Therefore, Biopano can show the nodes and regulations in the biological regulation network that probably has to do with the sequence (such as BioBrick sequece) the user inputs.<br />
</p><br />
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<p>University of Science and Technology of China</p><br />
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Hlx1996
http://2014.igem.org/Team:USTC-Software/biopano.php
Team:USTC-Software/biopano.php
2014-10-18T03:10:39Z
<p>Hlx1996: </p>
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<h4 id="overview">Overview</h4><br />
<div class="underline-small"></div><br />
<p>Designed specifically for biological research, BioPano is a software platform targeted for visualisation of biological relationships as well as cooperative net-building. You can set up your own network of biological relationship by adding information about genetic regulation and metabolic system to the network we already provided for you. Also, the software allows you to explore the links among the substances by just several clicks, and you can even look into the details of the interaction between the exogenous gene and the host. What is even more exciting is that our software will end your loneliness and frustration in research, since it is providing you with cloud cooperating system so that you can view massive amounts of resources in databases, together with build up groups to share information and set up mutual network with others.<br />
</p><br />
<br />
<h4 id="motivation">Motivation</h4><br />
<div class="underline-small"></div><br />
<p><br />
In recent years, people has made a lot of remarkable achievements <br />
in synthetic biology. However, scientists are often faced with <br />
many unpredictable problems when carrying out experiments. <br />
Each kind of biological substance is inextricably linked to the <br />
biological environment to which it belongs, so we have to consider <br />
a question: Can we attain the desired goal, if we simply follow the traditional ideas of synthetic biology and avoid the problem merely by engineering?<br />
</p><br />
<p><br />
A synthetic biologist, Chris Voigt, has successfully transferred a<br />
Toggle Switch, which usually works in the Bacillus <br />
subtilis, into E. coli. Unfortunately, it did not function properly. In <br />
fact, in experiments, due to the unexpected interactions between <br />
BioBrick and the host, it is very common that the designed path do <br />
not work as anticipated.<br />
</p><br />
<p><br />
In fact, the life system is so complex that there are many sorts of <br />
biological substance to support it with complex interations in it. <br />
In order to understand a phenomenon, we keep using new and <br />
sophisticated methods to refine our research and to explore every <br />
detail of life. However, if we widen our perspective, by looking at <br />
our research objectives from a more comprehensive perspective, <br />
we may have some unexpected discoveries.<br />
</p><br />
<br />
<h4 id="features">Features</h4><br />
<div class="underline-small"><br />
</div><br />
<p>Our software has many marvelous features, with which your biology research will become extremely easy and joyful.</p><br />
<ul><br />
<br />
<h5>1. Expansion of single node</h5><br />
<div class="row"><br />
<div class="large-6 columns"><p>In Biopano, every biology part of E.coli K-12 will be displayed as a node of different types and regulation relationship <br />
will be displayed as arc of different types. They are displayed in the biological network in a visualizational way. <br />
You just need to select a node and click “Expand”, and the nodes associated with it will be “expanded”. <br />
Nodes are connected to each other by all kinds of relationship, so users can see how biological parts are connected clearly, <br />
such as LacI Operon. </p></div><br />
<div class="large-6 columns"><img src="https://static.igem.org/mediawiki/2014/4/46/2014ustc-Feature-a.png"></div><br />
</div><br />
<br />
<div class="row"><br />
<div class="large-6 columns"><img src="https://static.igem.org/mediawiki/2014/9/9e/2014ustc-Feature-b.png"></div><br />
<div class="large-6 columns"><p>However, since there are so many biological parts connected to each other in various convoluted, <br />
the expansion of all nodes will give rise to extremely involved nets, which will fail to convey useful information to the users, <br />
even interfere their thoughts. So you can choose to expand the nodes in a way you see fit. Take Transcription factor CRP as an example. </p><br />
<p>Biopano displays the network dynamically, which makes you able to tease out the relationship among thousands of materials of <br />
E.coli K-12, satisfies your curiosity and helps you discover unknown biological field.</p></div><br />
</div><br />
<div class="underline-tiny"></div><br />
<br />
<br />
<br />
<h5>2. Link Finder</h5><br />
<div class="row"><br />
<div class="large-6 columns"><p>You can input two nodes that seem irrelevant, such as gene A and Transcription FactorB, and the software will <br />
search the route connecting the two nodes for you. Since some routes are too sinuous for further analysis or does not make sense, <br />
you can set a specific number k, Biopano will search and show the k shortest routes for you.</p></div><br />
<div class="large-6 columns"><img src="https://static.igem.org/mediawiki/2014/7/79/2014ustc-Feature-c.png"></div><br />
</div><br />
<div class="underline-tiny"></div><br />
<br />
<br />
<h5>3. BLAST</h5><br />
<div class="row"><br />
<div class="large-6 columns"><img src="https://static.igem.org/mediawiki/2014/7/71/2014ustc-Feature-e.png"></div><br />
<div class="large-6 columns"><p>By BLAST method, Biopano finds E.coli K-12 gene highly similar to the injected sequence. <br />
These genes are regulated by other parts in E.coli K-12, so can provide information of the host environment’s impact on injected <br />
exogenous sequence. Biopano also offers BioBrick helper, enabling you search all kinds of BioBricks on iGEM’s official website. <br />
By BLAST analysis, it helps you design correct gene route with appropriate BioBricks.</p></div><br />
</div><br />
<div class="underline-tiny"></div><br />
<br />
<br />
<h5>4. Data Sharing</h5><br />
<p>Hence, while offering various functions, Biopano also serves as a cooperative network building platform. When you create a project, you can add new nodes, name new biological parts and link them with respect to your comprehension to build a brand new net gradually. Meanwhile, Biopano provides log in service. You can sign up with Google or Baidu account and upload your network to the main database to make it more plentiful. Biopano also supports data importing in batch. You can even import data of a species and a database.</p><br />
<ul class="small-block-grid-2"><br />
<li><img src="https://static.igem.org/mediawiki/2014/2/2a/2014ustc-Feature-f.png"></li><br />
<li><img src="https://static.igem.org/mediawiki/2014/5/57/2014ustc-Feature-g.png"></li><br />
</ul><br />
<div class="underline-tiny"></div><br />
<br />
<h5>5. Details and Reference</h5><br />
<p>When you have already got the entire view and want to know more about the details, double-click the nodes and arcs and the details will be shown. More surprisingly, Biopano supports literature reading in the network. You can view literature corresponding to every node and arc along any gene route in the network, and you will understand how the nodes in the net are associated with each other in depth. If you cast doubt on the reliability of our database, you can verify your thought with authoritative literature.</p><br />
<br />
</ul><br />
<p></p><br />
<h4 id="demos">Demo</h4><br />
<div class="underline-small"><br />
</div><br />
<div><br />
<h4>Next we will demonstrate some common modules of E.coli k-12:</h4><br />
<br />
<h5>1, Lac Operon: When you input LacZYA, a Transcription Unit(TU) of Lac Operon and Expand the node:</h5><br />
<p>You will see four promoters, acZp1, lacZp2, lacZp3 and lacZp4 as<br />
upstream sequences and three structure genes, lacZ, lacY and lacA as <br />
downstream sequences. Meanwhile, you can see the TU belongs to <br />
the Operon lacZYA.<br />
</p><br />
<p>Above the node lacZYA, you also see three Transcription<br />
Factors, namely, CRP, H-NS and lacl. They suppress the expression of <br />
lazZYA.</p><br />
<p>Expand lacZ, lacY and lacA, and we get BgaL, LacY and ThgA<br />
respectively, of which Bgal and ThgA are Enzymes. They catalyze<br />
corresponding reactions. Expand Lacl and we get the gene lacl which<br />
codes it.</p><br />
<ul class="small-block-grid-2"><br />
<li><img src="https://static.igem.org/mediawiki/2014/4/47/2014ustc-B.png"></li><br />
<li><img src="https://static.igem.org/mediawiki/2014/e/ee/C.png"></li><br />
</ul><br />
<br />
<p>Continue to Expand lacZYA and lacl and we find more materials’<br />
connected with them. You can select and drag the nodes to arrange the <br />
network neatly; you can also click Full Screen and the network will be <br />
displayed in full screen.</p><br />
<ul class="small-block-grid-2"><br />
<li><img src="https://static.igem.org/mediawiki/2014/c/c5/2014ustc-D.png"></li><br />
<li><img src="https://static.igem.org/mediawiki/2014/3/3a/2014ustc-E.png"></li><br />
</ul><br />
<br />
<h5>2, Following the same steps, we can also get the regulation network of<br />
the Operon Trp.</h5><br />
<img src="https://static.igem.org/mediawiki/2014/9/9d/2014ustc-F.png"><br />
<br />
<br />
</div><br />
<br />
<br />
<h4 id="why">Why choose BioPano?</h4><br />
<div class="underline-small"></div><br />
<div><br />
<p> Biopano, do the experiment as you do in the lab.</p><br />
<p>In experiment, synthetic biologists always find gene circuits formed by BioBricks are incompatible with the host cell, thus cannot work as expected. However, Biopano uses sequence alignment to analyze the possible reasons of the failure and design more acute gene circuit for your consideration.</p><br />
<p>Our Blast algorism derives from NCBI. However, the original version only offers sequence alignment and fails to analyze what impact the host environment might have on the injected gene circuit, let along predicts whether it will work.</p><br />
<p>Firstly, Biopano offers BioBrick searching to make it convenient for you to study all standardized biological parts on the official website of iGEM. Secondly, you can input a BioBrick and even construct a brand new sequence. Biopano will find the gene nodes of E.coli K-12 sharing the deepest homology with it based on authoritative Blast algorithm. Then you can Expand these nodes to find out the possible regulation on them. In this way, Biopano helps you analyze whether the injected gene circuit will actually work.</p><br />
<p>Biopano abstracts biological parts and the regulation among them into nodes and arcs to realize data visualization, and displays gene regulation and metabolism network of E.coli K-12 dynamically by continually Expanding nodes. Single database cannot make an entire material network, so our back end combines Regulon DB, KEGG, Uniprot and abundant data. You can ceaselessly Expand the nodes in the network to comb the relationship among them and satisfy your curiosity.</p><br />
<br />
<p>Compared with Biopano, Cytoscape and Netscience mainly support file importing and network displaying without powerful database from the back end. Hence you cannot search for biological parts online and view the certain part of the biological network you need with them.</p><br />
<br />
<p>Now that there is enormous astonishing material relationship in biological body, more and more biologists hope to find the specific function route between two biological parts or even two biological blocks that seem not related to each other, such as c-di-GMP signalling and Quorum Sensing. Unfortunately, the interactions of the biological parts are saved in database as records and it is almost impossible to find the route in thousands of records. There haven’t been any software to offer any help before. Luckily, Biopano brings hope to this.</p><br />
<br />
<p>You can input two biological parts and set several shortest routes, then you will find their relationship. We used this powerful function to find the specific relationship betweem c-di-GMP signalling and Quorum Sensing, which was corroborated by corresponding literature. How amazing!</p><br />
<br />
<p>We have to admit that Biopano may show you wrong gene route. However, it provides you with direction of studying the relationship of two fields. It not only makes your goal for experiment designing clearer, but enables you to understand the connection inside body is so close as well.</p><br />
<br />
<p>While offering function services, Biopano serves as a platform for collaborative network building. You can define new nodes and arcs yourself and sign in with your Google or Baidu account to upload the network you build to our database. You can also invite several companions to complete a project together. Common biological software, such as Cytoscape and Netscience, doesn’t provide a good platform for communication, while Biopano enhances the communication of biological areas by data sharing.</p><br />
<br />
<p>Biopano, your right hand for biological research. Get it now!</p><br />
</div><br />
<br />
<h4 id="futurework">Future Work</h4><br />
<div class="underline-small"></div><br />
<div><br />
<h4>It is undeniable that we still have a lot to do to improve Biopano in many aspects in order to make it even better. We need to think more and develop it as we can. In the future, we hope to:<br />
</h4><br />
<br />
<p>1. Integrate more data in it. Currently, Biopano only integrates data of E.coli k-12 from Regulon DB, KEGG and Uniprot, and our data in regulatory interaction lack accurate numerical data to indicate its strength. etc. Therefore, not only will we update the existing data in the original species, we will also make complement of high-throughput data through other databases and papers, as well as expand information of other species, so that more biological researchers can benefit from our software.</p><br />
<br />
<p>2. Normalize users' rights, improve quality of data. With the increase of the number of users, the data synchronized every day become not only massive, but also in many different forms, and some of them have nevitable errors or redundant information, or there may be different kinds of comprehension of certain regulatory relations. So we want the machine to automatically recognize the validity of the data submitted by the user, and establish a evaluation criteria of credibility. Thus, only those reliable users will be selected, and only their data can be synchronized to the main database, and the redundancy or errors will be eliminated, and they also continue to enhance the credibility and value of the main database.</p><br />
<br />
<p>3. Enhance network analysis functions. When we add the high-throughput kinetic data for biological networks, we can build a variety of mathematical models on the network and carry out quantitative simulation analysis. For example, we can put the nodes that are closely related to one another together in a group. We can make out software automatically arrange the modules for different functions in the organism. We can even do things that are analogic to those in an electric circult. The network provides the entrance and the exit of the signals, and all you need to do is to enter the target product and we will help you find the substance needed for synthesizing it. </p><br />
<br />
<p>4. Supports more file formats. Currently, the file formats we provide to the users are only XML and SBOL. In the future we will make our software support more file formats, such as sif, EMBL, etc., and we will develop its ability to be capable with other biological softwares such as cytoscape and Netscience, seamlessly. You can import and export any file that are constantly used. From this aspect, we will greatly broadens the scope of the functions of the software.</p><br />
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<h5 style="color:#fff;font-weight:bold;margin-bottom: 25px;">Innovation Experiment Centre of Life Science (IEC)</h5><br />
<p>Building of Life Sciences, Room 363</p><br />
<p>University of Science and Technology of China</p><br />
<p>96, Jinzhai Rd, Shushan, Hefei</p><br />
<p>230026, Anhui, China</p><br />
<p>support@biopano.org</p><br />
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<h5 style="color:#fff;font-weight:bold;margin-bottom: 25px;">Innovation Experiment Centre of Life Science (IEC)</h5><br />
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Hlx1996
http://2014.igem.org/Team:USTC-Software/team.php
Team:USTC-Software/team.php
2014-10-18T03:08:13Z
<p>Hlx1996: </p>
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<img src="https://static.igem.org/mediawiki/2014/6/62/2014ustc-Xyc.jpg" alt="Xue Yuechuan"><br />
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<div class = "details"><img src="https://static.igem.org/mediawiki/2014/6/62/2014ustc-Xyc.jpg" alt="Xue Yuechuan" align="left"><p>captain<br>junior from physical electronics major<br>team leader and art designer</p><br />
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<img src="https://static.igem.org/mediawiki/2014/e/ee/2014ustc-Zss.jpg" alt="Zhao Shensen"><br />
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<div class = "details"><img src="https://static.igem.org/mediawiki/2014/e/ee/2014ustc-Zss.jpg" alt="Zhao Shensen" align="left"><p>vice captain<br>senior from physical electronics major<br>help team managing,join back end work</br>his words:Work which make idea true make me happy</p><br />
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<div class = "details"><img src="https://static.igem.org/mediawiki/2014/6/6e/2014ustc-Glz.jpg" alt="Gan Longzhi" align="left"><p>team manager<br>sophomore from school of earth and space science<br>help team managing,web and document writing<br>his words:Try hard, have fun.</p><br />
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<div class = "details"><img style="width:200px" src="https://static.igem.org/mediawiki/2014/6/6c/2014ustc-Ltx.jpg" alt="Lin Taixing" align="left"><p>member<br>junior from Atomic and molecular physics major<br>Responsible for web designing<br>his words:Dream what you want to dream; go where you want to go; be what you want to be, because you have only one life and one chance to do all the things you want to do. </p><br />
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<div class = "details"><img src="https://static.igem.org/mediawiki/2014/1/1e/2014ustc-Wws.jpg" alt="Wang Wenshuo" align="left"><p>member<br>Junior of the Special Class for the Gifted Young, majoring in Statistics<br>tranlates and document writing<br>his words:There is no fate but what we make.</p><br />
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<div class = "details"><img src="https://static.igem.org/mediawiki/2014/d/d0/2014ustc-Zzy.jpg" alt="Zhang Zhiyuan" align="left"><p>member<br>Senior of Hua Loo-Keng Talent Program in Mathematics, majoring in fundamental mathematics<br>tranlates and document writing<br>her words:To see, to ask, to search, to believe.</p><br />
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<img src="https://static.igem.org/mediawiki/2014/7/7d/2014ustc-Gyf.jpg" alt="Gao Yifan"><br />
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<div class = "details"><img src="https://static.igem.org/mediawiki/2014/7/7d/2014ustc-Gyf.jpg" alt="Yifan Gao" align="left"><p>member<br>junior from optics major<br>Responsible for back end work<br>his words:Perfection is achieved not when there is nothing more to add, but rather when there is nothing more to take away.</p><br />
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<img src="https://static.igem.org/mediawiki/2014/4/4b/2014ustc-Dcx.jpg" alt="Dong Chenxiao"><br />
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<div class = "details"><img src="https://static.igem.org/mediawiki/2014/4/4b/2014ustc-Dcx.jpg" alt="Dong Chenxiao" align="left"><p>member<br>sophomore from school of physics science<br>data hunting and organizing,software design and document writing<br>his words:All the time, try retroting any idea from team.</p><br />
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<img src="https://static.igem.org/mediawiki/2014/2/28/2014ustc-Jzy.jpg" alt="Haiyan Liu"><br />
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<div class = "details"><img src="https://static.igem.org/mediawiki/2014/2/28/2014ustc-Jzy.jpg" alt="Haiyan Liu" align="left"><p>member<br>sophomore from school of earth and space science<br>data hunting and organizing,software design and document writing<br>his words:Not most powerful, but highly responsible!</p><br />
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<img src="https://static.igem.org/mediawiki/2014/9/97/2014ustc-Zl.jpg" alt="Haiyan Liu"><br />
<div class ="nameplate"><a href="#">Zhou Long</a></div><br />
<div class = "details"><img src="https://static.igem.org/mediawiki/2014/9/97/2014ustc-Zl.jpg" alt="Haiyan Liu" align="left"><p>member<br>junior from Nuclear physics major<br>>Responsible for Front End work<br>his words:Simply Enjoy.</p><br />
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<img src="https://static.igem.org/mediawiki/2014/a/a1/2014ustc-Hlx.jpg" alt="Han Luxin"><br />
<div class ="nameplate"><a href="#">Han Luxin</a></div><br />
<div class = "details"><img src="https://static.igem.org/mediawiki/2014/a/a1/2014ustc-Hlx.jpg" alt="Han Luxin" align="left"><p>member<br>sophomore from school of computer science<br>Algorithm design and writing,web writing<br>his word:Where there is a will, there is a way.</p><br />
</div><br />
</li><br />
<br />
<li class ="profilewrap"><br />
<img src="https://static.igem.org/mediawiki/2014/8/8d/2014ustc-Ycp.jpg" alt="Yu Chuanping"><br />
<div class ="nameplate"><a href="#">Yu Chuanping</a></div><br />
<div class = "details"><img src="https://static.igem.org/mediawiki/2014/8/8d/2014ustc-Ycp.jpg" alt="Yu Chuanping" align="left"><p>member<br>senior from statistics major<br>translate<br>her words:Do one thing at a time, and do well.</p><br />
</div><br />
</li><br />
<br />
<li class ="profilewrap"><br />
<img src="https://static.igem.org/mediawiki/2014/4/44/2014ustc-Zhy.jpg" alt="Zhang Huayu"><br />
<div class ="nameplate"><a href="#">Zhang Huayu</a></div><br />
<div class = "details"><img src="https://static.igem.org/mediawiki/2014/4/44/2014ustc-Zhy.jpg" alt="Zhang Huayu" align="left"><p>member<br>sophomore from school of physics science<br>Front End work<br>his words:Be the best yourself, to be No.1. </p><br />
</div><br />
</li><br />
<br />
</li><br />
<br />
<li class ="profilewrap"><br />
<img src="https://static.igem.org/mediawiki/2014/9/96/2014ustc-Fyc.jpg" alt="Haiyan Liu"><br />
<div class ="nameplate"><a href="#">Fei Yicheng</a></div><br />
<div class = "details"><img src="https://static.igem.org/mediawiki/2014/9/96/2014ustc-Fyc.jpg" alt="Haiyan Liu" align="left"><p>member<br>sophomore from school of physics science<br>back end work<br>his words:Be the best yourself, to be No.1. </p><br />
</div><br />
</li><br />
<br />
<li class ="profilewrap"><br />
<img src="https://static.igem.org/mediawiki/2014/b/bc/2014ustc-Ctl.jpg" alt="Chen Tianlong"><br />
<div class ="nameplate"><a href="#">Chen Tianlong</a></div><br />
<div class = "details"><img src="https://static.igem.org/mediawiki/2014/b/bc/2014ustc-Ctl.jpg" alt="Chen Tianlong" align="left"><p>member<br>sophomore from school of matnematics<br>web design<br>his words:Be the best yourself, to be No.1. </p><br />
</div><br />
</li><br />
<br />
<li class ="profilewrap"><br />
<img src="https://static.igem.org/mediawiki/2014/e/e8/Clf.jpg" alt="Chen Lingfan"><br />
<div class ="nameplate"><a href="#">Chen Lingfan</a></div><br />
<div class = "details"><img src="https://static.igem.org/mediawiki/2014/e/e8/Clf.jpg" alt="Chen Lingfan" align="left"><p>member<br>junior from computational mathematics major<br>algorithm design<br>his words:Be the best yourself, to be No.1. </p><br />
</div><br />
</li><br />
<br />
</ul><br />
<h4 id="I_A">Instructors & Advisors</h4><br />
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<br />
<br />
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<img src="https://static.igem.org/mediawiki/2014/d/de/2014ustc-G.png" alt="Haiyan Liu"><br />
<div class ="nameplate"><a href="#">Haiyan Liu</a></div><br />
<div class = "details"><img src="https://static.igem.org/mediawiki/2014/d/de/2014ustc-G.png" alt="Haiyan Liu" ><br />
<p><b>Email:</b>hyliu@ustc.edu.cn</p><br />
<p><b>Brief Intro:</b>Haiyan Liu was born in Sichuan Province, China. He received his BS degree in Biology in 1990 and PhD degree in Biochemistry and Molecular Biology in 1996, both from USTC. Between 1993 and 1995 he was a visiting graduate student in Laboratory of Physical Chemistry of ETH, Zurich (Switzerland). From 1998 to 2000 he was post-doctoral research associate at Department of Chemistry, Duke University (USA) and Department of Biochemistry and Biophysics UNC-Chapel Hill (USA). Since 2001, he has been a professor of computational biology at School of Life Sciences, USTC.</p><br />
</div><br />
</li><br />
<br />
<br />
<li class ="profilewrap"><br />
<img src="https://static.igem.org/mediawiki/2014/a/af/2014ustc-H.png" alt="Zhi Liang"><br />
<div class ="nameplate"><a href="#">Zhi Liang</a></div><br />
<div class = "details"><img src="https://static.igem.org/mediawiki/2014/a/af/2014ustc-H.png" alt="Zhi Liang" ><br />
<p><b>Email:</b>liangzhi@ustc.edu.cn</p><br />
<p><b>Brief Intro:</b>Liang Zhi, Ph.D., Associate Professor Extraordinary . 2000 graduated from the school of Life Sciences in the University of Science and Technology of China, received bachelor's degree in biology and electronics and information engineering dual degree. 2006 graduated from the school of Life Sciences in the University of Science and Technology of China protein crystallography laboratory , PhD. From 2007 to 2012 in the school of Life Sciences in the University of Science and Technology of China Systems Biology Laboratory in systems biology postdoctoral research. Postdoctoral period has won China Postdoctoral Science Foundation funded second and Natural Science Foundation funding. 2012 University of Science and Technology of China Extraordinary Life Sciences Research Associate . Research results published on Nucleic Acids Res, Bioinformatics, Bioinformatics, J Biol Chem.</p><br />
</div><br />
</li><br />
<br />
<li class ="profilewrap"><br />
<img src="https://static.igem.org/mediawiki/2014/9/93/2014ustc-I.png"><br />
<div class ="nameplate"><a href="#">Jiong Hong</a></div><br />
<div class = "details"><img src="https://static.igem.org/mediawiki/2014/9/93/2014ustc-I.png" alt="Jiong Hong" ><br />
<p>Professor, School of Life Sciences University of Science & Technology of China</p><br />
<p><br />
<b>Email:</b> hjiong@ustc.edu.cn<br /><br /><br />
<b>Brief Intro:</b>Jiong Hong was born in Anhui Province, China. He received his BS degree in 1993 from Anhui Normal University, MSc degree in 1996 from Beijing Normal University, and Ph.D degree in 2003 from Kyoto University, all in Life Sciences. From 2006 to 2008, he did post-doctoral research in Virginia Tech University, USA. Since 2008, he has been introduced to the USTC as talented.<br />
</p><br />
</div><br />
</li><br />
<br />
<br />
<li class ="profilewrap"><br />
<img src="https://static.igem.org/mediawiki/2014/9/92/2014ustc-J.png" alt="Fan Jin"><br />
<div class ="nameplate"><a href="#">Fan Jin</a></div><br />
<div class = "details"><img src="https://static.igem.org/mediawiki/2014/9/92/2014ustc-J.png" alt="Fan Jin" ><br />
<br />
<br /><br /><br />
<p>1997.07-2002.07 B.S., Student, Department of Applied Chemistry, University of Science & Technology of China, P. R. China.<br />
Degree awarded: B.S. in chemistry, 07/2002</p><br />
<br />
<p>2003.08-2007.06 Ph.D. Candidate, Department of Chemistry, The Chinese University of Hong Kong.<br />
Degree awarded: Ph.D in chemistry, 06/2007</p><br />
<br />
<p>2002.07-2003.07 R.A., The Hefei National Laboratory of Physical Science at Microscale, Department of Chemical Physics, University of Science & Technology of China, P. R. China.</p><br />
<br />
<p>2007.06-2009.01 Postdoctoral Associate, Department of Chemistry, The Chinese University of Hong Kong.</p><br />
<br />
<p>2009.01-2009.11 Postdoctoral Associate, Department of Materials Science and Engineering, University of Illinois at Urbana Champaign.</p><br />
<br />
<p>2009.11-2011.8 Postdoctoral Associate, Department of Bioengineering, California Nanosystems Institute, University of California, Los Angeles. </p><br />
<br />
<p>2011.8-present Professor, Department of Polymer Materials Science and Engineering, University of Science and Technology of China, CAS Key Lab of Soft Matter Chemistry. </p><br />
<br />
<h4>Research Interests</h4><br />
<p>Polyelectrolyte and colloidal particles in the oil-water interface. </p><br />
<p>Interaction between Antibiotic peptides and lipids membrane. </p><br />
<p>Living cell image and living cell micro-manipulation.</p><br />
<p>Biological macromolecules, characterization of supramolecular assembly and its applications in drug delivery and gene transfection. </p><br />
<p>Bacterial communities. (Ex: signaling, motility, social organization in biofilms)</p><br />
<br />
<br />
<br />
</div><br />
</li><br />
</ul><br />
<br />
</div><br />
<br />
<br />
<h4 id="Additional_thanks">Additional Thanks</h4><br />
<div class="underline-small"><br />
<br />
</div><br />
<div style="line-height:200%"><br />
<li><br />
Thanks for financial assistance from Deutsche Bank, USTCIF and USTC Teaching Affair Office. Only with their help could we finish the competition;<br />
</li><br />
<li><br />
Thank data from RegulonDB, KEGG, Uniprot and NCBI. Only with their data and apis could we refine our database; <br />
</li><br />
<li><br />
Thank project guidance from Haiyan Liu, Zhi Liang, Fan Jin and Jiong Hong. Only with their guidance could our project be improved and deepened; <br />
</li><br />
<li><br />
Thank Chen Liao for participating in the use, evaluation and popularization of Biopano.He pointed out many deficiencies and bugs of our software.<br />
</li><br />
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<p>Building of Life Sciences, Room 363</p><br />
<p>University of Science and Technology of China</p><br />
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Hlx1996
http://2014.igem.org/Team:USTC-Software/human_practice.php
Team:USTC-Software/human practice.php
2014-10-18T02:57:55Z
<p>Hlx1996: </p>
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<p style="font-size:32px">Human Practice</p><br />
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<h4 id="management">Management</h4><br />
<div class="underline-small"><br />
<br />
</div><br />
<h5> iGEM, Efficiency, Environment and Enjoyment</h5><br />
<p>During the entire iGEM project, we adhered to the four elements,<br />
iGEM, efficiency, environment and enjoyment. When the project is drawing to a close,<br />
we tease out our project management experience according<br />
to them and put it online as reference for more people.</p><br />
<div class="underline-tiny"></div><br />
<h5>iGEM</h5><br />
<br />
<p>Since our project is for participating in iGEM,<br />
we always emphasized the leading position of iGEM in our project.<br />
We set up study group specifically for iGEM project. Independent of the working group,<br />
they worked on synthetic biology. Although some of their results turned out to be useless,<br />
they played a critical role in every phase of our project, such as the decision of our final project,<br />
the optimization of functions of the software and teaching other team members<br />
not majoring in biology some biological knowledge. A group focusing on the subject guarantees<br />
that the whole project runs smoothly on track. The experience above applies to project of any subject.<br />
Just replace “iGEM” with your own word.</p><br />
<div class="underline-tiny"></div><br />
<h5>Efficiency</h5><br />
<br />
<p>In any project, efficiency is always a significant factor.<br />
During our project, we took regular and necessary methods,<br />
such as wholesome team management system (team leader, team manager,<br />
group supervisor) and explicit regulations. In addition,<br />
we managed our team in an innovative way—electronic platform.<br />
All work plans are put on electronic notebook shared by all team members.<br />
We also built a platform for team members to report their working achievements periodically.<br />
Last but not least, we established a GitLab ourselves accessible to all team members,<br />
which avoided the detriment of environment caused by paper-based platform <br />
(this will be mentioned again later).</p><br />
<div class="underline-tiny"></div><br />
<h5>Environment</h5><br />
<br />
<p><br />
Environmental protection is one of the most compelling problems nowadays.<br />
We kept thinking about this while proceeding the project. As mentioned above,<br />
we built a paperless office, except for necessary invoices. Compared with previous iGEM teams of USTC,<br />
we saved a lot of paper. Meanwhile, we paid attention to keeping our working environment neat and clean.<br />
The workplace was cleaned by our team members every day.<br />
Garbage was classified and dropped in the garbage bin. We believe that<br />
appropriate regulation can ensure that working group of any project can <br />
do their work comfortably and protect the earth at the same time.<br />
</p><br />
<div class="underline-tiny"></div><br />
<h5>Enjoyment</h5><br />
<p><br />
Although there were a lot of work to do, our project experience was joyful.<br />
At the beginning of the project, team members with experience in software <br />
development prepared courses for other members. Well-prepared courses made us accomplish <br />
the assignments successfully and gain new knowledge. We also organized various kinds of <br />
activities to relax our team members. In the summer vacation, we had group activities <br />
after a whole day’s hard work, including having dinner outside, playing sports and even<br />
computer game competition. We also recommend these activities to every team. They not only<br />
relax team members, but also improve the relationship among team members, making the whole<br />
working experience enjoyable and unforgettable.<br />
<br />
</p><br />
<br />
<br />
<h3 id="hlxisveryhandsome">Software & Platforms We Used</h3><br />
<div class="underline-small"><br />
<br />
</div><br />
<br />
<h5>Google group</h5><br />
<br />
<p>At the formation of USTC-Software of 2014, the team leader of 2013 recommended Google group as an online platform for communication and team management. Although every team member was highly enthusiastic about iGEM, they had their own school work to worry about. Meanwhile, our team members lived in different areas of the campus. Hence it became a serious problem that how team members could receive notifications in time to accomplish the work separately while co-working time could not be guaranteed. Google group solved this problem. Google group offers open online platform to users and users can build their own platform for sharing. Messages on the platform are accessible to all users joining the group. Emails can also be pushed to users. We built a platform of our team, and all messages on the platform could be pushed to team members in time. By Google group, we were able to:</p><br />
<ul><br />
<li>1. send notifications and arrangements to all team members in time;</li><br />
<li>2. make team members share their thoughts and innovation conveniently;</li><br />
<li>3. make regulations, assessments and financal issues transparent by sharing work logs.</li><br />
</ul><br />
<p>We recommend Google group for project management based on our experience. It can enhance communication among team members by breaking through the limitations of time and space. It can also make team work transparent and increase management efficiency.</p><br />
<div class="underline-tiny"></div><br />
<h5>Wunderlist</h5><br />
<p>Conversation sharing of Google group became inconvenient as the project proceeded and our work became more and more complicated. So we chose to use Wunderlist at the same time.<br /><br />Wunderlist is specifically designed for work arrangement. People in charge can create lists for their part of work and invite other users to help them with the work. Specifically, they can assign different members for different tasks and set deadlines. Other members can give feedbacks to the list after the corresponding work is done, and people in charge can delete the work from the list. Another advantage of Wunderlist is that it is available for all platforms, including PC and mobile phone. This way, all team members could receive the latest work notices.<br /><br />During the project, we created lists based on our work, including iGEM-backend, iGEM-frontend, iGEM-wiki and iGEM-finance, etc. Complicated assignments were distributed to different people. We also used the feedback service of Wunderlist to monitor the work progress. The use of Wunderlist enabled us to assign tasks in a scientific way and keep us informed of the progress of our project all the time to make sure that everything goes according to the plan.<br />
<br />
</p><br />
<div class="underline-tiny"></div><br />
<h5>OneNote</h5><br />
<br />
<p><br />
For every team, the financial problem is a big one. Of course, you may think of separating money and account easily, but how do you keep two or more financial managers in the same stage? We chose to solve the problem by OneNote.<br /><br />OneNote is originally designed for instant creation and notes sharing, and so it can be applied to financial management smoothly. We could create notebooks according to different items and mark the accounts that have been cleared or have not yet been cleared. By inviting others, the team leader can supervise the manager about he financial situation timely and make sure about the accuracy of this.<br />
</p><br />
<div class="underline-tiny"></div><br />
<h5>Omni outliner & Mindmap</h5><br />
<br />
<p><br />
No matter you are in what stage of what project, when you need new thoughts, it is always quite a hard time to get a satisfying result. Brainstorm might be a really nice idea, but in most of the time you have to stare at a whiteboard full of messy ideas on it without action. To solve the problem, you need some kind of software for thought assistance, such as Omni Outliner and Mingmap.<br /><br />Software like Omni Outliner can help you sort out all the necessary points and arrange your thoughts when you are writing articles, and software like Mindmap can enable you to draw a succinct "map" of your ideas to clarify your thoughts and summarize the viewpoints. Therefore you can quickly extract a wonderful idea from the numerous viewpoints raised in the brainstorm.<br />
<br />
</p><br />
<div class="underline-tiny"></div><br />
<h5>Dropbox</h5><br />
<br />
<p><br />
During the project, all kinds of files were created unremittingly. To be specific, articles to read, work log to be displayed, finished program codes, relevant materials, photos of us, etc. How will you store the files? You don’t store all of them in only one person’s computer, for they are too many and other people may also need them. We have a great solution—Dropbox.<br /><br />Dropbox is a cloud storage platform. It allows users to store files in the cloud, and thus any team member, knowing the password of the account, has access to these files no matter when and where. In the meantime, cloud storage is also very secure. Even if you accidentally spill coffee on your computer or the manuscripts, you can still keep your files safe.<br />
</p><br />
<br />
<h3>Biological Cooperation</h3><br />
<div class="underline-small"><br />
<br />
</div><br />
<br />
<p>Fine communication in any field enhances the development of the field, especially when it comes to biological field. Nowadays, there are already some ways of communication in biology. They are traditional ways, however. Communication by literature publishing, meeting attending and emailing is relatively slow and hard to be used in global range. What’s more important is that communication in these ways will restrict a biologist’s research field. This suppresses the cross-field communication of biology. As we all know, communication of different fields will bring about amazing breakthroughs. Therefore, if the restriction can be broken, it will benefit the development of biology astonishingly.<br /><br />BioPano is based on an online server, so it supports communication and cooperation perfectly. Users can release their research results on our software platform. BioPano will record the information and all biologists using the software all over the world can see the modifications. What’s better, we add group function usually in social software into BioPano. Biologists from different fields can form a group with BioPano. They can communicate more conveniently in the group. Meanwhile, BioPano offers other project co-management services to help biologists from different fields complete the research together.<br /><br />Popularization of BioPano will surely improve the connection among biologists greatly and enhance the progress of biology. Furthermore, BioPano will change the frequency and pattern of research results updating of biology, and even show every single change of biology real-timely like Wikipedia. Every researcher can share the progress of biology, and biological research will stride into the information age.<br /><br />We have already reccomended BioPano to many biological researchers, and received great feedbacks.</p><br />
<br />
<h3>Summer Vacation Meetup</h3><br />
<div class="underline-small"><br />
<br />
</div><br />
<br />
<p>Since local competitions are not held this year, iGEM foundation encourages every district to organize communication activity themselves. We responded to the call and organized summer vacation meetup at University of Science and Technology of China.<br /><br />This summer, we invited several iGEM teams from China to USTC from August 15th to August 17th for project showing and ideas interchanging. SJTU-Software, SJTU-BioX-China, SYSU-Software, XMU-China, HFUT_China, USTC_Software and USTC-China paticipated in this activity.<br /><br />The meetup was successful. Firstly, iGEM teams from China got to know each other, and developed profound friendship. Secondly, we understood each other’s project, which would benefit the improvements of our projects. Thirdly, the meetup simulated the real competition segments. We felt the atmosphere of the competition and found the deficiency of our presentations. During the meetup, we also discussed a lot about iGEM, hoping that iGEM could get better and better.<br /><br />All teams attending the meetup make positive evaluations to the activity.</p><br />
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<h5 style="color:#fff;font-weight:bold;margin-bottom: 25px;">Innovation Experiment Centre of Life Science (IEC)</h5><br />
<p>Building of Life Sciences, Room 363</p><br />
<p>University of Science and Technology of China</p><br />
<p>96, Jinzhai Rd, Shushan, Hefei</p><br />
<p>230026, Anhui, China</p><br />
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Hlx1996
http://2014.igem.org/Team:USTC-Software/acknowledge.php
Team:USTC-Software/acknowledge.php
2014-10-18T02:57:34Z
<p>Hlx1996: </p>
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<h4 id="dbank">Deutsche Bank</h4><br />
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<p><br />
Deutsche Bank is a German global banking and financial services company with its<br />
headquarters in the Deutsche Bank Twin Towers in Frankfurt. It has more than 100,000<br />
employees in over 70 countries, and has a large presence in Europe, the Americas, Asia-<br />
Pacific and the emerging markets. In 2009, Deutsche Bank was the largest foreign exchange<br />
dealer in the world with a market share of 21 percent.<br />
Deutsche Bank has offices in major financial centres including London, New York City,<br />
Singapore, Hong Kong, Tokyo, Paris, Moscow, Sydney, Toronto, Jakarta, Istanbul, Madrid,<br />
Dublin, Amsterdam, Warsaw, Mumbai, Kuala Lumpur, São Paulo, Dubai, Riyadh, Bangkok,<br />
Karachi, Belgrade, Manila and George Town (Cayman Islands).<br />
The bank offers financial products and services for corporate and institutional clients along<br />
with private and business clients. Services include sales, trading, research and origination of<br />
debt and equity; mergers and acquisitions (M&A); risk management products, such as<br />
derivatives, corporate finance, wealth management, retail banking, fund management, and<br />
transaction banking<br />
</p><br />
<br />
<h4 id="ustcif">USTCIF</h4><br />
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<p><br />
USTCIF, The University of Science and Technology of China Initiative Foundation, is a educational NGO serves to help with the development of USTC. As one of USTC's alumni foundations, its purpose is to enhence the alumni foundations to make USTC better. USTIF is the first college alumni foundation indepentant from the university.<br />
</p><br />
<br />
<h4 id="utao">USTC Teaching Affair Office</h4><br />
<div class="underline-small"><br />
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<p><br />
http://www.teach.ustc.edu.cn/<br />
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<img src="https://static.igem.org/mediawiki/2014/4/43/2014ustc-RegulonDB.jpg" style="height:100px"></a></li><br />
<li><a href="http://www.kegg.jp/"><br />
<img src="https://static.igem.org/mediawiki/2014/c/ca/2014ustc-Kegg.jpg" style="height:100px"></a></li><br />
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<img src="https://static.igem.org/mediawiki/2014/5/55/2014ustc-NCBI.jpg" style="height:100px"></a></li><br />
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<img src="https://static.igem.org/mediawiki/2014/4/47/2014ustc-Uniprot.png" style="height:100px"></a></li><br />
</ul><br />
<p>We would like to thank RegulonDB, Kegg, NCBI and uniprot for their data, without which Biopano can never be finished. Thanks again for their work and effort.</p><br />
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<h5 style="color:#fff;font-weight:bold;margin-bottom: 25px;">Innovation Experiment Centre of Life Science (IEC)</h5><br />
<p>Building of Life Sciences, Room 363</p><br />
<p>University of Science and Technology of China</p><br />
<p>96, Jinzhai Rd, Shushan, Hefei</p><br />
<p>230026, Anhui, China</p><br />
<p>ustc-software-2014@googlegroups.com </p><br />
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Hlx1996
http://2014.igem.org/Team:USTC-Software/requirements.php
Team:USTC-Software/requirements.php
2014-10-18T02:56:22Z
<p>Hlx1996: </p>
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<p style="font-size:32px">Requirements</p><br />
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<h4 id="medals">Medals</h4><br />
<div class="underline-small"><br />
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<br />
<br />
<h4><img src="https://static.igem.org/mediawiki/2014/4/4c/2014ustc-Bronze.png" width="60" height="60" alt="Bronze" >Bronze</h4><br />
<p> The following 4 goals must be achieved:</p><br />
<br />
<br />
<br />
<h5><img src="https://static.igem.org/mediawiki/2014/c/c1/Hfut-A.png" width="30" height="30" alt="Complete" ><br />
Register the team, have a great summer, and have fun attending the Jamboree in Boston.<br />
</h5><br />
<br />
<br />
<br />
<br />
<h5><img src="https://static.igem.org/mediawiki/2014/c/c1/Hfut-A.png" width="30" height="30" alt="Complete" ><br />
Create and share a description of the team's project via the iGEM wiki.<br />
</h5><br />
<br />
<br />
<br />
<br />
<h5><img src="https://static.igem.org/mediawiki/2014/c/c1/Hfut-A.png" width="30" height="30" alt="Complete" ><br />
Present a Poster and Talk at the Regional Jamboree and World Championship Jamboree.<br />
</h5><br />
<br />
<br />
<br />
<br />
<h5><img src="https://static.igem.org/mediawiki/2014/c/c1/Hfut-A.png" width="30" height="30" alt="Complete" ><br />
Develop and make available via The Registry of Software Tools, an open source software tool that supports Synthetic Biology based on Standard Parts.<br />
</h5><br />
You can directly enter the precise number of Standard Part, you can get its all types in BioBrick Assistant Windows.<br />
<div class="large-12 columns text-center"><br />
<img style="margin:1em" src="https://static.igem.org/mediawiki/2014/c/ce/2014ustc-medal1.png"><br />
</div> <br />
<p>&nbsp;</p><br />
<br />
<div class="underline-tiny"></div> <br />
<br />
<h4><img src="https://static.igem.org/mediawiki/2014/c/c6/2014ustc-Silver.png" width="60" height="60" alt="Sliver" >Silver</h4><br />
<p> In addition to the Bronze Medal requirements, the following 4 goals must be achieved:</p><br />
<br />
<br />
<br />
<br />
<h5><img src="https://static.igem.org/mediawiki/2014/c/c1/Hfut-A.png" width="30" height="30" alt="Complete" ><br />
Demonstrate the relevance of your development for Synthetic Biology based on standard Parts.<br />
</h5><br />
<p>You can directly enter the precise number of Standard Part, you can get its types in BioBrick Assistant Windows .then you can use blast tool with the sequence from BioBrick Assistant.By comparing the homology between the sequence of the part and in our database, we could predict its impact on the target body when injected to some extent.</p><br />
<div class="large-12 columns text-center"><br />
<img style="margin:1em" src="https://static.igem.org/mediawiki/2014/e/ee/2014ustc-medal2.png"><br />
</div><br />
<br />
<br />
<br />
<br />
<br />
<h5><img src="https://static.igem.org/mediawiki/2014/c/c1/Hfut-A.png" width="30" height="30" alt="Complete" ><br />
Provide a comprehensive and well-designed User Guide. (Be creative! An instructional video may work as well.)<br />
</h5><br />
<p>We have a complete user manual <a href="biopanohelp.pdf">here!</a></p><br />
<br />
<br />
<br />
<br />
<h5><img src="https://static.igem.org/mediawiki/2014/c/c1/Hfut-A.png" width="30" height="30" alt="Complete" ><br />
Provide detailed API documentation, preferably, automatically built from source code documentation (use tools like doxygen, yard, rdoc, naturaldocs, etc).<br />
</h5><br />
<p>We use toc to automatically produce api document. <a href="./api.html">Here!</a></p><br />
<br />
<br />
<br />
<br />
<h5><img src="https://static.igem.org/mediawiki/2014/c/c1/Hfut-A.png" width="30" height="30" alt="Complete" ><br />
Demonstrate that you followed best practises in software development so that other developers can modify, use and reuse your code. Provide more than one realistic test case. Examples of best practices are automated unit testing and documentation of test coverage , bug tracking facilities, documentation of releases and changes between releases.<br />
</h5><br />
<p><b><a href="http://bug.biopano.org">Problem feedback and bug tracking</a>:</b> You can cast inquiry on us by GitHub, GitLab and YouTrack. Meanwhile, YouTrack is also used for bug tracking, ensuring your feedback goes to the developer as soon as possible. <br />
<br /><br /><br />
<b><a href="http://ci.biopano.org"> Automated Deployment</a>:</b> Our server has automated deployment capabilities. Server-side applications are bound with the Product branch of Git. All codes pushed to the Product branch will be deployed to many servers over the world in ten seconds. In order to prevent fault codes from being deployed to the servers by mistake, all the testing branches will be deployed to the testing server real-timely to be tested by developers.<br />
<br /><br /><br />
<b>Unit Testing:</b> Our server applies automated unit testing to dealing with uploaded back end codes. It will test the basic legitimacy and function of the codes, including robustness testing with respect to illegitimate uploaded parameters, legitimacy testing on data legitimacy, status testing of the database and testing of function realizaton, etc.</p><br />
<br />
<p>&nbsp;</p><br />
<div class="underline-tiny"></div><br />
<h4><img src="https://static.igem.org/mediawiki/2014/8/88/2014ustc-Gold.png" width="60" height="60" alt="Gold" >Gold</h4><br />
<p> In addition to the Bronze and Silver Medal requirements, two additional goals must be achieved:</p><br />
<br />
<br />
<br />
<br />
<h5><img src="https://static.igem.org/mediawiki/2014/c/c1/Hfut-A.png" width="30" height="30" alt="Complete" ><br />
Provide a convincing validation, testing the performance of the development -- experimentally (can be outsourced) or by other teams and users. Note, even if the algorithm or tool turns out not to work that well, the Gold requirement is fulfilled if the test is good and the analysis convincing. Validation may include: preferably experiments, informatics analysis (complexity, run time) of an algorithm, or user studies.<br />
</h5><br />
<p><b>Analysis of pathway finder (k-shortest pathway search):</b><br /><br />
We use a specail heuristic algorithm , <a href="http://en.wikipedia.org/wiki/A*_search_algorithm">A* search algorithm</a>, to find more than one path connected two nodes in a given network.The run time of A* depends on structure of the given network. The space complexity is the number of edges plus the number of nodes. In our back end, we test this algorithm. The average of time which database reading costs is 1"40, the average of time which Vars initialization costs is 0"70, the average of time which <a href="http://en.wikipedia.org/wiki/Shortest_Path_Faster_Algorithm">SPFA(abbreviation for Shortest Path Faster Algorithm)</a> costs is 0"37, and the average of time which Serialize costs is 0"21.</p> <br />
<br />
<br />
<h4><br />
And the second goal can be any one of the following:<br />
</h4><br />
<br />
<br />
<br />
<br />
<h5><img src="https://static.igem.org/mediawiki/2014/c/c1/Hfut-A.png" width="30" height="30" alt="Complete" ><br />
Make your software interact / interface with the Registry.<br />
</h5><p>You can directly enter the precise number of Standard Part, you can get its types in BioBrick Assistant Windows .then you can use blast tool with the sequence from BioBrick Assistant.By comparing the homology between the sequence of the part and in our database, we could predict its impact on the target body when injected to some extent.</p><br />
<br />
<div class="large-12 columns text-center"><br />
<img style="margin:1em" src="https://static.igem.org/mediawiki/2014/c/ce/2014ustc-medal1.png"><br />
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<br />
<br />
<br />
<br />
<h5><img src="https://static.igem.org/mediawiki/2014/c/c1/Hfut-A.png" width="30" height="30" alt="Complete" ><br />
Re-use and further develop previous iGEM software projects (or parts thereof) or use and/or improvement of existing synthetic biology tools or frameworks.<br />
</h5><br />
<p>We use blast code from <a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi">ncbi </a>to comparing the homology.</p><br />
<br />
<br />
<br />
<br />
<br />
<h5><img src="https://static.igem.org/mediawiki/2014/c/c1/Hfut-A.png" width="30" height="30" alt="Complete" ><br />
Develop a well documented library or API for other developers (rather than “only” a stand-alone app for end users.)<br />
</h5><br />
<p>We use toc to automatically produce api document. <a href="./docs/">Here!</a></p><br />
<br />
<br />
<br />
<br />
<h5><img src="https://static.igem.org/mediawiki/2014/c/c1/Hfut-A.png" width="30" height="30" alt="Complete" ><br />
Support and use the SBOL and / or SBOLv standard.<br />
</h5><br />
<p>Biopano supports file format conversion to sbol perfectly.</p><br />
<div class="large-12 columns text-center"><br />
<img style="margin:1em" src="https://static.igem.org/mediawiki/2014/d/dd/2014ustc-medal3.png"><br />
</div><br />
<br />
<p></p><br />
<h4 id="safety">Safety</h4><br />
<div class="underline-small"> </div><br />
<h5>1. Are you using the iGEM Software repository at github.com/igemsoftware? If you have instead stored your code elsewhere, please explain where and why you have put it there. If your code is not in the iGEM repository, a re you using any version control system such as Git, CVS, or SVN?<br />
</h5><br />
<p>Yes, we use the iGEM Software repository at github.com/igemsoftware.<br />
</p><br />
<h5> 2. Does your software store any private data supplied by the user? (For example: the user's name and email address, passwords, DNA sequences, circuit designs, etc.) If yes, please describe what kind of data is stored. If no, skip the rest of this question and move on to question 3.<br />
</h5><br />
<p>We store the user's name, the email address (if he/she logs in using Gmail account) or the username (if logged in using Baidu account), and the user's all data designed with our software.<br />
Especially, we DO NOT store the user's password because we only allow users to log in with their Gmail account or Baidu account using OAuth2.0 ,<br />
which is a very secure protocol describing a third-party login pattern.<br />
</p><br />
<h5>3. Does your software include any other security features? Please describe them here. </h5><br />
<p><br />
We use OAuth technology in user system. So users can log in with their GOOGLE account or BAIDU account without telling us their passwords.<br />
</p> <br />
<h5> 4. Does your software let the user create a design by choosing parts/genes from a list/database, such as the Registry? If so, which lists/databases are included? Is there any restriction on which parts/ genes the user can choose?</h5><br />
<p> <br />
Yes, users can use database built by our team to assist themself to create a design. The database we build is the result of merging and reforming parts of KEGG, RegulonDB, Uniport.<br />
</p><br />
<h5>5. Does your software allow users to write new data into any public lists or databases? If so, do you check the new data for errors before allowing it to be written?</h5><br />
<p><br />
Yes, users can upload their data to our database anytime.<br /><br />Yes, we will check validation and format of data before it is written in the back end.<br />
</p><br />
<h5>6. Does your software include any other features that encourage the user to create safe designs? Please describe them. </h5><br />
<p>No.</p><br />
<br />
<h5>7. Is your team also doing biological work in a wet lab ? </h5><br />
<p>No.</p><br />
<p></p><br />
<h4 id="collaboration">Collaboration</h4><br />
<div class="underline-small"><br />
<br />
</div><br />
<p>While preparing for iGEM, we always hope we can accomplish more and more people can join this great project. Luckily, by cooperation with others, all these hopes come ture.</p><br />
<li>Collaboration with professors</li> <br />
<p></p><br />
<p>While completing our project, we encountered all kinds of problems, of which some could hardly solve by ourselves. We solved them by discussing and cooperating with many professors of USTC. At the same time, we knew more about the original thoughts of synthetic biological researchers. So we tried to combine their needs and our project, hoping we could also help them. Now, we believe that we realized our original intention.</p><br />
<li>Collaboration with Chinese iGEMers</li><br />
<p></p><br />
<p>One reason why iGEM competition is unforgettable is that it makes us know more like-minded people. This year, we hoped iGEM teams could communicate more with each other, so we organized iGEM meetup this summer. Teams from China got familiar through the meetup, and we kept in touch after it. We not only got to know each other by frequent communication, but helped each other with their problems to bring about good results for us all as well.</p><br />
<li>Collaboration with HFUT_CHINA</li><br />
<p></p><br />
<p>While enjoying iGEM, we hoped more people could join us. This year, HFUT_CHINA sent a team for iGEM for the first time. As a team new to iGEM, it would surely encounter more problems. As their neighbor, we kept in touch with them and did everything we could to help them with their project. Through the course, we got to know a lot of people enthusiastic about iGEM of our age. We are glad that they also join iGEM.</p><br />
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<p>Hlx1996: </p>
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<h3 id="front_end">Front End</h3><br />
<div class="underline-small"></div><br />
<p>The work of front end is various and complicated. We generally divided it into 4 large parts as below:</p><br />
<ul><br />
<li>UI Framework</li><br />
<li>Canvas System</li><br />
<li>Project & Cloud System</li><br />
<li>Functional Units</li><br />
</ul><br />
<p></p><br />
<p>In concise, users can create a biological network on the Canvas, save or browse their work as Projects, get or share biological information by Cloud, and analyze biological data with Functional Units, all of which happen in the friendly environment provided by the UI Framework.</p><br />
<p></p><br />
<p>We based our program on Adobe Air 15.0 platform, with programming language Action Script 3.0 (AS 3.0). AS 3.0 is powerful in vector illustration processing, and provides rich interactions and responsiveness, these two features meet the demand of our project exactly.</p><br />
<p></p><br />
<p>The major techniques we used are as following: Smart Canvas, Operation Track, Multi-Threading and Heterogeneous computing.</p><br />
<p></p><br />
<div class="underline-tiny"> </div><br />
<h5>UI Framework</h5><br />
<p>In order to provide a better user experience, we designed a completely new UI Framework, in which most of the operations can be directly performed while the interface keeps simple and tidy. Meanwhile, this new framework aims for demonstrating information clearly, so there are fewer containers but richer contents. We also added guiding animation responding to most operations so that all the processes are smooth and easy to understand.</p><br />
<p></p><br />
<div class="underline-tiny"> </div><br />
<h5>Canvas System (Smart Canvas)</h5><br />
<p>The canvas to display the biological network is the most important part of this software, so this receives the most concern. A simple canvas with all objects sticking on could not meet the demand of a boundless and highly complicated visual network. So we need to design the structure of both data and displaying object to guarantee the capability of performing mass information while consuming limited system resources. After several trials and analyses, we build our canvas in two major layers and five sub layers:</p><br />
<p></p><br />
<ul><br />
<li>1. Node Layer<br />
<ul><br />
<li>a) Float layer</li><br />
<li>b) Compressed partitioned layer</li><br />
</ul><br />
</li><br />
<li>2. Link Layer<br />
<ul><br />
<li>a) Fast redraw layer</li><br />
<li>b) Float layer</li><br />
<li>c) Compressed layer</li><br />
</ul><br />
</li><br />
</ul><br />
<p>For float layer, objects exist independently, which means they have their own RAM and Graphic. These independent objects have many event listeners that can interact with users easily. Specifically, users can simply move, double-click and edit them. Though a few dozens of objects working in this way together will be quite well, more (thousands of) objects exist in the float layer at the same time will consume a great amount of resources with an unacceptable low speed.</p><br />
<p></p><br />
<p>A biological network can be huge and highly convoluted. To meet the requirement of higher efficiency, we use compressed layer, on which objects are drawn together as one or several (partitioned) bitmaps, to solve this problem. These bitmaps draw fast with GPU acceleration and cost much fewer resources, but they are not interactive. So a significant task we have done is to translate an operation towards an object drawn in compressed layer to the real object by calculating its geometry characteristic. Once a focus intension is traced, the object will emerge to the float layer to interact with the user, and when it loses focus, it will submerge into the compressed layer again and the RAM space will be cleared.</p><br />
<p></p><br />
<p>In most of time, objects stay in compressed layers. But there is still another problem: the graph may be too large to draw at one time while most part of the graph is out of screen. So we use partitioned bitmap blocks (for nodes) and fast drawing layer (for links) in place of one huge bitmap, and redrawing only happens to the blocks (for nodes) or the range (for lines) shown on the screen.</p><br />
<p></p><br />
<p>With all these methods, we could save over 90% costs of system resources while providing an enjoyable user experience.</p><br />
<div class="underline-tiny"> </div><br />
<h5>Project System</h5><br />
<p>Project is the basic unit to manage a biological network. Three kinds of information are saved in a project:</p><br />
<ul><br />
<li>1. Node information</li><br />
<li>2. Link information</li><br />
<li>3. Project information</li><br />
</ul><br />
<p>You can import nodes and links to the project from cloud database or add yours; both can be saved into one project. Meanwhile, two ways are provided to store a project, storing locally and on cloud.</p><br />
<p></p><br />
<p>For a local project, information saved as an XML file, so you can open, save or copy it like any other kind of document.</p><br />
<p></p><br />
<p>Building projects on cloud is strongly recommended, for not only these projects can be open and edit on any computer with your account, but the existence of the nodes and links in the project are recorded in the global biological network database, in which all the nodes and links exist together as well. With more projects uploaded to the cloud, the global database will be extended, thus more information will be provided to users and an ultimate biological network will be built up someday.</p><br />
<p></p><br />
<p>With projects on cloud, researchers worldwide will be able to share and quote the findings of each other or directly build one project together by registering as colleagues. For more information about project management, see documentation of the Back End.</p><br />
<div class="underline-tiny"> </div><br />
<h5>Functional Units</h5><br />
<p><b>BioBrick Assistant:</b><br />BioBrick Assistant will get the BioPart in the form of XML from the official website when the user inputs keywords. Then we extract the important information by using Actionscript XML processing functions in the form of a table.</p><br />
<p></p><br />
<p><b>Google API:</b><br />When the user inputs the keyword, it will be searched on Google. Then we parse the returned HTML, and save the title, author, abstract, and URL of the literature, which is convenient for the user.</p><br />
<p></p><br />
<p><b>Layout Algorithm:</b></p><br />
<p></p><br />
<p>1. Even Layout: First we calculate the border region which the user selected, namely the minimum and maximum of X and Y. So that we can get the height and width of the area. During the process, the number of nodes is gotten. Then we select the value of m and n as below: m, n are integers, m / n is closest to the width / height and m*n is no smaller than the number of the nodes. After m and n are set, the nodes will be arranged that the horizontal interval between horizontally adjacent nodes is width / m, and the vertical interval between vertically adjacent nodes is height / n.</p><br />
<p>2. Plasmid Arrangement: the arrangement of the radius of the circle size is in proportion to the number of nodes selected. Node will be sorted according to the type and arranged on the circle.</p><br />
<p>3. Force-directed Arrangement: Imagine that we assign each node with a positive charge, those nodes are mutually exclusive, and the repulsive force is inversely proportional to the square of the distance. Imagine that every edge is a spring, the force it applies on the nodes at its ends is proportional to the length of the spring. By calculating the force applied to each node, we can determine the direction and magnitude of its displacement. This process is called an iteration. After fifty times of iteration, all the nodes will be in steady state. We make their positions now their final positions for arrangement. The parameters of gravitation and repulsion are determined by experiments. The advantage of the algorithm is that it can arrange the graph like a tree and reduce the cross of edges greatly to show the relationships among the nodes more lucidly.<br />
<br />Force-directed algorithm and GPU acceleration: the time complexity of the arrangement algorithm is O(n^2), so it will take a long time if the number of the nodes is large. So we spill the algorithm among several threads (users can still operate while the back end is calculating) and use the powerful ability for floating-point computation and parallel computation of GPU to accelerate the calculation. Taken multi-platform support into consideration, we use opencl as our programming language. The acceleration uses socket communication for data transfer. The front end send the amount of the nodes, the number and position of each node, the amount of the links and the number of nodes each edge connects to the calculation end. The calculation end spill the computation that the computation of each node is done in a single thread. Visit all the nodes and edges only once and we can get the acceleration of each node. When the computation is done, the calculation end sends every node’s position to the front end.</p><br />
<p></p><br />
<h3 id="back_end">Back End</h3><br />
<div class="underline-small"><br />
</div><br />
<h5>Framework</h5><br />
<p>Our server uses Linux as operating system, MongoDB to manage abundant biological data, including information of millions of nodes, and MySQL database to store data of users and information of projects and species. Our server-side program is based on Django development, and is optimized for multi-node and remote-controlling circumstances, ensuring that your request will be answered wherever you are. When a node breaks down, our server will separate the node from the group and realize automatic failover.</p> <br />
<br />
<br />
<br />
<br />
<div class="underline-tiny"> </div><br />
<h5>Account System:</h5><br />
<p>Oauth is used as login credential. You just need to provide your Google or Baidu account and use Biopano conveniently without signing up. Meanwhile, Oauth is decoupled with local account system, providing convenience for developers to offer more ways for authentication.</p><br />
<br />
<div class="underline-tiny"> </div><br />
<h5>Rapid Server Deployment:</h5> <br />
<P>We do not recommend users to build at local Biopano server, for one of the main advantages of Biopano is data sharing. However, for special cases such as intranet, you could use the docker repository we provide to deploy a Biopano server rapidly. We encapsulate basic databases to offer powerful basic biological data support for your intranet server.</P><br />
<br />
<div class="underline-tiny"> </div><br />
<h5>Interface Design:</h5><br />
<p>The server communicate with front end based on HTTP protocol. It uses interfaces of RESTful style. It is a kind of completely public and universal interface and offers detailed documentation. You can develop your own applications based on these interfaces. These interfaces have been optimized a lot for Biopano-client, so the communication efficiency has been enhanced significantly.</p><br />
<br />
<div class="underline-tiny"> </div><br />
<h5>Automated Deployment:</h5><br />
<p>Our server has automated deployment capabilities. Server-side applications are bound with the Product branch of Git. All codes pushed to the Product branch will be deployed to many servers over the world in ten seconds. In order to prevent fault codes from being deployed to the servers by mistake, all the testing branches will be deployed to the testing server real-timely to be tested by developers.</p><br />
<br />
<div class="underline-tiny"> </div><br />
<h5>Unit Testing:</h5><br />
<p>Our server applies automated unit testing to dealing with uploaded back end codes. It will test the basic legitimacy and function of the codes, including robustness testing with respect to illegitimate uploaded parameters, legitimacy testing on data legitimacy, status testing of the database and testing of function realizaton, etc.</p><br />
<br />
<h3 id="alogrithm">Alogrithm</h3><br />
<div class = "underline-small"></div> <br />
<h5>Pathway Finder Alogrithm:</h5><br />
<p>The software can search for paths between two selected nodes. We used a-stark short-path algorithm to achieve the function of discovering potential relationship in the biological network.<br />
A* algorithm is a search algorithm based on greedy, which can always visit fewer nodes and get a better solution at the same time.<br />
In this way, however, we get the shortest path in graph theory. By giving different and appopraite weights to different edges, the algorithm can find the shortest path in the sense of biology.</p><br />
<br />
<div class="underline-tiny"> </div><br />
<h5>BLAST:</h5><br />
<p><br />
We use two packages, namely, NCBI_Blast and the Python package called for NCBI_Blast. Different from NCBI, our alignment database combines RegulonDB and user-define databases. When the user inputs a sequence (such as a BioBrick sequence), Biopano will the node that shares the deepest homology with it in the server database, and show other nodes connected with it. Therefore, Biopano can show the nodes and regulations in the biological regulation network that probably has to do with the sequence (such as BioBrick sequece) the user inputs.<br />
</p><br />
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<p>University of Science and Technology of China</p><br />
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Hlx1996
http://2014.igem.org/Team:USTC-Software/biopano.php
Team:USTC-Software/biopano.php
2014-10-18T02:54:44Z
<p>Hlx1996: </p>
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<p style="font-size:64px;height:100%;line-height:100%;color:rgb(144,144,144)">Meet Biopano</p><br />
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<div class="large-12 columns large-centered"><br />
<br />
<p></p><br />
<h4 id="overview">Overview</h4><br />
<div class="underline-small"></div><br />
<p>Designed specifically for biological research, BioPano is a software platform targeted for visualisation of biological relationships as well as cooperative net-building. You can set up your own network of biological relationship by adding information about genetic regulation and metabolic system to the network we already provided for you. Also, the software allows you to explore the links among the substances by just several clicks, and you can even look into the details of the interaction between the exogenous gene and the host. What is even more exciting is that our software will end your loneliness and frustration in research, since it is providing you with cloud cooperating system so that you can view massive amounts of resources in databases, together with build up groups to share information and set up mutual network with others.<br />
</p><br />
<br />
<h4 id="motivation">Motivation</h4><br />
<div class="underline-small"></div><br />
<p><br />
In recent years, people has made a lot of remarkable achievements <br />
in synthetic biology. However, scientists are often faced with <br />
many unpredictable problems when carrying out experiments. <br />
Each kind of biological substance is inextricably linked to the <br />
biological environment to which it belongs, so we have to consider <br />
a question: Can we attain the desired goal, if we simply follow the traditional ideas of synthetic biology and avoid the problem merely by engineering?<br />
</p><br />
<p><br />
A synthetic biologist, Chris Voigt, has successfully transferred a<br />
Toggle Switch, which usually works in the Bacillus <br />
subtilis, into E. coli. Unfortunately, it did not function properly. In <br />
fact, in experiments, due to the unexpected interactions between <br />
BioBrick and the host, it is very common that the designed path do <br />
not work as anticipated.<br />
</p><br />
<p><br />
In fact, the life system is so complex that there are many sorts of <br />
biological substance to support it with complex interations in it. <br />
In order to understand a phenomenon, we keep using new and <br />
sophisticated methods to refine our research and to explore every <br />
detail of life. However, if we widen our perspective, by looking at <br />
our research objectives from a more comprehensive perspective, <br />
we may have some unexpected discoveries.<br />
</p><br />
<br />
<h4 id="features">Features</h4><br />
<div class="underline-small"><br />
</div><br />
<p>Our software has many marvelous features, with which your biology research will become extremely easy and joyful.</p><br />
<ul><br />
<br />
<h5>1. Expansion of single node</h5><br />
<div class="row"><br />
<div class="large-6 columns"><p>In Biopano, every biology part of E.coli K-12 will be displayed as a node of different types and regulation relationship <br />
will be displayed as arc of different types. They are displayed in the biological network in a visualizational way. <br />
You just need to select a node and click “Expand”, and the nodes associated with it will be “expanded”. <br />
Nodes are connected to each other by all kinds of relationship, so users can see how biological parts are connected clearly, <br />
such as LacI Operon. </p></div><br />
<div class="large-6 columns"><img src="https://static.igem.org/mediawiki/2014/4/46/2014ustc-Feature-a.png"></div><br />
</div><br />
<br />
<div class="row"><br />
<div class="large-6 columns"><img src="https://static.igem.org/mediawiki/2014/9/9e/2014ustc-Feature-b.png"></div><br />
<div class="large-6 columns"><p>However, since there are so many biological parts connected to each other in various convoluted, <br />
the expansion of all nodes will give rise to extremely involved nets, which will fail to convey useful information to the users, <br />
even interfere their thoughts. So you can choose to expand the nodes in a way you see fit. Take Transcription factor CRP as an example. </p><br />
<p>Biopano displays the network dynamically, which makes you able to tease out the relationship among thousands of materials of <br />
E.coli K-12, satisfies your curiosity and helps you discover unknown biological field.</p></div><br />
</div><br />
<div class="underline-tiny"></div><br />
<br />
<br />
<br />
<h5>2. Link Finder</h5><br />
<div class="row"><br />
<div class="large-6 columns"><p>You can input two nodes that seem irrelevant, such as gene A and Transcription FactorB, and the software will <br />
search the route connecting the two nodes for you. Since some routes are too sinuous for further analysis or does not make sense, <br />
you can set a specific number k, Biopano will search and show the k shortest routes for you.</p></div><br />
<div class="large-6 columns"><img src="https://static.igem.org/mediawiki/2014/7/79/2014ustc-Feature-c.png"></div><br />
</div><br />
<div class="underline-tiny"></div><br />
<br />
<br />
<h5>3. BLAST</h5><br />
<div class="row"><br />
<div class="large-6 columns"><img src="https://static.igem.org/mediawiki/2014/7/71/2014ustc-Feature-e.png"></div><br />
<div class="large-6 columns"><p>By BLAST method, Biopano finds E.coli K-12 gene highly similar to the injected sequence. <br />
These genes are regulated by other parts in E.coli K-12, so can provide information of the host environment’s impact on injected <br />
exogenous sequence. Biopano also offers BioBrick helper, enabling you search all kinds of BioBricks on iGEM’s official website. <br />
By BLAST analysis, it helps you design correct gene route with appropriate BioBricks.</p></div><br />
</div><br />
<div class="underline-tiny"></div><br />
<br />
<br />
<h5>4. Data Sharing</h5><br />
<p>Hence, while offering various functions, Biopano also serves as a cooperative network building platform. When you create a project, you can add new nodes, name new biological parts and link them with respect to your comprehension to build a brand new net gradually. Meanwhile, Biopano provides log in service. You can sign up with Google or Baidu account and upload your network to the main database to make it more plentiful. Biopano also supports data importing in batch. You can even import data of a species and a database.</p><br />
<ul class="small-block-grid-2"><br />
<li><img src="https://static.igem.org/mediawiki/2014/2/2a/2014ustc-Feature-f.png"></li><br />
<li><img src="https://static.igem.org/mediawiki/2014/5/57/2014ustc-Feature-g.png"></li><br />
</ul><br />
<div class="underline-tiny"></div><br />
<br />
<h5>5. Details and Reference</h5><br />
<p>When you have already got the entire view and want to know more about the details, double-click the nodes and arcs and the details will be shown. More surprisingly, Biopano supports literature reading in the network. You can view literature corresponding to every node and arc along any gene route in the network, and you will understand how the nodes in the net are associated with each other in depth. If you cast doubt on the reliability of our database, you can verify your thought with authoritative literature.</p><br />
<br />
</ul><br />
<p></p><br />
<h4 id="demos">Demo</h4><br />
<div class="underline-small"><br />
</div><br />
<div><br />
<h4>Next we will demonstrate some common modules of E.coli k-12:</h4><br />
<br />
<h5>1, Lac Operon: When you input LacZYA, a Transcription Unit(TU) of Lac Operon and Expand the node:</h5><br />
<p>You will see four promoters, acZp1, lacZp2, lacZp3 and lacZp4 as<br />
upstream sequences and three structure genes, lacZ, lacY and lacA as <br />
downstream sequences. Meanwhile, you can see the TU belongs to <br />
the Operon lacZYA.<br />
</p><br />
<p>Above the node lacZYA, you also see three Transcription<br />
Factors, namely, CRP, H-NS and lacl. They suppress the expression of <br />
lazZYA.</p><br />
<p>Expand lacZ, lacY and lacA, and we get BgaL, LacY and ThgA<br />
respectively, of which Bgal and ThgA are Enzymes. They catalyze<br />
corresponding reactions. Expand Lacl and we get the gene lacl which<br />
codes it.</p><br />
<ul class="small-block-grid-2"><br />
<li><img src="https://static.igem.org/mediawiki/2014/4/47/2014ustc-B.png"></li><br />
<li><img src="https://static.igem.org/mediawiki/2014/e/ee/C.png"></li><br />
</ul><br />
<br />
<p>Continue to Expand lacZYA and lacl and we find more materials’<br />
connected with them. You can select and drag the nodes to arrange the <br />
network neatly; you can also click Full Screen and the network will be <br />
displayed in full screen.</p><br />
<ul class="small-block-grid-2"><br />
<li><img src="https://static.igem.org/mediawiki/2014/c/c5/2014ustc-D.png"></li><br />
<li><img src="https://static.igem.org/mediawiki/2014/3/3a/2014ustc-E.png"></li><br />
</ul><br />
<br />
<h5>2, Following the same steps, we can also get the regulation network of<br />
the Operon Trp.</h5><br />
<img src="https://static.igem.org/mediawiki/2014/9/9d/2014ustc-F.png"><br />
<br />
<br />
</div><br />
<br />
<br />
<h4 id="why">Why choose BioPano?</h4><br />
<div class="underline-small"></div><br />
<div><br />
<p> Biopano, do the experiment as you do in the lab.</p><br />
<p>In experiment, synthetic biologists always find gene circuits formed by BioBricks are incompatible with the host cell, thus cannot work as expected. However, Biopano uses sequence alignment to analyze the possible reasons of the failure and design more acute gene circuit for your consideration.</p><br />
<p>Our Blast algorism derives from NCBI. However, the original version only offers sequence alignment and fails to analyze what impact the host environment might have on the injected gene circuit, let along predicts whether it will work.</p><br />
<p>Firstly, Biopano offers BioBrick searching to make it convenient for you to study all standardized biological parts on the official website of iGEM. Secondly, you can input a BioBrick and even construct a brand new sequence. Biopano will find the gene nodes of E.coli K-12 sharing the deepest homology with it based on authoritative Blast algorithm. Then you can Expand these nodes to find out the possible regulation on them. In this way, Biopano helps you analyze whether the injected gene circuit will actually work.</p><br />
<p>Biopano abstracts biological parts and the regulation among them into nodes and arcs to realize data visualization, and displays gene regulation and metabolism network of E.coli K-12 dynamically by continually Expanding nodes. Single database cannot make an entire material network, so our back end combines Regulon DB, KEGG, Uniprot and abundant data. You can ceaselessly Expand the nodes in the network to comb the relationship among them and satisfy your curiosity.</p><br />
<br />
<p>Compared with Biopano, Cytoscape and Netscience mainly support file importing and network displaying without powerful database from the back end. Hence you cannot search for biological parts online and view the certain part of the biological network you need with them.</p><br />
<br />
<p>Now that there is enormous astonishing material relationship in biological body, more and more biologists hope to find the specific function route between two biological parts or even two biological blocks that seem not related to each other, such as c-di-GMP signalling and Quorum Sensing. Unfortunately, the interactions of the biological parts are saved in database as records and it is almost impossible to find the route in thousands of records. There haven’t been any software to offer any help before. Luckily, Biopano brings hope to this.</p><br />
<br />
<p>You can input two biological parts and set several shortest routes, then you will find their relationship. We used this powerful function to find the specific relationship betweem c-di-GMP signalling and Quorum Sensing, which was corroborated by corresponding literature. How amazing!</p><br />
<br />
<p>We have to admit that Biopano may show you wrong gene route. However, it provides you with direction of studying the relationship of two fields. It not only makes your goal for experiment designing clearer, but enables you to understand the connection inside body is so close as well.</p><br />
<br />
<p>While offering function services, Biopano serves as a platform for collaborative network building. You can define new nodes and arcs yourself and sign in with your Google or Baidu account to upload the network you build to our database. You can also invite several companions to complete a project together. Common biological software, such as Cytoscape and Netscience, doesn’t provide a good platform for communication, while Biopano enhances the communication of biological areas by data sharing.</p><br />
<br />
<p>Biopano, your right hand for biological research. Get it now!</p><br />
</div><br />
<br />
<h4 id="futurework">Future Work</h4><br />
<div class="underline-small"></div><br />
<div><br />
<h4>It is undeniable that we still have a lot to do to improve Biopano in many aspects in order to make it even better. We need to think more and develop it as we can. In the future, we hope to:<br />
</h4><br />
<br />
<p>1. Integrate more data in it. Currently, Biopano only integrates data of E.coli k-12 from Regulon DB, KEGG and Uniprot, and our data in regulatory interaction lack accurate numerical data to indicate its strength. etc. Therefore, not only will we update the existing data in the original species, we will also make complement of high-throughput data through other databases and papers, as well as expand information of other species, so that more biological researchers can benefit from our software.</p><br />
<br />
<p>2. Normalize users' rights, improve quality of data. With the increase of the number of users, the data synchronized every day become not only massive, but also in many different forms, and some of them have nevitable errors or redundant information, or there may be different kinds of comprehension of certain regulatory relations. So we want the machine to automatically recognize the validity of the data submitted by the user, and establish a evaluation criteria of credibility. Thus, only those reliable users will be selected, and only their data can be synchronized to the main database, and the redundancy or errors will be eliminated, and they also continue to enhance the credibility and value of the main database.</p><br />
<br />
<p>3. Enhance network analysis functions. When we add the high-throughput kinetic data for biological networks, we can build a variety of mathematical models on the network and carry out quantitative simulation analysis. For example, we can put the nodes that are closely related to one another together in a group. We can make out software automatically arrange the modules for different functions in the organism. We can even do things that are analogic to those in an electric circult. The network provides the entrance and the exit of the signals, and all you need to do is to enter the target product and we will help you find the substance needed for synthesizing it. </p><br />
<br />
<p>4. Supports more file formats. Currently, the file formats we provide to the users are only XML and SBOL. In the future we will make our software support more file formats, such as sif, EMBL, etc., and we will develop its ability to be capable with other biological softwares such as cytoscape and Netscience, seamlessly. You can import and export any file that are constantly used. From this aspect, we will greatly broadens the scope of the functions of the software.</p><br />
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Hlx1996
http://2014.igem.org/Team:USTC-Software
Team:USTC-Software
2014-10-18T02:45:03Z
<p>Hlx1996: </p>
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Hlx1996
http://2014.igem.org/Team:USTC-Software/server.php
Team:USTC-Software/server.php
2014-10-18T02:43:15Z
<p>Hlx1996: </p>
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global: { <br />
useUTC: false <br />
} <br />
}); <br />
<br />
var chart,str="<br />",info=[],status=[];<br />
for(h in data2){<br />
if(data2[h].status=="up"){<br />
info.push({<br />
name:data2[h].database_center+"@"+data2[h].location,<br />
data:data2[h].history<br />
});<br />
}<br />
status.push({<br />
name:data2[h].database_center+"@"+data2[h].location,<br />
status:data2[h].status,<br />
load:data2[h].lavg_1<br />
});<br />
<br />
} <br />
for(s in status){<br />
if(status[s].status=="up")<br />
{<br />
if (status[s].load < 8)<br />
img = '<img src="img/green.png" style="width:20px;padding: 0;margin-right:0.5em ">'; <br />
else<br />
img = '<img src="img/yellow.png" style="width:20px;padding: 0;margin-right:0.5em">';<br />
}else {<br />
img = '<img src="img/red.png" style="width:20px;padding: 0;margin-right:0.5em">';<br />
}<br />
str = str + img + status[s].name+"<br /><br />";<br />
}<br />
$("#server_status").html(str);<br />
<br />
$('#container').highcharts({ <br />
chart: { <br />
type: 'spline', <br />
animation: Highcharts.svg, // don't animate in old IE <br />
marginRight: 10, <br />
}, <br />
title: { <br />
text: 'Server Load Status in Hours' //主标题 <br />
}, <br />
xAxis: { //X轴 <br />
type: 'datetime', <br />
tickPixelInterval: 150 <br />
}, <br />
yAxis: { //Y轴 <br />
title: { <br />
text: 'Load Status' <br />
}, <br />
plotLines: [{ <br />
value: 0, <br />
width: 1, <br />
color: '#808080' <br />
}] <br />
}, <br />
tooltip: { <br />
formatter: function() { <br />
return '<b>'+ this.series.name +'</b><br>'+ <br />
Highcharts.dateFormat('%Y-%m-%d %H:%M:%S', this.x) +'<br>'+<br />
Highcharts.numberFormat(this.y, 2); <br />
} <br />
}, <br />
legend: { <br />
enabled: false <br />
}, <br />
exporting: { <br />
enabled: false <br />
}, <br />
series:info <br />
}); <br />
<br />
<br />
}); <br />
<br />
}); <br />
</script><br />
<div class="main-content"><br />
<div class="row large-12 columns large-centered"><br />
<br />
<div id="container" style="min-width:400px;height:400px;"></div><br />
<div id="server_status" style="padding:2em"><br />
<br />
</div><br />
</div><br />
</div><br />
<br />
<div id="last-info" class="hide-for-small"><br />
<div class="row fullWidth"><br />
<div class="large-3 medium-3 columns " style="margin-top:5em"><br />
<img src="https://static.igem.org/mediawiki/2014/7/78/2014ustc-software2.png"><br />
</div><br />
<div class="large-6 medium-6 columns" style="color:#fff"><br />
<h5 style="color:#fff;font-weight:bold;margin-bottom: 25px;">Innovation Experiment Centre of Life Science (IEC)</h5><br />
<p>Building of Life Sciences, Room 363</p><br />
<p>University of Science and Technology of China</p><br />
<p>96, Jinzhai Rd, Shushan, Hefei</p><br />
<p>230026, Anhui, China</p><br />
<p>ustc-software-2014@googlegroups.com </p><br />
</div><br />
<div class="large-3 medium-3 columns " style="margin-top:5em"><br />
<br />
<a href="https://www.db.com" target="_blank"><img src="https://static.igem.org/mediawiki/2014/c/c0/2014ustc-Dbank.png" style="margin-top:2em"></a><br />
</div><br />
<br />
<br />
</div><br />
</div><br />
<br />
<div class="ltx-footer-bottom"><br />
<div class="row" ><br />
<div class="medium-4 medium-4 push-9 columns"><br />
<ul class="home-social"><br />
<li><a href="http://www.twitter.com/USTC_Software" class="twitter"></a></li><br />
<li><a href="http://www.facebook.com/USTCSoftware" class="facebook"></a></li><br />
<li><a href="#contactus" class="mail"></a></li><br />
</ul><br />
</div><br />
<div class="medium-8 medium-8 pull-5 columns"><br />
<a href="http://en.ustc.edu.cn"><h4 style="color:antiquewhite">University of Science and Technology of China</h4></a><br />
<p class="copyright">© 2014 USTC-Software,University of Science and Technology of China. All rights reserved.</p><br />
</div><br />
</div><br />
</div><br />
<br />
<script><br />
$(function(){<br />
$('.row .nameplate').click(function(){<br />
var description = $(this).parent().find('.details').html();<br />
var titleText = $(this).text();//text();<br />
$('#pop_up_content').html('<h2>' + titleText + '</h2>' + description);<br />
$('#pop_up').fadeIn();<br />
$(document.body).css("overflow","hidden");//禁止body 滚动条<br />
$("html").css("overflow","hidden");<br />
return false;<br />
});<br />
$('.row .profilewrap').click(function(){<br />
var description = $(this).find('.details').html();<br />
var titleText = $(this).find('.nameplate').text();//text();<br />
$('#pop_up_content').html('<h2>' + titleText + '</h2>' + description);<br />
$('#pop_up').fadeIn();<br />
$(document.body).css("overflow","hidden");//禁止body 滚动条<br />
$("html").css("overflow","hidden");<br />
return false;<br />
}); <br />
$('#pop_up #pop_up_close').click(function(){<br />
$('#pop_up').fadeOut();<br />
$(document.body).css("overflow","auto");<br />
$("html").css("overflow","auto");<br />
});<br />
$('#pop_up #pop_up_underlay').click(function(){<br />
$('#pop_up').fadeOut();<br />
$(document.body).css("overflow","auto");<br />
$("html").css("overflow","auto");<br />
});<br />
});<br />
</script><br />
<script src="https://2014.igem.org/Team:USTC-Software/main.js?action=raw&ctype=text/javascript"></script> <!-- Resource jQuery --><br />
<br />
<script src="https://2014.igem.org/Team:USTC-Software/foundation.min.js?action=raw&ctype=text/javascript"></script><br />
<script><br />
$(document).foundation();<br />
</script><br />
<style type="text/css"><br />
#totop_item {<br />
display: none;<br />
width: 60px;<br />
height: 100px;<br />
position: fixed;<br />
right: 2px;<br />
bottom: 10px;<br />
-webkit-transition: opacity .4s ease-in-out;<br />
-moz-transition: opacity .4s ease-in-out;<br />
-o-transition: opacity .4s ease-in-out;<br />
opacity: 1;<br />
z-index: 100000000;<br />
}<br />
<br />
#totop {<br />
display: block;<br />
width: 60px;<br />
height: 50px;<br />
background: url(https://static.igem.org/mediawiki/2014/3/31/2014ustc-Totop.png) center center no-repeat;<br />
background-color: #444;<br />
background-color: rgba(0,0,0,.6);<br />
border-radius: 2px;<br />
box-shadow: 0 1px 3px rgba(0,0,0,.2);<br />
cursor: pointer;<br />
margin-bottom: 10px;<br />
}<br />
<br />
</style><br />
<div id="totop_item" class=""> <br />
<a id="totop" onclick="return false;" title="回到顶部"></a> <br />
</div><br />
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{<br />
$(window).scroll(function(e) {<br />
if($(window).scrollTop()>300)<br />
$("#totop_item").fadeIn(1000);<br />
else<br />
$("#totop_item").fadeOut(1000);<br />
});<br />
};<br />
$(function(){<br />
$("#totop").click(function(e) {<br />
$('body,html').animate({scrollTop:0},1000);<br />
});<br />
goTop();<br />
});<br />
</script><br />
<br />
<br />
</body><br />
</html></div>
Hlx1996
http://2014.igem.org/Team:USTC-Software/server.php
Team:USTC-Software/server.php
2014-10-18T02:41:27Z
<p>Hlx1996: </p>
<hr />
<div><html class="no-js" lang="en"><br />
<head><br />
<meta charset="utf-8" /><br />
<meta name="viewport" content="width=device-width, initial-scale=1.0" /><br />
<title>USTC-Software | Welcome</title><br />
<br />
<meta name="description" content="iGEM"><br />
<meta name="author" content="Taixing Lin"><br />
<meta name="copyright" content="USTC-Software, inc. Copyright (c) 2014"><br />
<br />
<link href="https://2014.igem.org/Team:USTC-Software/fixed-igemHead.css?action=raw&ctype=text/css" rel="stylesheet" type="text/css" /><br />
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<link href='http://fonts.googleapis.com/css?family=Lobster' rel='stylesheet' type='text/css'><br />
<link rel="stylesheet" href="https://2014.igem.org/Team:USTC-Software/reset.css?action=raw&ctype=text/css"> <!-- CSS reset --><br />
<br />
<link rel="stylesheet" href="https://2014.igem.org/Team:USTC-Software/foundation.css?action=raw&ctype=text/css" /><br />
<br />
<link rel="stylesheet" href="https://2014.igem.org/Team:USTC-Software/main-new.css?action=raw&ctype=text/css" /><br />
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<script src="https://2014.igem.org/Team:USTC-Software/jquery.js?action=raw&ctype=text/javascript"></script><br />
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<link href="http://huodong.ustc.edu.cn/Web/igem2014-website/css/ie.css" media="screen" rel="stylesheet" /><br />
<![endif]--><br />
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<script src="http://huodong.ustc.edu.cn/Web/igem2014-website/js/html5.js"></script><br />
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<br />
<nav class="top-bar" data-topbar role="navigation"><br />
<ul class="title-area"><br />
<li class="name" ><br />
<h1><a href="/Team:USTC-Software" style="font-family: 'Lobster', cursive;">USTC-Software</a></h1><br />
</li><br />
<li class="toggle-topbar menu-icon"><a href="#"></a></li><br />
</ul><br />
<!-- --------------------------------------><br />
<br />
<section class="top-bar-section"><br />
<ul class="right"><br />
<br />
<li class="divider"></li><br />
<li class="has-dropdown"><br />
<a href="/Team:USTC-Software/biopano.php" class="">BioPano</a><br />
<ul class="dropdown"><br />
<li><a href="/Team:USTC-Software/biopano.php#overview">Overview</a></li><br />
<li><a href="/Team:USTC-Software/biopano.php#motivation">Motivation</a></li><br />
<li><a href="/Team:USTC-Software/biopano.php#features">Features</a></li><br />
<li><a href="/Team:USTC-Software/biopano.php#demos">Demos</a></li><br />
<li><a href="/Team:USTC-Software/biopano.php#why">Why choose BioPano?</a></li><br />
<li><a href="/Team:USTC-Software/biopano.php#futurework">Future work</a></li><br />
</ul><br />
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<a href="/Team:USTC-Software/develop.php" class="">Technology</a><br />
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<li><a href="/Team:USTC-Software/develop.php#alogrithm">Alogrithm</a></li><br />
</ul><br />
</li><br />
<li class="divider"></li><br />
<li><br />
<a href="server.php" class="">Server</a><br />
</li><br />
<br />
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<a href="/Team:USTC-Software/requirements.php" class="">Requirements</a><br />
<ul class="dropdown"><br />
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<li><a href="/Team:USTC-Software/human_practice.php#management">Management</a></li><br />
<li><a href="/Team:USTC-Software/human_practice.php#hlxisveryhandsome">Software & Platform We Used</a></li><br />
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<a href="/Team:USTC-Software/team.php" class="">Team</a><br />
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<li><a href="/Team:USTC-Software/team.php#team_members">Team Members</a></li><br />
<li><a href="/Team:USTC-Software/team.php#I_A">Instructors & Advisors</a></li><br />
<li><a href="/Team:USTC-Software/team.php#Additional_thanks">Additional Thanks</a></li><br />
</ul><br />
</li><br />
<li class="divider"></li><br />
<li class="has-dropdown"><br />
<a href="/Team:USTC-Software/acknowledge.php" class="">Acknowledge</a><br />
<ul class="dropdown"><br />
<li><a href="/Team:USTC-Software/acknowledge.php#dbank">Deutsche Bank</a></li><br />
<li><a href="/Team:USTC-Software/acknowledge.php#ustcif">USTCIF</a></li><br />
<li><a href="/Team:USTC-Software/acknowledge.php#utao">USTC Teaching Affair Office</a></li><br />
<li><a href="/Team:USTC-Software/acknowledge.php#database">Database</a></li><br />
</ul><br />
</li><br />
<ul><br />
</section><br />
<br />
</nav><br />
<script type="text/javascript" src="http://code.highcharts.com/highcharts.js"></script><br />
<script type="text/javascript" src="http://monitor.biopano.org/status.js"></script><br />
<script><br />
$(function () { <br />
$(document).ready(function() { <br />
Highcharts.setOptions({ <br />
global: { <br />
useUTC: false <br />
} <br />
}); <br />
<br />
var chart,str="<br />",info=[],status=[];<br />
for(h in data2){<br />
if(data2[h].status=="up"){<br />
info.push({<br />
name:data2[h].database_center+"@"+data2[h].location,<br />
data:data2[h].history<br />
});<br />
}<br />
status.push({<br />
name:data2[h].database_center+"@"+data2[h].location,<br />
status:data2[h].status,<br />
load:data2[h].lavg_1<br />
});<br />
<br />
} <br />
for(s in status){<br />
if(status[s].status=="up" && status[s].load < 8){<br />
img = '<img src="img/green.png" style="width:20px;padding: 0;margin-right:0.5em ">';<br />
<br />
}<br />
if (status[s].status=="up" && status[s].load > 8) {<br />
img = '<img src="img/yellow.png" style="width:20px;padding: 0;margin-right:0.5em">';<br />
}<br />
if (status[s].status!="up" ) {<br />
img = '<img src="img/red.png" style="width:20px;padding: 0;margin-right:0.5em">';<br />
}<br />
str = str + img + status[s].name+"<br /><br />";<br />
}<br />
$("#server_status").html(str);<br />
<br />
$('#container').highcharts({ <br />
chart: { <br />
type: 'spline', <br />
animation: Highcharts.svg, // don't animate in old IE <br />
marginRight: 10, <br />
}, <br />
title: { <br />
text: 'Server Load Status in Hours' //主标题 <br />
}, <br />
xAxis: { //X轴 <br />
type: 'datetime', <br />
tickPixelInterval: 150 <br />
}, <br />
yAxis: { //Y轴 <br />
title: { <br />
text: 'Load Status' <br />
}, <br />
plotLines: [{ <br />
value: 0, <br />
width: 1, <br />
color: '#808080' <br />
}] <br />
}, <br />
tooltip: { <br />
formatter: function() { <br />
return '<b>'+ this.series.name +'</b><br>'+ <br />
Highcharts.dateFormat('%Y-%m-%d %H:%M:%S', this.x) +'<br>'+<br />
Highcharts.numberFormat(this.y, 2); <br />
} <br />
}, <br />
legend: { <br />
enabled: false <br />
}, <br />
exporting: { <br />
enabled: false <br />
}, <br />
series:info <br />
}); <br />
<br />
<br />
}); <br />
<br />
}); <br />
</script><br />
<div class="main-content"><br />
<div class="row large-12 columns large-centered"><br />
<br />
<div id="container" style="min-width:400px;height:400px;"></div><br />
<div id="server_status" style="padding:2em"><br />
<br />
</div><br />
</div><br />
</div><br />
<br />
<div id="last-info" class="hide-for-small"><br />
<div class="row fullWidth"><br />
<div class="large-3 medium-3 columns " style="margin-top:5em"><br />
<img src="https://static.igem.org/mediawiki/2014/7/78/2014ustc-software2.png"><br />
</div><br />
<div class="large-6 medium-6 columns" style="color:#fff"><br />
<h5 style="color:#fff;font-weight:bold;margin-bottom: 25px;">Innovation Experiment Centre of Life Science (IEC)</h5><br />
<p>Building of Life Sciences, Room 363</p><br />
<p>University of Science and Technology of China</p><br />
<p>96, Jinzhai Rd, Shushan, Hefei</p><br />
<p>230026, Anhui, China</p><br />
<p>ustc-software-2014@googlegroups.com </p><br />
</div><br />
<div class="large-3 medium-3 columns " style="margin-top:5em"><br />
<br />
<a href="https://www.db.com" target="_blank"><img src="https://static.igem.org/mediawiki/2014/c/c0/2014ustc-Dbank.png" style="margin-top:2em"></a><br />
</div><br />
<br />
<br />
</div><br />
</div><br />
<br />
<div class="ltx-footer-bottom"><br />
<div class="row" ><br />
<div class="medium-4 medium-4 push-9 columns"><br />
<ul class="home-social"><br />
<li><a href="http://www.twitter.com/USTC_Software" class="twitter"></a></li><br />
<li><a href="http://www.facebook.com/USTCSoftware" class="facebook"></a></li><br />
<li><a href="#contactus" class="mail"></a></li><br />
</ul><br />
</div><br />
<div class="medium-8 medium-8 pull-5 columns"><br />
<a href="http://en.ustc.edu.cn"><h4 style="color:antiquewhite">University of Science and Technology of China</h4></a><br />
<p class="copyright">© 2014 USTC-Software,University of Science and Technology of China. All rights reserved.</p><br />
</div><br />
</div><br />
</div><br />
<br />
<script><br />
$(function(){<br />
$('.row .nameplate').click(function(){<br />
var description = $(this).parent().find('.details').html();<br />
var titleText = $(this).text();//text();<br />
$('#pop_up_content').html('<h2>' + titleText + '</h2>' + description);<br />
$('#pop_up').fadeIn();<br />
$(document.body).css("overflow","hidden");//禁止body 滚动条<br />
$("html").css("overflow","hidden");<br />
return false;<br />
});<br />
$('.row .profilewrap').click(function(){<br />
var description = $(this).find('.details').html();<br />
var titleText = $(this).find('.nameplate').text();//text();<br />
$('#pop_up_content').html('<h2>' + titleText + '</h2>' + description);<br />
$('#pop_up').fadeIn();<br />
$(document.body).css("overflow","hidden");//禁止body 滚动条<br />
$("html").css("overflow","hidden");<br />
return false;<br />
}); <br />
$('#pop_up #pop_up_close').click(function(){<br />
$('#pop_up').fadeOut();<br />
$(document.body).css("overflow","auto");<br />
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$('#pop_up #pop_up_underlay').click(function(){<br />
$('#pop_up').fadeOut();<br />
$(document.body).css("overflow","auto");<br />
$("html").css("overflow","auto");<br />
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});<br />
</script><br />
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<script><br />
$(document).foundation();<br />
</script><br />
<style type="text/css"><br />
#totop_item {<br />
display: none;<br />
width: 60px;<br />
height: 100px;<br />
position: fixed;<br />
right: 2px;<br />
bottom: 10px;<br />
-webkit-transition: opacity .4s ease-in-out;<br />
-moz-transition: opacity .4s ease-in-out;<br />
-o-transition: opacity .4s ease-in-out;<br />
opacity: 1;<br />
z-index: 100000000;<br />
}<br />
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display: block;<br />
width: 60px;<br />
height: 50px;<br />
background: url(https://static.igem.org/mediawiki/2014/3/31/2014ustc-Totop.png) center center no-repeat;<br />
background-color: #444;<br />
background-color: rgba(0,0,0,.6);<br />
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box-shadow: 0 1px 3px rgba(0,0,0,.2);<br />
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margin-bottom: 10px;<br />
}<br />
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<div id="totop_item" class=""> <br />
<a id="totop" onclick="return false;" title="回到顶部"></a> <br />
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$(window).scroll(function(e) {<br />
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$("#totop_item").fadeIn(1000);<br />
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$(function(){<br />
$("#totop").click(function(e) {<br />
$('body,html').animate({scrollTop:0},1000);<br />
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goTop();<br />
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</html></div>
Hlx1996
http://2014.igem.org/Team:USTC-Software/requirements.php
Team:USTC-Software/requirements.php
2014-10-18T02:35:01Z
<p>Hlx1996: </p>
<hr />
<div><html class="no-js" lang="en"><br />
<head><br />
<meta charset="utf-8" /><br />
<meta name="viewport" content="width=device-width, initial-scale=1.0" /><br />
<title>USTC-Software | Welcome</title><br />
<br />
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<p style="font-size:32px">Requirements</p><br />
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<h4 id="medals">Medals</h4><br />
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<h4><img src="https://static.igem.org/mediawiki/2014/4/4c/2014ustc-Bronze.png" width="60" height="60" alt="Bronze" >Bronze</h4><br />
<p> The following 4 goals must be achieved:</p><br />
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<h5><img src="https://static.igem.org/mediawiki/2014/c/c1/Hfut-A.png" width="30" height="30" alt="Complete" ><br />
Register the team, have a great summer, and have fun attending the Jamboree in Boston.<br />
</h5><br />
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<h5><img src="https://static.igem.org/mediawiki/2014/c/c1/Hfut-A.png" width="30" height="30" alt="Complete" ><br />
Create and share a description of the team's project via the iGEM wiki.<br />
</h5><br />
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<h5><img src="https://static.igem.org/mediawiki/2014/c/c1/Hfut-A.png" width="30" height="30" alt="Complete" ><br />
Present a Poster and Talk at the Regional Jamboree and World Championship Jamboree.<br />
</h5><br />
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<h5><img src="https://static.igem.org/mediawiki/2014/c/c1/Hfut-A.png" width="30" height="30" alt="Complete" ><br />
Develop and make available via The Registry of Software Tools, an open source software tool that supports Synthetic Biology based on Standard Parts.<br />
</h5><br />
You can directly enter the precise number of Standard Part, you can get its all types in BioBrick Assistant Windows.<br />
<div class="large-12 columns text-center"><br />
<img style="margin:1em" src="https://static.igem.org/mediawiki/2014/c/ce/2014ustc-medal1.png"><br />
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<p>&nbsp;</p><br />
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<div class="underline-tiny"></div> <br />
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<h4><img src="https://static.igem.org/mediawiki/2014/c/c6/2014ustc-Silver.png" width="60" height="60" alt="Sliver" >Silver</h4><br />
<p> In addition to the Bronze Medal requirements, the following 4 goals must be achieved:</p><br />
<br />
<br />
<br />
<br />
<h5><img src="https://static.igem.org/mediawiki/2014/c/c1/Hfut-A.png" width="30" height="30" alt="Complete" ><br />
Demonstrate the relevance of your development for Synthetic Biology based on standard Parts.<br />
</h5><br />
<p>You can directly enter the precise number of Standard Part, you can get its types in BioBrick Assistant Windows .then you can use blast tool with the sequence from BioBrick Assistant.By comparing the homology between the sequence of the part and in our database, we could predict its impact on the target body when injected to some extent.</p><br />
<div class="large-12 columns text-center"><br />
<img style="margin:1em" src="https://static.igem.org/mediawiki/2014/e/ee/2014ustc-medal2.png"><br />
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<h5><img src="https://static.igem.org/mediawiki/2014/c/c1/Hfut-A.png" width="30" height="30" alt="Complete" ><br />
Provide a comprehensive and well-designed User Guide. (Be creative! An instructional video may work as well.)<br />
</h5><br />
<p>We have a complete user manual <a href="biopanohelp.pdf">here!</a></p><br />
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<h5><img src="https://static.igem.org/mediawiki/2014/c/c1/Hfut-A.png" width="30" height="30" alt="Complete" ><br />
Provide detailed API documentation, preferably, automatically built from source code documentation (use tools like doxygen, yard, rdoc, naturaldocs, etc).<br />
</h5><br />
<p>We use toc to automatically produce api document. <a href="./api.html">Here!</a></p><br />
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<h5><img src="https://static.igem.org/mediawiki/2014/c/c1/Hfut-A.png" width="30" height="30" alt="Complete" ><br />
Demonstrate that you followed best practises in software development so that other developers can modify, use and reuse your code. Provide more than one realistic test case. Examples of best practices are automated unit testing and documentation of test coverage , bug tracking facilities, documentation of releases and changes between releases.<br />
</h5><br />
<p><b><a href="http://bug.biopano.org">Problem feedback and bug tracking</a>:</b> You can cast inquiry on us by GitHub, GitLab and YouTrack. Meanwhile, YouTrack is also used for bug tracking, ensuring your feedback goes to the developer as soon as possible. <br />
<br /><br /><br />
<b><a href="http://ci.biopano.org"> Automated Deployment</a>:</b> Our server has automated deployment capabilities. Server-side applications are bound with the Product branch of Git. All codes pushed to the Product branch will be deployed to many servers over the world in ten seconds. In order to prevent fault codes from being deployed to the servers by mistake, all the testing branches will be deployed to the testing server real-timely to be tested by developers.<br />
<br /><br /><br />
<b>Unit Testing:</b> Our server applies automated unit testing to dealing with uploaded back end codes. It will test the basic legitimacy and function of the codes, including robustness testing with respect to illegitimate uploaded parameters, legitimacy testing on data legitimacy, status testing of the database and testing of function realizaton, etc.</p><br />
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<p>&nbsp;</p><br />
<div class="underline-tiny"></div><br />
<h4><img src="https://static.igem.org/mediawiki/2014/8/88/2014ustc-Gold.png" width="60" height="60" alt="Gold" >Gold</h4><br />
<p> In addition to the Bronze and Silver Medal requirements, two additional goals must be achieved:</p><br />
<br />
<br />
<br />
<br />
<h5><img src="https://static.igem.org/mediawiki/2014/c/c1/Hfut-A.png" width="30" height="30" alt="Complete" ><br />
Provide a convincing validation, testing the performance of the development -- experimentally (can be outsourced) or by other teams and users. Note, even if the algorithm or tool turns out not to work that well, the Gold requirement is fulfilled if the test is good and the analysis convincing. Validation may include: preferably experiments, informatics analysis (complexity, run time) of an algorithm, or user studies.<br />
</h5><br />
<p><b>Analysis of pathway finder (k-shortest pathway search):</b><br /><br />
We use a specail heuristic algorithm , <a href="http://en.wikipedia.org/wiki/A*_search_algorithm">A* search algorithm</a>, to find more than one path connected two nodes in a given network.The run time of A* depends on structure of the given network. The space complexity is the number of edges plus the number of nodes. In our back end, we test this algorithm. The average of time which database reading costs is 1"40, the average of time which Vars initialization costs is 0"70, the average of time which <a href="http://en.wikipedia.org/wiki/Shortest_Path_Faster_Algorithm">SPFA(abbreviation for Shortest Path Faster Algorithm)</a> costs is 0"37, and the average of time which Serialize costs is 0"21.</p> <br />
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<br />
<h4><br />
And the second goal can be any one of the following:<br />
</h4><br />
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<h5><img src="https://static.igem.org/mediawiki/2014/c/c1/Hfut-A.png" width="30" height="30" alt="Complete" ><br />
Make your software interact / interface with the Registry.<br />
</h5><p>You can directly enter the precise number of Standard Part, you can get its types in BioBrick Assistant Windows .then you can use blast tool with the sequence from BioBrick Assistant.By comparing the homology between the sequence of the part and in our database, we could predict its impact on the target body when injected to some extent.</p><br />
<br />
<div class="large-12 columns text-center"><br />
<img style="margin:1em" src="https://static.igem.org/mediawiki/2014/c/ce/2014ustc-medal1.png"><br />
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<h5><img src="https://static.igem.org/mediawiki/2014/c/c1/Hfut-A.png" width="30" height="30" alt="Complete" ><br />
Re-use and further develop previous iGEM software projects (or parts thereof) or use and/or improvement of existing synthetic biology tools or frameworks.<br />
</h5><br />
<p>We use blast code from <a href="http://blast.ncbi.nlm.nih.gov/Blast.cgi">ncbi </a>to comparing the homology.</p><br />
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<h5><img src="https://static.igem.org/mediawiki/2014/c/c1/Hfut-A.png" width="30" height="30" alt="Complete" ><br />
Develop a well documented library or API for other developers (rather than “only” a stand-alone app for end users.)<br />
</h5><br />
<p>We use toc to automatically produce api document. <a href="./docs/">Here!</a></p><br />
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<br />
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<h5><img src="https://static.igem.org/mediawiki/2014/c/c1/Hfut-A.png" width="30" height="30" alt="Complete" ><br />
Support and use the SBOL and / or SBOLv standard.<br />
</h5><br />
<p>Biopano supports file format conversion to sbol perfectl</p><br />
<div class="large-12 columns text-center"><br />
<img style="margin:1em" src="https://static.igem.org/mediawiki/2014/d/dd/2014ustc-medal3.png"><br />
</div><br />
<br />
<p></p><br />
<h4 id="safety">Safety</h4><br />
<div class="underline-small"> </div><br />
<h5>1. Are you using the iGEM Software repository at github.com/igemsoftware? If you have instead stored your code elsewhere, please explain where and why you have put it there. If your code is not in the iGEM repository, a re you using any version control system such as Git, CVS, or SVN?<br />
</h5><br />
<p>Yes, we use the iGEM Software repository at github.com/igemsoftware.<br />
</p><br />
<h5> 2. Does your software store any private data supplied by the user? (For example: the user's name and email address, passwords, DNA sequences, circuit designs, etc.) If yes, please describe what kind of data is stored. If no, skip the rest of this question and move on to question 3.<br />
</h5><br />
<p>We store the user's name, the email address (if he/she logs in using Gmail account) or the username (if logged in using Baidu account), and the user's all data designed with our software.<br />
Especially, we DO NOT store the user's password because we only allow users to log in with their Gmail account or Baidu account using OAuth2.0 ,<br />
which is a very secure protocol describing a third-party login pattern.<br />
</p><br />
<h5>3. Does your software include any other security features? Please describe them here. </h5><br />
<p><br />
We use OAuth technology in user system. So users can log in with their GOOGLE account or BAIDU account without telling us their passwords.<br />
</p> <br />
<h5> 4. Does your software let the user create a design by choosing parts/genes from a list/database, such as the Registry? If so, which lists/databases are included? Is there any restriction on which parts/ genes the user can choose?</h5><br />
<p> <br />
Yes, users can use database built by our team to assist themself to create a design. The database we build is the result of merging and reforming parts of KEGG, RegulonDB, Uniport.<br />
</p><br />
<h5>5. Does your software allow users to write new data into any public lists or databases? If so, do you check the new data for errors before allowing it to be written?</h5><br />
<p><br />
Yes, users can upload their data to our database anytime.<br /><br />Yes, we will check validation and format of data before it is written in the back end.<br />
</p><br />
<h5>6. Does your software include any other features that encourage the user to create safe designs? Please describe them. </h5><br />
<p>No.</p><br />
<br />
<h5>7. Is your team also doing biological work in a wet lab ? </h5><br />
<p>No.</p><br />
<p></p><br />
<h4 id="collaboration">Collaboration</h4><br />
<div class="underline-small"><br />
<br />
</div><br />
<p>While preparing for iGEM, we always hope we can accomplish more and more people can join this great project. Luckily, by cooperation with others, all these hopes come ture.</p><br />
<li>Collaboration with professors</li> <br />
<p></p><br />
<p>While completing our project, we encountered all kinds of problems, of which some could hardly solve by ourselves. We solved them by discussing and cooperating with many professors of USTC. At the same time, we knew more about the original thoughts of synthetic biological researchers. So we tried to combine their needs and our project, hoping we could also help them. Now, we believe that we realized our original intention.</p><br />
<li>Collaboration with Chinese iGEMers</li><br />
<p></p><br />
<p>One reason why iGEM competition is unforgettable is that it makes us know more like-minded people. This year, we hoped iGEM teams could communicate more with each other, so we organized iGEM meetup this summer. Teams from China got familiar through the meetup, and we kept in touch after it. We not only got to know each other by frequent communication, but helped each other with their problems to bring about good results for us all as well.</p><br />
<li>Collaboration with HFUT_CHINA</li><br />
<p></p><br />
<p>While enjoying iGEM, we hoped more people could join us. This year, HFUT_CHINA sent a team for iGEM for the first time. As a team new to iGEM, it would surely encounter more problems. As their neighbor, we kept in touch with them and did everything we could to help them with their project. Through the course, we got to know a lot of people enthusiastic about iGEM of our age. We are glad that they also join iGEM.</p><br />
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Hlx1996
http://2014.igem.org/Team:USTC-Software/acknowledge.php
Team:USTC-Software/acknowledge.php
2014-10-18T02:34:22Z
<p>Hlx1996: </p>
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<h4 id="dbank">Deutsche Bank</h4><br />
<div class="underline-small"></div><br />
<p><br />
Deutsche Bank is a German global banking and financial services company with its<br />
headquarters in the Deutsche Bank Twin Towers in Frankfurt. It has more than 100,000<br />
employees in over 70 countries, and has a large presence in Europe, the Americas, Asia-<br />
Pacific and the emerging markets. In 2009, Deutsche Bank was the largest foreign exchange<br />
dealer in the world with a market share of 21 percent.<br />
Deutsche Bank has offices in major financial centres including London, New York City,<br />
Singapore, Hong Kong, Tokyo, Paris, Moscow, Sydney, Toronto, Jakarta, Istanbul, Madrid,<br />
Dublin, Amsterdam, Warsaw, Mumbai, Kuala Lumpur, São Paulo, Dubai, Riyadh, Bangkok,<br />
Karachi, Belgrade, Manila and George Town (Cayman Islands).<br />
The bank offers financial products and services for corporate and institutional clients along<br />
with private and business clients. Services include sales, trading, research and origination of<br />
debt and equity; mergers and acquisitions (M&A); risk management products, such as<br />
derivatives, corporate finance, wealth management, retail banking, fund management, and<br />
transaction banking<br />
</p><br />
<br />
<h4 id="ustcif">USTCIF</h4><br />
<div class="underline-small"></div><br />
<p><br />
USTCIF, The University of Science and Technology of China Initiative Foundation, is a educational NGO serves to help with the development of USTC. As one of USTC's alumni foundations, its purpose is to enhence the alumni foundations to make USTC better. USTIF is the first college alumni foundation indepentant from the university.<br />
</p><br />
<br />
<h4 id="utao">USTC Teaching Affair Office</h4><br />
<div class="underline-small"><br />
<br />
</div><br />
<p><br />
http://www.teach.ustc.edu.cn/<br />
</p><br />
<h4></h4><br />
<div class="underline-small"><br />
<br />
</div><br />
<br />
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<li><a href="http://regulondb.ccg.unam.mx/"><br />
<img src="https://static.igem.org/mediawiki/2014/4/43/2014ustc-RegulonDB.jpg" style="height:100px"></a></li><br />
<li><a href="http://www.kegg.jp/"><br />
<img src="https://static.igem.org/mediawiki/2014/c/ca/2014ustc-Kegg.jpg" style="height:100px"></a></li><br />
<li><a href="http://www.ncbi.nlm.nih.gov/"><br />
<img src="https://static.igem.org/mediawiki/2014/5/55/2014ustc-NCBI.jpg" style="height:100px"></a></li><br />
<li><a href=" http://www.uniprot.org/"><br />
<img src="https://static.igem.org/mediawiki/2014/4/47/2014ustc-Uniprot.png" style="height:100px"></a></li><br />
</ul><br />
<p>We would like to thank RegulonDB, Kegg, NCBI and uniprot for their data, without which Biopano can never be finished. Thanks again for their work and effort.</p><br />
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<div class="large-6 medium-6 columns" style="color:#fff"><br />
<h5 style="color:#fff;font-weight:bold;margin-bottom: 25px;">Innovation Experiment Centre of Life Science (IEC)</h5><br />
<p>Building of Life Sciences, Room 363</p><br />
<p>University of Science and Technology of China</p><br />
<p>96, Jinzhai Rd, Shushan, Hefei</p><br />
<p>230026, Anhui, China</p><br />
<p>ustc-software-2014@googlegroups.com </p><br />
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<a href="http://en.ustc.edu.cn"><h4 style="color:antiquewhite">University of Science and Technology of China</h4></a><br />
<p class="copyright">© 2014 USTC-Software,University of Science and Technology of China. All rights reserved.</p><br />
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Hlx1996
http://2014.igem.org/Team:USTC-Software/team.php
Team:USTC-Software/team.php
2014-10-18T02:33:52Z
<p>Hlx1996: </p>
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<img src="https://static.igem.org/mediawiki/2014/6/62/2014ustc-Xyc.jpg" alt="Xue Yuechuan"><br />
<div class ="nameplate"><a href="#">Xue Yuechuan</a></div><br />
<div class = "details"><img src="https://static.igem.org/mediawiki/2014/6/62/2014ustc-Xyc.jpg" alt="Xue Yuechuan" align="left"><p>captain<br>junior from physical electronics major<br>team leader and art designer</p><br />
</div><br />
</li><br />
<br />
<li class ="profilewrap"><br />
<img src="https://static.igem.org/mediawiki/2014/e/ee/2014ustc-Zss.jpg" alt="Zhao Shensen"><br />
<div class ="nameplate"><a href="#">Zhao Shensen</a></div><br />
<div class = "details"><img src="https://static.igem.org/mediawiki/2014/e/ee/2014ustc-Zss.jpg" alt="Zhao Shensen" align="left"><p>vice captain<br>senior from physical electronics major<br>help team managing,join back end work</br>his words:Work which make idea true make me happy</p><br />
</div><br />
</li><br />
<li class ="profilewrap"><br />
<img src="https://static.igem.org/mediawiki/2014/6/6e/2014ustc-Glz.jpg" alt="Gan Longzhi"><br />
<div class ="nameplate"><a href="#">Gan Longzhi</a></div><br />
<div class = "details"><img src="https://static.igem.org/mediawiki/2014/6/6e/2014ustc-Glz.jpg" alt="Gan Longzhi" align="left"><p>team manager<br>sophomore from school of earth and space science<br>help team managing,web and document writing<br>his words:Try hard, have fun.</p><br />
</div><br />
</li><br />
<li class ="profilewrap"><br />
<img src="https://static.igem.org/mediawiki/2014/6/6c/2014ustc-Ltx.jpg" alt="Lin Taixing"><br />
<div class ="nameplate"><a href="#">Lin Taixing</a></div><br />
<div class = "details"><img style="width:200px" src="https://static.igem.org/mediawiki/2014/6/6c/2014ustc-Ltx.jpg" alt="Lin Taixing" align="left"><p>member<br>junior from Atomic and molecular physics major<br>Responsible for web designing<br>his words:Dream what you want to dream; go where you want to go; be what you want to be, because you have only one life and one chance to do all the things you want to do. </p><br />
</div><br />
</li><br />
<li class ="profilewrap"><br />
<img src="https://static.igem.org/mediawiki/2014/1/1e/2014ustc-Wws.jpg" alt="Wang Wenshuo"><br />
<div class ="nameplate"><a href="#">Wang Wenshuo</a></div><br />
<div class = "details"><img src="https://static.igem.org/mediawiki/2014/1/1e/2014ustc-Wws.jpg" alt="Wang Wenshuo" align="left"><p>member<br>Junior of the Special Class for the Gifted Young, majoring in Statistics<br>tranlates and document writing<br>his words:There is no fate but what we make.</p><br />
</div><br />
</li><br />
<li class ="profilewrap"><br />
<img src="https://static.igem.org/mediawiki/2014/d/d0/2014ustc-Zzy.jpg" alt="Zhang Zhiyuan"><br />
<div class ="nameplate"><a href="#">Zhang Zhiyuan</a></div><br />
<div class = "details"><img src="https://static.igem.org/mediawiki/2014/d/d0/2014ustc-Zzy.jpg" alt="Zhang Zhiyuan" align="left"><p>member<br>Senior of Hua Loo-Keng Talent Program in Mathematics, majoring in fundamental mathematics<br>tranlates and document writing<br>his words:To see, to ask, to search, to believe.</p><br />
</div><br />
</li><br />
<br />
<li class ="profilewrap"><br />
<img src="https://static.igem.org/mediawiki/2014/7/7d/2014ustc-Gyf.jpg" alt="Gao Yifan"><br />
<div class ="nameplate"><a href="#">Gao Yifan</a></div><br />
<div class = "details"><img src="https://static.igem.org/mediawiki/2014/7/7d/2014ustc-Gyf.jpg" alt="Yifan Gao" align="left"><p>member<br>junior from optics major<br>Responsible for back end work<br>his words:Perfection is achieved not when there is nothing more to add, but rather when there is nothing more to take away.</p><br />
</div><br />
</li><br />
<li class ="profilewrap"><br />
<img src="https://static.igem.org/mediawiki/2014/4/4b/2014ustc-Dcx.jpg" alt="Dong Chenxiao"><br />
<div class ="nameplate"><a href="#">Dong Chenxiao</a></div><br />
<div class = "details"><img src="https://static.igem.org/mediawiki/2014/4/4b/2014ustc-Dcx.jpg" alt="Dong Chenxiao" align="left"><p>member<br>sophomore from school of physics science<br>data hunting and organizing,software design and document writing<br>his words:All the time, try retroting any idea from team.</p><br />
</div><br />
</li><br />
<br />
<li class ="profilewrap"><br />
<img src="https://static.igem.org/mediawiki/2014/2/28/2014ustc-Jzy.jpg" alt="Haiyan Liu"><br />
<div class ="nameplate"><a href="#">Jin Zeyu</a></div><br />
<div class = "details"><img src="https://static.igem.org/mediawiki/2014/2/28/2014ustc-Jzy.jpg" alt="Haiyan Liu" align="left"><p>member<br>sophomore from school of earth and space science<br>data hunting and organizing,software design and document writing<br>his words:Not most powerful, but highly responsible!</p><br />
</div><br />
</li><br />
<br />
<li class ="profilewrap"><br />
<img src="https://static.igem.org/mediawiki/2014/9/97/2014ustc-Zl.jpg" alt="Haiyan Liu"><br />
<div class ="nameplate"><a href="#">Zhou Long</a></div><br />
<div class = "details"><img src="https://static.igem.org/mediawiki/2014/9/97/2014ustc-Zl.jpg" alt="Haiyan Liu" align="left"><p>member<br>junior from Nuclear physics major<br>>Responsible for Front End work<br>his words:Simply Enjoy.</p><br />
</div><br />
</li><br />
<br />
<li class ="profilewrap"><br />
<img src="https://static.igem.org/mediawiki/2014/a/a1/2014ustc-Hlx.jpg" alt="Han Luxin"><br />
<div class ="nameplate"><a href="#">Han Luxin</a></div><br />
<div class = "details"><img src="https://static.igem.org/mediawiki/2014/a/a1/2014ustc-Hlx.jpg" alt="Han Luxin" align="left"><p>member<br>sophomore from school of computer science<br>Algorithm design and writing,web writing<br>his word:Where there is a will, there is a way.</p><br />
</div><br />
</li><br />
<br />
<li class ="profilewrap"><br />
<img src="https://static.igem.org/mediawiki/2014/8/8d/2014ustc-Ycp.jpg" alt="Yu Chuanping"><br />
<div class ="nameplate"><a href="#">Yu Chuanping</a></div><br />
<div class = "details"><img src="https://static.igem.org/mediawiki/2014/8/8d/2014ustc-Ycp.jpg" alt="Yu Chuanping" align="left"><p>member<br>senior from statistics major<br>translate<br>his words:Do one thing at a time, and do well.</p><br />
</div><br />
</li><br />
<br />
<li class ="profilewrap"><br />
<img src="https://static.igem.org/mediawiki/2014/4/44/2014ustc-Zhy.jpg" alt="Zhang Huayu"><br />
<div class ="nameplate"><a href="#">Zhang Huayu</a></div><br />
<div class = "details"><img src="https://static.igem.org/mediawiki/2014/4/44/2014ustc-Zhy.jpg" alt="Zhang Huayu" align="left"><p>member<br>sophomore from school of physics science<br>Front End work<br>his words:Be the best yourself, to be No.1. </p><br />
</div><br />
</li><br />
<br />
</li><br />
<br />
<li class ="profilewrap"><br />
<img src="https://static.igem.org/mediawiki/2014/9/96/2014ustc-Fyc.jpg" alt="Haiyan Liu"><br />
<div class ="nameplate"><a href="#">Fei Yicheng</a></div><br />
<div class = "details"><img src="https://static.igem.org/mediawiki/2014/9/96/2014ustc-Fyc.jpg" alt="Haiyan Liu" align="left"><p>member<br>sophomore from school of physics science<br>back end work<br>his words:Be the best yourself, to be No.1. </p><br />
</div><br />
</li><br />
<br />
<li class ="profilewrap"><br />
<img src="https://static.igem.org/mediawiki/2014/b/bc/2014ustc-Ctl.jpg" alt="Chen Tianlong"><br />
<div class ="nameplate"><a href="#">Chen Tianlong</a></div><br />
<div class = "details"><img src="https://static.igem.org/mediawiki/2014/b/bc/2014ustc-Ctl.jpg" alt="Chen Tianlong" align="left"><p>member<br>sophomore from school of matnematics<br>web design<br>his words:Be the best yourself, to be No.1. </p><br />
</div><br />
</li><br />
<br />
<li class ="profilewrap"><br />
<img src="https://static.igem.org/mediawiki/2014/e/e8/Clf.jpg" alt="Chen Lingfan"><br />
<div class ="nameplate"><a href="#">Chen Lingfan</a></div><br />
<div class = "details"><img src="https://static.igem.org/mediawiki/2014/e/e8/Clf.jpg" alt="Chen Lingfan" align="left"><p>member<br>junior from computational mathematics major<br>algorithm design<br>his words:Be the best yourself, to be No.1. </p><br />
</div><br />
</li><br />
<br />
</ul><br />
<h4 id="I_A">Instructors & Advisors</h4><br />
<div class="underline-small"></div><br />
<br />
<br />
<div><br />
<ul class="large-block-grid-6 medium-block-grid-4 small-block-grid-2 text-center"><br />
<li class ="profilewrap"><br />
<img src="https://static.igem.org/mediawiki/2014/d/de/2014ustc-G.png" alt="Haiyan Liu"><br />
<div class ="nameplate"><a href="#">Haiyan Liu</a></div><br />
<div class = "details"><img src="https://static.igem.org/mediawiki/2014/d/de/2014ustc-G.png" alt="Haiyan Liu" ><br />
<p><b>Email:</b>hyliu@ustc.edu.cn</p><br />
<p><b>Brief Intro:</b>Haiyan Liu was born in Sichuan Province, China. He received his BS degree in Biology in 1990 and PhD degree in Biochemistry and Molecular Biology in 1996, both from USTC. Between 1993 and 1995 he was a visiting graduate student in Laboratory of Physical Chemistry of ETH, Zurich (Switzerland). From 1998 to 2000 he was post-doctoral research associate at Department of Chemistry, Duke University (USA) and Department of Biochemistry and Biophysics UNC-Chapel Hill (USA). Since 2001, he has been a professor of computational biology at School of Life Sciences, USTC.</p><br />
</div><br />
</li><br />
<br />
<br />
<li class ="profilewrap"><br />
<img src="https://static.igem.org/mediawiki/2014/a/af/2014ustc-H.png" alt="Zhi Liang"><br />
<div class ="nameplate"><a href="#">Zhi Liang</a></div><br />
<div class = "details"><img src="https://static.igem.org/mediawiki/2014/a/af/2014ustc-H.png" alt="Zhi Liang" ><br />
<p><b>Email:</b>liangzhi@ustc.edu.cn</p><br />
<p><b>Brief Intro:</b>Liang Zhi, Ph.D., Associate Professor Extraordinary . 2000 graduated from the school of Life Sciences in the University of Science and Technology of China, received bachelor's degree in biology and electronics and information engineering dual degree. 2006 graduated from the school of Life Sciences in the University of Science and Technology of China protein crystallography laboratory , PhD. From 2007 to 2012 in the school of Life Sciences in the University of Science and Technology of China Systems Biology Laboratory in systems biology postdoctoral research. Postdoctoral period has won China Postdoctoral Science Foundation funded second and Natural Science Foundation funding. 2012 University of Science and Technology of China Extraordinary Life Sciences Research Associate . Research results published on Nucleic Acids Res, Bioinformatics, Bioinformatics, J Biol Chem.</p><br />
</div><br />
</li><br />
<br />
<li class ="profilewrap"><br />
<img src="https://static.igem.org/mediawiki/2014/9/93/2014ustc-I.png"><br />
<div class ="nameplate"><a href="#">Jiong Hong</a></div><br />
<div class = "details"><img src="https://static.igem.org/mediawiki/2014/9/93/2014ustc-I.png" alt="Jiong Hong" ><br />
<p>Professor, School of Life Sciences University of Science & Technology of China</p><br />
<p><br />
<b>Email:</b> hjiong@ustc.edu.cn<br /><br /><br />
<b>Brief Intro:</b>Jiong Hong was born in Anhui Province, China. He received his BS degree in 1993 from Anhui Normal University, MSc degree in 1996 from Beijing Normal University, and Ph.D degree in 2003 from Kyoto University, all in Life Sciences. From 2006 to 2008, he did post-doctoral research in Virginia Tech University, USA. Since 2008, he has been introduced to the USTC as talented.<br />
</p><br />
</div><br />
</li><br />
<br />
<br />
<li class ="profilewrap"><br />
<img src="https://static.igem.org/mediawiki/2014/9/92/2014ustc-J.png" alt="Fan Jin"><br />
<div class ="nameplate"><a href="#">Fan Jin</a></div><br />
<div class = "details"><img src="https://static.igem.org/mediawiki/2014/9/92/2014ustc-J.png" alt="Fan Jin" ><br />
<br />
<br /><br /><br />
<p>1997.07-2002.07 B.S., Student, Department of Applied Chemistry, University of Science & Technology of China, P. R. China.<br />
Degree awarded: B.S. in chemistry, 07/2002</p><br />
<br />
<p>2003.08-2007.06 Ph.D. Candidate, Department of Chemistry, The Chinese University of Hong Kong.<br />
Degree awarded: Ph.D in chemistry, 06/2007</p><br />
<br />
<p>2002.07-2003.07 R.A., The Hefei National Laboratory of Physical Science at Microscale, Department of Chemical Physics, University of Science & Technology of China, P. R. China.</p><br />
<br />
<p>2007.06-2009.01 Postdoctoral Associate, Department of Chemistry, The Chinese University of Hong Kong.</p><br />
<br />
<p>2009.01-2009.11 Postdoctoral Associate, Department of Materials Science and Engineering, University of Illinois at Urbana Champaign.</p><br />
<br />
<p>2009.11-2011.8 Postdoctoral Associate, Department of Bioengineering, California Nanosystems Institute, University of California, Los Angeles. </p><br />
<br />
<p>2011.8-present Professor, Department of Polymer Materials Science and Engineering, University of Science and Technology of China, CAS Key Lab of Soft Matter Chemistry. </p><br />
<br />
<h4>Research Interests</h4><br />
<p>Polyelectrolyte and colloidal particles in the oil-water interface. </p><br />
<p>Interaction between Antibiotic peptides and lipids membrane. </p><br />
<p>Living cell image and living cell micro-manipulation.</p><br />
<p>Biological macromolecules, characterization of supramolecular assembly and its applications in drug delivery and gene transfection. </p><br />
<p>Bacterial communities. (Ex: signaling, motility, social organization in biofilms)</p><br />
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<br />
<br />
</div><br />
</li><br />
</ul><br />
<br />
</div><br />
<br />
<br />
<h4 id="Additional_thanks">Additional Thanks</h4><br />
<div class="underline-small"><br />
<br />
</div><br />
<div style="line-height:200%"><br />
<li><br />
Thanks for financial assistance from Deutsche Bank, USTCIF and USTC Teaching Affair Office. Only with their help could we finish the competition;<br />
</li><br />
<li><br />
Thank data from RegulonDB, KEGG, Uniprot and NCBI. Only with their data and apis could we refine our database; <br />
</li><br />
<li><br />
Thank project guidance from Haiyan Liu, Zhi Liang, Fan Jin and Jiong Hong. Only with their guidance could our project be improved and deepened; <br />
</li><br />
<li><br />
Thank Chen Liao for participating in the use, evaluation and popularization of Biopano.He pointed out many deficiencies and bugs of our software.<br />
</li><br />
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Hlx1996
http://2014.igem.org/Team:USTC-Software/human_practice.php
Team:USTC-Software/human practice.php
2014-10-18T02:33:28Z
<p>Hlx1996: </p>
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<p style="font-size:32px">Human Practice</p><br />
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<div class="row large-12 columns large-centered"><br />
<h4 id="management">Management</h4><br />
<div class="underline-small"><br />
<br />
</div><br />
<h5> iGEM, Efficiency, Environment and Enjoyment</h5><br />
<p>During the entire iGEM project, we adhered to the four elements,<br />
iGEM, efficiency, environment and enjoyment. When the project is drawing to a close,<br />
we tease out our project management experience according<br />
to them and put it online as reference for more people.</p><br />
<div class="underline-tiny"></div><br />
<h5>iGEM</h5><br />
<br />
<p>Since our project is for participating in iGEM,<br />
we always emphasized the leading position of iGEM in our project.<br />
We set up study group specifically for iGEM project. Independent of the working group,<br />
they worked on synthetic biology. Although some of their results turned out to be useless,<br />
they played a critical role in every phase of our project, such as the decision of our final project,<br />
the optimization of functions of the software and teaching other team members<br />
not majoring in biology some biological knowledge. A group focusing on the subject guarantees<br />
that the whole project runs smoothly on track. The experience above applies to project of any subject.<br />
Just replace “iGEM” with your own word.</p><br />
<div class="underline-tiny"></div><br />
<h5>Efficiency</h5><br />
<br />
<p>In any project, efficiency is always a significant factor.<br />
During our project, we took regular and necessary methods,<br />
such as wholesome team management system (team leader, team manager,<br />
group supervisor) and explicit regulations. In addition,<br />
we managed our team in an innovative way—electronic platform.<br />
All work plans are put on electronic notebook shared by all team members.<br />
We also built a platform for team members to report their working achievements periodically.<br />
Last but not least, we established a GitLab ourselves accessible to all team members,<br />
which avoided the detriment of environment caused by paper-based platform <br />
(this will be mentioned again later).</p><br />
<div class="underline-tiny"></div><br />
<h5>Environment</h5><br />
<br />
<p><br />
Environmental protection is one of the most compelling problems nowadays.<br />
We kept thinking about this while proceeding the project. As mentioned above,<br />
we built a paperless office, except for necessary invoices. Compared with previous iGEM teams of USTC,<br />
we saved a lot of paper. Meanwhile, we paid attention to keeping our working environment neat and clean.<br />
The workplace was cleaned by our team members every day.<br />
Garbage was classified and dropped in the garbage bin. We believe that<br />
appropriate regulation can ensure that working group of any project can <br />
do their work comfortably and protect the earth at the same time.<br />
</p><br />
<div class="underline-tiny"></div><br />
<h5>Enjoyment</h5><br />
<p><br />
Although there were a lot of work to do, our project experience was joyful.<br />
At the beginning of the project, team members with experience in software <br />
development prepared courses for other members. Well-prepared courses made us accomplish <br />
the assignments successfully and gain new knowledge. We also organized various kinds of <br />
activities to relax our team members. In the summer vacation, we had group activities <br />
after a whole day’s hard work, including having dinner outside, playing sports and even<br />
computer game competition. We also recommend these activities to every team. They not only<br />
relax team members, but also improve the relationship among team members, making the whole<br />
working experience enjoyable and unforgettable.<br />
<br />
</p><br />
<br />
<br />
<h3 id="hlxisveryhandsome">Software & Platforms We Used</h3><br />
<div class="underline-small"><br />
<br />
</div><br />
<br />
<h5>Google group</h5><br />
<br />
<p>At the formation of USTC-Software of 2014, the team leader of 2013 recommended Google group as an online platform for communication and team management. Although every team member was highly enthusiastic about iGEM, they had their own school work to worry about. Meanwhile, our team members lived in different areas of the campus. Hence it became a serious problem that how team members could receive notifications in time to accomplish the work separately while co-working time could not be guaranteed. Google group solved this problem. Google group offers open online platform to users and users can build their own platform for sharing. Messages on the platform are accessible to all users joining the group. Emails can also be pushed to users. We built a platform of our team, and all messages on the platform could be pushed to team members in time. By Google group, we were able to:</p><br />
<ul><br />
<li>1. send notifications and arrangements to all team members in time;</li><br />
<li>2. make team members share their thoughts and innovation conveniently;</li><br />
<li>3. make regulations, assessments and financal issues transparent by sharing work logs.</li><br />
</ul><br />
<p>We recommend Google group for project management based on our experience. It can enhance communication among team members by breaking through the limitations of time and space. It can also make team work transparent and increase management efficiency.</p><br />
<div class="underline-tiny"></div><br />
<h5>Wunderlist</h5><br />
<br />
</p><br />
<div class="underline-tiny"></div><br />
<h5>OneNote</h5><br />
<br />
<p><br />
For every team, the financial problem is a big one. Of course, you may think of separating money and account easily, but how do you keep two or more financial managers in the same stage? We chose to solve the problem by OneNote.<br /><br />OneNote is originally designed for instant creation and notes sharing, and so it can be applied to financial management smoothly. We could create notebooks according to different items and mark the accounts that have been cleared or have not yet been cleared. By inviting others, the team leader can supervise the manager about he financial situation timely and make sure about the accuracy of this.<br />
</p><br />
<div class="underline-tiny"></div><br />
<h5>Omni outliner & Mindmap</h5><br />
<br />
<p><br />
No matter you are in what stage of what project, when you need new thoughts, it is always quite a hard time to get a satisfying result. Brainstorm might be a really nice idea, but in most of the time you have to stare at a whiteboard full of messy ideas on it without action. To solve the problem, you need some kind of software for thought assistance, such as Omni Outliner and Mingmap.<br /><br />Software like Omni Outliner can help you sort out all the necessary points and arrange your thoughts when you are writing articles, and software like Mindmap can enable you to draw a succinct "map" of your ideas to clarify your thoughts and summarize the viewpoints. Therefore you can quickly extract a wonderful idea from the numerous viewpoints raised in the brainstorm.<br />
<br />
</p><br />
<div class="underline-tiny"></div><br />
<h5>Dropbox</h5><br />
<br />
<p><br />
During the project, all kinds of files were created unremittingly. To be specific, articles to read, work log to be displayed, finished program codes, relevant materials, photos of us, etc. How will you store the files? You don’t store all of them in only one person’s computer, for they are too many and other people may also need them. We have a great solution—Dropbox.<br /><br />Dropbox is a cloud storage platform. It allows users to store files in the cloud, and thus any team member, knowing the password of the account, has access to these files no matter when and where. In the meantime, cloud storage is also very secure. Even if you accidentally spill coffee on your computer or the manuscripts, you can still keep your files safe.<br />
</p><br />
<br />
<h3>Biological Cooperation</h3><br />
<div class="underline-small"><br />
<br />
</div><br />
<br />
<p>Fine communication in any field enhances the development of the field, especially when it comes to biological field. Nowadays, there are already some ways of communication in biology. They are traditional ways, however. Communication by literature publishing, meeting attending and emailing is relatively slow and hard to be used in global range. What’s more important is that communication in these ways will restrict a biologist’s research field. This suppresses the cross-field communication of biology. As we all know, communication of different fields will bring about amazing breakthroughs. Therefore, if the restriction can be broken, it will benefit the development of biology astonishingly.<br /><br />BioPano is based on an online server, so it supports communication and cooperation perfectly. Users can release their research results on our software platform. BioPano will record the information and all biologists using the software all over the world can see the modifications. What’s better, we add group function usually in social software into BioPano. Biologists from different fields can form a group with BioPano. They can communicate more conveniently in the group. Meanwhile, BioPano offers other project co-management services to help biologists from different fields complete the research together.<br /><br />Popularization of BioPano will surely improve the connection among biologists greatly and enhance the progress of biology. Furthermore, BioPano will change the frequency and pattern of research results updating of biology, and even show every single change of biology real-timely like Wikipedia. Every researcher can share the progress of biology, and biological research will stride into the information age.<br /><br />We have already reccomended BioPano to many biological researchers, and received great feedbacks.</p><br />
<br />
<h3>Summer Vacation Meetup</h3><br />
<div class="underline-small"><br />
<br />
</div><br />
<br />
<p>Since local competitions are not held this year, iGEM foundation encourages every district to organize communication activity themselves. We responded to the call and organized summer vacation meetup at University of Science and Technology of China.<br /><br />This summer, we invited several iGEM teams from China to USTC from August 15th to August 17th for project showing and ideas interchanging. SJTU-Software, SJTU-BioX-China, SYSU-Software, XMU-China, HFUT_China, USTC_Software and USTC-China paticipated in this activity.<br /><br />The meetup was successful. Firstly, iGEM teams from China got to know each other, and developed profound friendship. Secondly, we understood each other’s project, which would benefit the improvements of our projects. Thirdly, the meetup simulated the real competition segments. We felt the atmosphere of the competition and found the deficiency of our presentations. During the meetup, we also discussed a lot about iGEM, hoping that iGEM could get better and better.<br /><br />All teams attending the meetup make positive evaluations to the activity.</p><br />
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<p>Building of Life Sciences, Room 363</p><br />
<p>University of Science and Technology of China</p><br />
<p>96, Jinzhai Rd, Shushan, Hefei</p><br />
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Hlx1996
http://2014.igem.org/Team:USTC-Software/server.php
Team:USTC-Software/server.php
2014-10-18T02:31:59Z
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<h5 style="color:#fff;font-weight:bold;margin-bottom: 25px;">Innovation Experiment Centre of Life Science (IEC)</h5><br />
<p>Building of Life Sciences, Room 363</p><br />
<p>University of Science and Technology of China</p><br />
<p>96, Jinzhai Rd, Shushan, Hefei</p><br />
<p>230026, Anhui, China</p><br />
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Hlx1996
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2014-10-18T02:31:31Z
<p>Hlx1996: </p>
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<div class="large-12 columns large-centered"><br />
<h3 id="front_end">Front End</h3><br />
<div class="underline-small"></div><br />
<p>The work of front end is various and complicated. We generally divided it into 4 large parts as below:</p><br />
<ul><br />
<li>UI Framework</li><br />
<li>Canvas System</li><br />
<li>Project & Cloud System</li><br />
<li>Functional Units</li><br />
</ul><br />
<p></p><br />
<p>In concise, users can create a biological network on the Canvas, save or browse their work as Projects, get or share biological information by Cloud, and analyze biological data with Functional Units, all of which happen in the friendly environment provided by the UI Framework.</p><br />
<p></p><br />
<p>We based our program on Adobe Air 15.0 platform, with programming language Action Script 3.0 (AS 3.0). AS 3.0 is powerful in vector illustration processing, and provides rich interactions and responsiveness, these two features meet the demand of our project exactly.</p><br />
<p></p><br />
<p>The major techniques we used are as following: Smart Canvas, Operation Track, Multi-Threading and Heterogeneous computing.</p><br />
<p></p><br />
<div class="underline-tiny"> </div><br />
<h5>UI Framework</h5><br />
<p>In order to provide a better user experience, we designed a completely new UI Framework, in which most of the operations can be directly performed while the interface keeps simple and tidy. Meanwhile, this new framework aims for demonstrating information clearly, so there are fewer containers but richer contents. We also added guiding animation responding to most operations so that all the processes are smooth and easy to understand.</p><br />
<p></p><br />
<div class="underline-tiny"> </div><br />
<h5>Canvas System (Smart Canvas)</h5><br />
<p>The canvas to display the biological network is the most important part of this software, so this receives the most concern. A simple canvas with all objects sticking on could not meet the demand of a boundless and highly complicated visual network. So we need to design the structure of both data and displaying object to guarantee the capability of performing mass information while consuming limited system resources. After several trials and analyses, we build our canvas in two major layers and five sub layers:</p><br />
<p></p><br />
<ul><br />
<li>1. Node Layer<br />
<ul><br />
<li>a) Float layer</li><br />
<li>b) Compressed partitioned layer</li><br />
</ul><br />
</li><br />
<li>2. Link Layer<br />
<ul><br />
<li>a) Fast redraw layer</li><br />
<li>b) Float layer</li><br />
<li>c) Compressed layer</li><br />
</ul><br />
</li><br />
</ul><br />
<p>For float layer, objects exist independently, which means they have their own RAM and Graphic. These independent objects have many event listeners that can interact with users easily. Specifically, users can simply move, double-click and edit them. Though a few dozens of objects working in this way together will be quite well, more (thousands of) objects exist in the float layer at the same time will consume a great amount of resources with an unacceptable low speed.</p><br />
<p></p><br />
<p>A biological network can be huge and highly convoluted. To meet the requirement of higher efficiency, we use compressed layer, on which objects are drawn together as one or several (partitioned) bitmaps, to solve this problem. These bitmaps draw fast with GPU acceleration and cost much fewer resources, but they are not interactive. So a significant task we have done is to translate an operation towards an object drawn in compressed layer to the real object by calculating its geometry characteristic. Once a focus intension is traced, the object will emerge to the float layer to interact with the user, and when it loses focus, it will submerge into the compressed layer again and the RAM space will be cleared.</p><br />
<p></p><br />
<p>In most of time, objects stay in compressed layers. But there is still another problem: the graph may be too large to draw at one time while most part of the graph is out of screen. So we use partitioned bitmap blocks (for nodes) and fast drawing layer (for links) in place of one huge bitmap, and redrawing only happens to the blocks (for nodes) or the range (for lines) shown on the screen.</p><br />
<p></p><br />
<p>With all these methods, we could save over 90% costs of system resources while providing an enjoyable user experience.</p><br />
<div class="underline-tiny"> </div><br />
<h5>Project System</h5><br />
<p>Project is the basic unit to manage a biological network. Three kinds of information are saved in a project:</p><br />
<ul><br />
<li>1. Node information</li><br />
<li>2. Link information</li><br />
<li>3. Project information</li><br />
</ul><br />
<p>You can import nodes and links to the project from cloud database or add yours; both can be saved into one project. Meanwhile, two ways are provided to store a project, storing locally and on cloud.</p><br />
<p></p><br />
<p>For a local project, information saved as an XML file, so you can open, save or copy it like any other kind of document.</p><br />
<p></p><br />
<p>Building projects on cloud is strongly recommended, for not only these projects can be open and edit on any computer with your account, but the existence of the nodes and links in the project are recorded in the global biological network database, in which all the nodes and links exist together as well. With more projects uploaded to the cloud, the global database will be extended, thus more information will be provided to users and an ultimate biological network will be built up someday.</p><br />
<p></p><br />
<p>With projects on cloud, researchers worldwide will be able to share and quote the findings of each other or directly build one project together by registering as colleagues. For more information about project management, see documentation of the Back End.</p><br />
<div class="underline-tiny"> </div><br />
<h5>Functional Units</h5><br />
<p><b>BioBrick Assistant:</b><br />BioBrick Assistant will get the BioPart in the form of XML from the official website when the user inputs keywords. Then we extract the important information by using Actionscript XML processing functions in the form of a table.</p><br />
<p></p><br />
<p><b>Google API:</b><br />When the user inputs the keyword, it will be searched on Google. Then we parse the returned HTML, and save the title, author, abstract, and URL of the literature, which is convenient for the user.</p><br />
<p></p><br />
<p><b>Layout Algorithm:</b></p><br />
<p></p><br />
<p>1. Even Layout: First we calculate the border region which the user selected, namely the minimum and maximum of X and Y. So that we can get the height and width of the area. During the process, the number of nodes is gotten. Then we select the value of m and n as below: m, n are integers, m / n is closest to the width / height and m*n is no smaller than the number of the nodes. After m and n are set, the nodes will be arranged that the horizontal interval between horizontally adjacent nodes is width / m, and the vertical interval between vertically adjacent nodes is height / n.</p><br />
<p>2. Plasmid Arrangement: the arrangement of the radius of the circle size is in proportion to the number of nodes selected. Node will be sorted according to the type and arranged on the circle.</p><br />
<p>3. Force-directed Arrangement: Imagine that we assign each node with a positive charge, those nodes are mutually exclusive, and the repulsive force is inversely proportional to the square of the distance. Imagine that every edge is a spring, the force it applies on the nodes at its ends is proportional to the length of the spring. By calculating the force applied to each node, we can determine the direction and magnitude of its displacement. This process is called an iteration. After fifty times of iteration, all the nodes will be in steady state. We make their positions now their final positions for arrangement. The parameters of gravitation and repulsion are determined by experiments. The advantage of the algorithm is that it can arrange the graph like a tree and reduce the cross of edges greatly to show the relationships among the nodes more lucidly.<br />
<br />Force-directed algorithm and GPU acceleration: the time complexity of the arrangement algorithm is O(n^2), so it will take a long time if the number of the nodes is large. So we spill the algorithm among several threads (users can still operate while the back end is calculating) and use the powerful ability for floating-point computation and parallel computation of GPU to accelerate the calculation. Taken multi-platform support into consideration, we use opencl as our programming language. The acceleration uses socket communication for data transfer. The front end send the amount of the nodes, the number and position of each node, the amount of the links and the number of nodes each edge connects to the calculation end. The calculation end spill the computation that the computation of each node is done in a single thread. Visit all the nodes and edges only once and we can get the acceleration of each node. When the computation is done, the calculation end sends every node’s position to the front end.</p><br />
<p></p><br />
<h3 id="back_end">Back End</h3><br />
<div class="underline-small"><br />
</div><br />
<h5>Framework</h5><br />
<p>Our server uses Linux as operating system, MongoDB to manage abundant biological data, including information of millions of nodes, and MySQL database to store data of users and information of projects and species. Our server-side program is based on Django development, and is optimized for multi-node and remote-controlling circumstances, ensuring that your request will be answered wherever you are. When a node breaks down, our server will separate the node from the group and realize automatic failover.</p> <br />
<br />
<br />
<br />
<br />
<div class="underline-tiny"> </div><br />
<h5>Account System:</h5><br />
<p>Oauth is used as login credential. You just need to provide your Google or Baidu account and use Biopano conveniently without signing up. Meanwhile, Oauth is decoupled with local account system, providing convenience for developers to offer more ways for authentication.</p><br />
<br />
<div class="underline-tiny"> </div><br />
<h5>Rapid Server Deployment:</h5> <br />
<P>We do not recommend users to build at local Biopano server, for one of the main advantages of Biopano is data sharing. However, for special cases such as intranet, you could use the docker repository we provide to deploy a Biopano server rapidly. We encapsulate basic databases to offer powerful basic biological data support for your intranet server.</P><br />
<br />
<div class="underline-tiny"> </div><br />
<h5>Interface Design:</h5><br />
<p>The server communicate with front end based on HTTP protocol. It uses interfaces of RESTful style. It is a kind of completely public and universal interface and offers detailed documentation. You can develop your own applications based on these interfaces. These interfaces have been optimized a lot for Biopano-client, so the communication efficiency has been enhanced significantly.</p><br />
<br />
<div class="underline-tiny"> </div><br />
<h5>Automated Deployment:</h5><br />
<p>Our server has automated deployment capabilities. Server-side applications are bound with the Product branch of Git. All codes pushed to the Product branch will be deployed to many servers over the world in ten seconds. In order to prevent fault codes from being deployed to the servers by mistake, all the testing branches will be deployed to the testing server real-timely to be tested by developers.</p><br />
<br />
<div class="underline-tiny"> </div><br />
<h5>Unit Testing:</h5><br />
<p>Our server applies automated unit testing to dealing with uploaded back end codes. It will test the basic legitimacy and function of the codes, including robustness testing with respect to illegitimate uploaded parameters, legitimacy testing on data legitimacy, status testing of the database and testing of function realizaton, etc.</p><br />
<br />
<h3 id="alogrithm">Alogrithm</h3><br />
<div class = "underline-small"></div> <br />
<h5>Pathway Finder Alogrithm:</h5><br />
<p>The software can search for paths between two selected nodes. We used a-stark short-path algorithm to achieve the function of discovering potential relationship in the biological network.<br />
A* algorithm is a search algorithm based on greedy, which can always visit fewer nodes and get a better solution at the same time.<br />
In this way, however, we get the shortest path in graph theory. By giving different and appopraite weights to different edges, the algorithm can find the shortest path in the sense of biology.</p><br />
<br />
<div class="underline-tiny"> </div><br />
<h5>BLAST:</h5><br />
<p><br />
We use two packages, namely, NCBI_Blast and the Python package called for NCBI_Blast. Different from NCBI, our alignment database combines RegulonDB and user-define databases. When the user inputs a sequence (such as a BioBrick sequence), Biopano will the node that shares the deepest homology with it in the server database, and show other nodes connected with it. Therefore, Biopano can show the nodes and regulations in the biological regulation network that probably has to do with the sequence (such as BioBrick sequece) the user inputs.<br />
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<h5 style="color:#fff;font-weight:bold;margin-bottom: 25px;">Innovation Experiment Centre of Life Science (IEC)</h5><br />
<p>Building of Life Sciences, Room 363</p><br />
<p>University of Science and Technology of China</p><br />
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Hlx1996
http://2014.igem.org/Team:USTC-Software/biopano.php
Team:USTC-Software/biopano.php
2014-10-18T02:30:50Z
<p>Hlx1996: </p>
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<p style="font-size:64px;height:100%;line-height:100%;color:rgb(144,144,144)">Meet Biopano</p><br />
<br />
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<div class="row"><br />
<div class="large-12 columns large-centered"><br />
<br />
<p></p><br />
<h4 id="overview">Overview</h4><br />
<div class="underline-small"></div><br />
<p>Designed specifically for biological research, BioPano is a software platform targeted for visualisation of biological relationships as well as cooperative net-building. You can set up your own network of biological relationship by adding information about genetic regulation and metabolic system to the network we already provided for you. Also, the software allows you to explore the links among the substances by just several clicks, and you can even look into the details of the interaction between the exogenous gene and the host. What is even more exciting is that our software will end your loneliness and frustration in research, since it is providing you with cloud cooperating system so that you can view massive amounts of resources in databases, together with build up groups to share information and set up mutual network with others.<br />
</p><br />
<br />
<h4 id="motivation">Motivation</h4><br />
<div class="underline-small"></div><br />
<p><br />
In recent years, people has made a lot of remarkable achievements <br />
in synthetic biology. However, scientists are often faced with <br />
many unpredictable problems when carrying out experiments. <br />
Each kind of biological substance is inextricably linked to the <br />
biological environment to which it belongs, so we have to consider <br />
a question: Can we attain the desired goal, if we simply follow the traditional ideas of synthetic biology and avoid the problem merely by engineering?<br />
</p><br />
<p><br />
A synthetic biologist, Chris Voigt, has successfully transferred a<br />
Toggle Switch, which usually works in the Bacillus <br />
subtilis, into E. coli. Unfortunately, it did not function properly. In <br />
fact, in experiments, due to the unexpected interactions between <br />
BioBrick and the host, it is very common that the designed path do <br />
not work as anticipated.<br />
</p><br />
<p><br />
In fact, the life system is so complex that there are many sorts of <br />
biological substance to support it with complex interations in it. <br />
In order to understand a phenomenon, we keep using new and <br />
sophisticated methods to refine our research and to explore every <br />
detail of life. However, if we widen our perspective, by looking at <br />
our research objectives from a more comprehensive perspective, <br />
we may have some unexpected discoveries.<br />
</p><br />
<br />
<h4 id="features">Features</h4><br />
<div class="underline-small"><br />
</div><br />
<p>Our software has many marvelous features, with which your biology research will become extremely easy and joyful.</p><br />
<ul><br />
<br />
<h5>1. Expansion of single node</h5><br />
<div class="row"><br />
<div class="large-6 columns"><p>In Biopano, every biology part of E.coli K-12 will be displayed as a node of different types and regulation relationship <br />
will be displayed as arc of different types. They are displayed in the biological network in a visualizational way. <br />
You just need to select a node and click “Expand”, and the nodes associated with it will be “expanded”. <br />
Nodes are connected to each other by all kinds of relationship, so users can see how biological parts are connected clearly, <br />
such as LacI Operon. </p></div><br />
<div class="large-6 columns"><img src="https://static.igem.org/mediawiki/2014/4/46/2014ustc-Feature-a.png"></div><br />
</div><br />
<br />
<div class="row"><br />
<div class="large-6 columns"><img src="https://static.igem.org/mediawiki/2014/9/9e/2014ustc-Feature-b.png"></div><br />
<div class="large-6 columns"><p>However, since there are so many biological parts connected to each other in various convoluted, <br />
the expansion of all nodes will give rise to extremely involved nets, which will fail to convey useful information to the users, <br />
even interfere their thoughts. So you can choose to expand the nodes in a way you see fit. Take Transcription factor CRP as an example. </p><br />
<p>Biopano displays the network dynamically, which makes you able to tease out the relationship among thousands of materials of <br />
E.coli K-12, satisfies your curiosity and helps you discover unknown biological field.</p></div><br />
</div><br />
<div class="underline-tiny"></div><br />
<br />
<br />
<br />
<h5>2. Link Finder</h5><br />
<div class="row"><br />
<div class="large-6 columns"><p>You can input two nodes that seem irrelevant, such as gene A and Transcription FactorB, and the software will <br />
search the route connecting the two nodes for you. Since some routes are too sinuous for further analysis or does not make sense, <br />
you can set a specific number k, Biopano will search and show the k shortest routes for you.</p></div><br />
<div class="large-6 columns"><img src="https://static.igem.org/mediawiki/2014/7/79/2014ustc-Feature-c.png"></div><br />
</div><br />
<div class="underline-tiny"></div><br />
<br />
<br />
<h5>3. BLAST</h5><br />
<div class="row"><br />
<div class="large-6 columns"><img src="https://static.igem.org/mediawiki/2014/7/71/2014ustc-Feature-e.png"></div><br />
<div class="large-6 columns"><p>By BLAST method, Biopano finds E.coli K-12 gene highly similar to the injected sequence. <br />
These genes are regulated by other parts in E.coli K-12, so can provide information of the host environment’s impact on injected <br />
exogenous sequence. Biopano also offers BioBrick helper, enabling you search all kinds of BioBricks on iGEM’s official website. <br />
By BLAST analysis, it helps you design correct gene route with appropriate BioBricks.</p></div><br />
</div><br />
<div class="underline-tiny"></div><br />
<br />
<br />
<h5>4. Data Sharing</h5><br />
<p>Hence, while offering various functions, Biopano also serves as a cooperative network building platform. When you create a project, you can add new nodes, name new biological parts and link them with respect to your comprehension to build a brand new net gradually. Meanwhile, Biopano provides log in service. You can sign up with Google or Baidu account and upload your network to the main database to make it more plentiful. Biopano also supports data importing in batch. You can even import data of a species and a database.</p><br />
<ul class="small-block-grid-2"><br />
<li><img src="https://static.igem.org/mediawiki/2014/2/2a/2014ustc-Feature-f.png"></li><br />
<li><img src="https://static.igem.org/mediawiki/2014/5/57/2014ustc-Feature-g.png"></li><br />
</ul><br />
<div class="underline-tiny"></div><br />
<br />
<h5>5. Details and Reference</h5><br />
<p>When you have already got the entire view and want to know more about the details, double-click the nodes and arcs and the details will be shown. More surprisingly, Biopano supports literature reading in the network. You can view literature corresponding to every node and arc along any gene route in the network, and you will understand how the nodes in the net are associated with each other in depth. If you cast doubt on the reliability of our database, you can verify your thought with authoritative literature.</p><br />
<br />
</ul><br />
<p></p><br />
<h4 id="demos">Demo</h4><br />
<div class="underline-small"><br />
</div><br />
<div><br />
<h4>Next we will demonstrate some common modules of E.coli k-12:</h4><br />
<br />
<h5>1, Lac Operon: When you input LacZYA, a Transcription Unit(TU) of Lac Operon and Expand the node:</h5><br />
<p>You will see four promoters, acZp1, lacZp2, lacZp3 and lacZp4 as<br />
upstream sequences and three structure genes, lacZ, lacY and lacA as <br />
downstream sequences. Meanwhile, you can see the TU belongs to <br />
the Operon lacZYA.<br />
</p><br />
<p>Above the node lacZYA, you also see three Transcription<br />
Factors, namely, CRP, H-NS and lacl. They suppress the expression of <br />
lazZYA.</p><br />
<p>Expand lacZ, lacY and lacA, and we get BgaL, LacY and ThgA<br />
respectively, of which Bgal and ThgA are Enzymes. They catalyze<br />
corresponding reactions. Expand Lacl and we get the gene lacl which<br />
codes it.</p><br />
<ul class="small-block-grid-2"><br />
<li><img src="https://static.igem.org/mediawiki/2014/4/47/2014ustc-B.png"></li><br />
<li><img src="https://static.igem.org/mediawiki/2014/e/ee/C.png"></li><br />
</ul><br />
<br />
<p>Continue to Expand lacZYA and lacl and we find more materials’<br />
connected with them. You can select and drag the nodes to arrange the <br />
network neatly; you can also click Full Screen and the network will be <br />
displayed in full screen.</p><br />
<ul class="small-block-grid-2"><br />
<li><img src="https://static.igem.org/mediawiki/2014/c/c5/2014ustc-D.png"></li><br />
<li><img src="https://static.igem.org/mediawiki/2014/3/3a/2014ustc-E.png"></li><br />
</ul><br />
<br />
<h5>2, Following the same steps, we can also get the regulation network of<br />
the Operon Trp.</h5><br />
<img src="https://static.igem.org/mediawiki/2014/9/9d/2014ustc-F.png"><br />
<br />
<br />
</div><br />
<br />
<br />
<h4 id="why">Why choose BioPano?</h4><br />
<div class="underline-small"></div><br />
<div><br />
<p> Biopano, do the experiment as you do in the lab.</p><br />
<p>In experiment, synthetic biologists always find gene circuits formed by BioBricks are incompatible with the host cell, thus cannot work as expected. However, Biopano uses sequence alignment to analyze the possible reasons of the failure and design more acute gene circuit for your consideration.</p><br />
<p>Our Blast algorism derives from NCBI. However, the original version only offers sequence alignment and fails to analyze what impact the host environment might have on the injected gene circuit, let along predicts whether it will work.</p><br />
<p>Firstly, Biopano offers BioBrick searching to make it convenient for you to study all standardized biological parts on the official website of iGEM. Secondly, you can input a BioBrick and even construct a brand new sequence. Biopano will find the gene nodes of E.coli K-12 sharing the deepest homology with it based on authoritative Blast algorithm. Then you can Expand these nodes to find out the possible regulation on them. In this way, Biopano helps you analyze whether the injected gene circuit will actually work.</p><br />
<p>Biopano abstracts biological parts and the regulation among them into nodes and arcs to realize data visualization, and displays gene regulation and metabolism network of E.coli K-12 dynamically by continually Expanding nodes. Single database cannot make an entire material network, so our back end combines Regulon DB, KEGG, Uniprot and abundant data. You can ceaselessly Expand the nodes in the network to comb the relationship among them and satisfy your curiosity.</p><br />
<br />
<p>Compared with Biopano, Cytoscape and Netscience mainly support file importing and network displaying without powerful database from the back end. Hence you cannot search for biological parts online and view the certain part of the biological network you need with them.</p><br />
<br />
<p>Now that there is enormous astonishing material relationship in biological body, more and more biologists hope to find the specific function route between two biological parts or even two biological blocks that seem not related to each other, such as c-di-GMP signalling and Quorum Sensing. Unfortunately, the interactions of the biological parts are saved in database as records and it is almost impossible to find the route in thousands of records. There haven’t been any software to offer any help before. Luckily, Biopano brings hope to this.</p><br />
<br />
<p>You can input two biological parts and set several shortest routes, then you will find their relationship. We used this powerful function to find the specific relationship betweem c-di-GMP signalling and Quorum Sensing, which was corroborated by corresponding literature. How amazing!</p><br />
<br />
<p>We have to admit that Biopano may show you wrong gene route. However, it provides you with direction of studying the relationship of two fields. It not only makes your goal for experiment designing clearer, but enables you to understand the connection inside body is so close as well.</p><br />
<br />
<p>While offering function services, Biopano serves as a platform for collaborative network building. You can define new nodes and arcs yourself and sign in with your Google or Baidu account to upload the network you build to our database. You can also invite several companions to complete a project together. Common biological software, such as Cytoscape and Netscience, doesn’t provide a good platform for communication, while Biopano enhances the communication of biological areas by data sharing.</p><br />
<br />
<p>Biopano, your right hand for biological research. Get it now!</p><br />
</div><br />
<br />
<h4 id="futurework">Future Work</h4><br />
<div class="underline-small"></div><br />
<div><br />
<h4>It is undeniable that we still have a lot to do to improve Biopano in many aspects in order to make it even better. We need to think more and develop it as we can. In the future, we hope to:<br />
</h4><br />
<br />
<p>1. Integrate more data in it. Currently, Biopano only integrates data of E.coli k-12 from Regulon DB, KEGG and Uniprot, and our data in regulatory interaction lack accurate numerical data to indicate its strength. etc. Therefore, not only will we update the existing data in the original species, we will also make complement of high-throughput data through other databases and papers, as well as expand information of other species, so that more biological researchers can benefit from our software.</p><br />
<br />
<p>2. Normalize users' rights, improve quality of data. With the increase of the number of users, the data synchronized every day become not only massive, but also in many different forms, and some of them have nevitable errors or redundant information, or there may be different kinds of comprehension of certain regulatory relations. So we want the machine to automatically recognize the validity of the data submitted by the user, and establish a evaluation criteria of credibility. Thus, only those reliable users will be selected, and only their data can be synchronized to the main database, and the redundancy or errors will be eliminated, and they also continue to enhance the credibility and value of the main database.</p><br />
<br />
<p>3. Enhance network analysis functions. When we add the high-throughput kinetic data for biological networks, we can build a variety of mathematical models on the network and carry out quantitative simulation analysis. For example, we can put the nodes that are closely related to one another together in a group. We can make out software automatically arrange the modules for different functions in the organism. We can even do things that are analogic to those in an electric circult. The network provides the entrance and the exit of the signals, and all you need to do is to enter the target product and we will help you find the substance needed for synthesizing it. </p><br />
<br />
<p>4. Supports more file formats. Currently, the file formats we provide to the users are only XML and SBOL. In the future we will make our software support more file formats, such as sif, EMBL, etc., and we will develop its ability to be capable with other biological softwares such as cytoscape and Netscience, seamlessly. You can import and export any file that are constantly used. From this aspect, we will greatly broadens the scope of the functions of the software.</p><br />
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<h5 style="color:#fff;font-weight:bold;margin-bottom: 25px;">Innovation Experiment Centre of Life Science (IEC)</h5><br />
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<p>University of Science and Technology of China</p><br />
<p>96, Jinzhai Rd, Shushan, Hefei</p><br />
<p>230026, Anhui, China</p><br />
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Team:USTC-Software/main-new.css
2014-10-18T02:26:00Z
<p>Hlx1996: </p>
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top:100px;<br />
left: 0;<br />
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}<br />
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background:url("../img/MainBackgroundback2.jpg");<br />
background-repeat: no-repeat;<br />
background-size: 100% 100%;<br />
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width: 100%;<br />
height: auto;<br />
position: relative;<br />
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}*/<br />
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background-color: #FFDFB9;padding:2em;margin-top:2em;<br />
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Hlx1996
http://2014.igem.org/Team:USTC-Software
Team:USTC-Software
2014-10-18T01:46:05Z
<p>Hlx1996: </p>
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<h5 style="color:#fff;font-weight:bold;margin-bottom: 25px;">Innovation Experiment Centre of Life Science (IEC)</h5><br />
<p>Building of Life Sciences, Room 363</p><br />
<p>University of Science and Technology of China</p><br />
<p>96, Jinzhai Rd, Shushan, Hefei</p><br />
<p>230026, Anhui, China</p><br />
<p>ustc-software-2014@googlegroups.com </p><br />
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Hlx1996
http://2014.igem.org/Team:USTC-Software
Team:USTC-Software
2014-10-18T01:43:42Z
<p>Hlx1996: </p>
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2014-10-18T01:36:22Z
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<h5 style="color:#fff;font-weight:bold;margin-bottom: 25px;">Innovation Experiment Centre of Life Science (IEC)</h5><br />
<p>Building of Life Sciences, Room 363</p><br />
<p>University of Science and Technology of China</p><br />
<p>96, Jinzhai Rd, Shushan, Hefei</p><br />
<p>230026, Anhui, China</p><br />
<p>ustc-software-2014@googlegroups.com </p><br />
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Hlx1996
http://2014.igem.org/File:2014ustc-medal3.png
File:2014ustc-medal3.png
2014-10-18T01:00:22Z
<p>Hlx1996: </p>
<hr />
<div></div>
Hlx1996
http://2014.igem.org/File:2014ustc-medal2.png
File:2014ustc-medal2.png
2014-10-18T00:57:20Z
<p>Hlx1996: </p>
<hr />
<div></div>
Hlx1996
http://2014.igem.org/File:2014ustc-medal1.png
File:2014ustc-medal1.png
2014-10-18T00:56:52Z
<p>Hlx1996: </p>
<hr />
<div></div>
Hlx1996
http://2014.igem.org/File:2014ustc-Gold.png
File:2014ustc-Gold.png
2014-10-18T00:54:56Z
<p>Hlx1996: </p>
<hr />
<div></div>
Hlx1996
http://2014.igem.org/File:2014ustc-Silver.png
File:2014ustc-Silver.png
2014-10-18T00:53:21Z
<p>Hlx1996: </p>
<hr />
<div></div>
Hlx1996
http://2014.igem.org/File:2014ustc-Bronze.png
File:2014ustc-Bronze.png
2014-10-18T00:51:38Z
<p>Hlx1996: </p>
<hr />
<div></div>
Hlx1996
http://2014.igem.org/File:2014ustc-Page4.jpg
File:2014ustc-Page4.jpg
2014-10-18T00:39:37Z
<p>Hlx1996: </p>
<hr />
<div></div>
Hlx1996
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Team:USTC-Software/main-new.css
2014-10-17T14:40:50Z
<p>Hlx1996: </p>
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Hlx1996
http://2014.igem.org/File:2014ustc-Hlx.jpg
File:2014ustc-Hlx.jpg
2014-10-17T12:39:23Z
<p>Hlx1996: uploaded a new version of &quot;File:2014ustc-Hlx.jpg&quot;</p>
<hr />
<div></div>
Hlx1996
http://2014.igem.org/File:2014ustc-Hlx.jpg
File:2014ustc-Hlx.jpg
2014-10-17T12:38:17Z
<p>Hlx1996: uploaded a new version of &quot;File:2014ustc-Hlx.jpg&quot;</p>
<hr />
<div></div>
Hlx1996
http://2014.igem.org/Meetups:August_USTC_software/photo.html
Meetups:August USTC software/photo.html
2014-08-19T13:34:00Z
<p>Hlx1996: </p>
<hr />
<div><html class="no-js"><br />
<head><br />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" /><br />
<title>Photo of Meetup</title><br />
<link rel="stylesheet" href="http://home.ustc.edu.cn/~hlx1996/photo/css/reset.css" media="screen" /><br />
<link rel="stylesheet" href="http://home.ustc.edu.cn/~hlx1996/photo/css/style.css" media="screen" /><br />
<link rel="stylesheet" href="http://home.ustc.edu.cn/~hlx1996/photo/css/css3_3d.css" media="screen" /><br />
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<br />
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<li><br />
<div class="details"><h3>SJTU-BioX-Shanghai's Presentation</h3></div><br />
<a href="http://home.ustc.edu.cn/~hlx1996/photo/images/600/1.jpg" rel="lightbox"><img src="http://home.ustc.edu.cn/~hlx1996/photo/images/290/1.jpg" /></a><br />
</li><br />
<li><br />
<div class="details"><h3>SJTU-Software's Presentation</h3></div><br />
<a href="http://home.ustc.edu.cn/~hlx1996/photo/images/600/2.jpg" rel="lightbox"><img src="http://home.ustc.edu.cn/~hlx1996/photo/images/290/2.jpg" /></a><br />
</li><br />
<li class="end"><br />
<div class="details"><h3>HFUT_China's Presentation</h3></div><br />
<a href="http://home.ustc.edu.cn/~hlx1996/photo/images/600/3.jpg" rel="lightbox"><img src="http://home.ustc.edu.cn/~hlx1996/photo/images/290/3.jpg" /></a><br />
</li><br />
<li><br />
<div class="details"><h3>Free chat: Future of the iGEM Software</h3></div><br />
<a href="http://home.ustc.edu.cn/~hlx1996/photo/images/600/4.jpg" rel="lightbox"><img src="http://home.ustc.edu.cn/~hlx1996/photo/images/290/4.jpg" /></a><br />
</li><br />
<li><br />
<div class="details"><h3>USTC_Software's Presentation</h3></div><br />
<a href="http://home.ustc.edu.cn/~hlx1996/photo/images/600/5.jpg" rel="lightbox"><img src="http://home.ustc.edu.cn/~hlx1996/photo/images/290/5.jpg" /></a><br />
</li><br />
<li class="end"><br />
<div class="details"><h3>NEAU_China's Presentation</h3></div><br />
<a href="http://home.ustc.edu.cn/~hlx1996/photo/images/600/6.jpg" rel="lightbox"><img src="http://home.ustc.edu.cn/~hlx1996/photo/images/290/6.jpg" /></a><br />
</li><br />
<li><br />
<div class="details"><h3>Brainstorming</h3></div><br />
<a href="http://home.ustc.edu.cn/~hlx1996/photo/images/600/7.jpg" rel="lightbox"><img src="http://home.ustc.edu.cn/~hlx1996/photo/images/290/7.jpg" /></a><br />
</li><br />
<li><br />
<div class="details"><h3>Lunch Time</h3></div><br />
<a href="http://home.ustc.edu.cn/~hlx1996/photo/images/600/8.jpg" rel="lightbox"><img src="http://home.ustc.edu.cn/~hlx1996/photo/images/290/8.jpg" /></a><br />
</li><br />
<li class="end"><br />
<div class="details"><h3>SYSU-Software</h3></div><br />
<a href="http://home.ustc.edu.cn/~hlx1996/photo/images/600/9.jpg" rel="lightbox"><img src="http://home.ustc.edu.cn/~hlx1996/photo/images/290/9.jpg" /></a><br />
</li><br />
<li><br />
<div class="details"><h3>SJTU-Software</h3></div><br />
<a href="http://home.ustc.edu.cn/~hlx1996/photo/images/600/10.jpg" rel="lightbox"><img src="http://home.ustc.edu.cn/~hlx1996/photo/images/290/10.jpg" /></a><br />
</li><br />
<li><br />
<div class="details"><h3>SJTU-Software</h3></div><br />
<a href="http://home.ustc.edu.cn/~hlx1996/photo/images/600/11.jpg" rel="lightbox"><img src="http://home.ustc.edu.cn/~hlx1996/photo/images/290/11.jpg" /></a><br />
</li><br />
<li class="end"><br />
<div class="details"><h3>HFUT_China: BioFunctional Designer</h3></div><br />
<a href="http://home.ustc.edu.cn/~hlx1996/photo/images/600/12.jpg" rel="lightbox"><img src="http://home.ustc.edu.cn/~hlx1996/photo/images/290/12.jpg" /></a><br />
</li><br />
<li><br />
<div class="details"><h3>Welcome Address by Professor Liu</h3></div><br />
<a href="http://home.ustc.edu.cn/~hlx1996/photo/images/600/13.jpg" rel="lightbox"><img src="http://home.ustc.edu.cn/~hlx1996/photo/images/290/13.jpg" /></a><br />
</li><br />
<li><br />
<div class="details"><h3>SYSU-Software's Presentation</h3></div><br />
<a href="http://home.ustc.edu.cn/~hlx1996/photo/images/600/14.jpg" rel="lightbox"><img src="http://home.ustc.edu.cn/~hlx1996/photo/images/290/14.jpg" /></a><br />
</li><br />
<li class="end"><br />
<div class="details"><h3>Comments by Dr. Liang</h3></div><br />
<a href="http://home.ustc.edu.cn/~hlx1996/photo/images/600/15.jpg" rel="lightbox"><img src="http://home.ustc.edu.cn/~hlx1996/photo/images/290/15.jpg" /></a><br />
</li><br />
<li><br />
<div class="details"><h3>Experience Exchangement hold by Nie Peng</h3></div><br />
<a href="http://home.ustc.edu.cn/~hlx1996/photo/images/600/16.jpg" rel="lightbox"><img src="http://home.ustc.edu.cn/~hlx1996/photo/images/290/16.jpg" /></a><br />
</li><br />
<li><br />
<div class="details"><h3>SYSU-Software</h3></div><br />
<a href="http://home.ustc.edu.cn/~hlx1996/photo/images/600/17.jpg" rel="lightbox"><img src="http://home.ustc.edu.cn/~hlx1996/photo/images/290/17.jpg" /></a><br />
</li><br />
<li class="end"><br />
<div class="details"><h3>Zhang People Win and His girls</h3></div><br />
<a href="http://home.ustc.edu.cn/~hlx1996/photo/images/600/18.jpg" rel="lightbox"><img src="http://home.ustc.edu.cn/~hlx1996/photo/images/290/18.jpg" /></a><br />
</li><br />
<li><br />
<div class="details"><h3>XMU</h3></div><br />
<a href="http://home.ustc.edu.cn/~hlx1996/photo/images/600/19.jpg" rel="lightbox"><img src="http://home.ustc.edu.cn/~hlx1996/photo/images/290/19.jpg" /></a><br />
</li><br />
<li><br />
<div class="details"><h3>NEAU_China</h3></div><br />
<a href="http://home.ustc.edu.cn/~hlx1996/photo/images/600/20.jpg" rel="lightbox"><img src="http://home.ustc.edu.cn/~hlx1996/photo/images/290/20.jpg" /></a><br />
</li><br />
<li class="end"><br />
<div class="details"><h3>Group Photo</h3></div><br />
<a href="http://home.ustc.edu.cn/~hlx1996/photo/images/600/21.jpg" rel="lightbox"><img src="http://home.ustc.edu.cn/~hlx1996/photo/images/290/21.jpg" /></a><br />
</li><br />
<li><br />
<div class="details"><h3>Comment by Dr. Liang</h3></div><br />
<a href="http://home.ustc.edu.cn/~hlx1996/photo/images/600/22.jpg" rel="lightbox"><img src="http://home.ustc.edu.cn/~hlx1996/photo/images/290/22.jpg" /></a><br />
</li><br />
<li><br />
<div class="details"><h3>USTC_Software and SJTU-Software at Tianzhu Mountain</h3></div><br />
<a href="http://home.ustc.edu.cn/~hlx1996/photo/images/600/23.jpg" rel="lightbox"><img src="http://home.ustc.edu.cn/~hlx1996/photo/images/290/23.jpg" /></a><br />
</li><br />
<li class="end"><br />
<div class="details"><h3>Group Photo at Tianzhu Mountain</h3></div><br />
<a href="http://home.ustc.edu.cn/~hlx1996/photo/images/600/24.jpg" rel="lightbox"><img src="http://home.ustc.edu.cn/~hlx1996/photo/images/290/24.jpg" /></a><br />
</li><br />
<br />
</ul><br />
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Hlx1996