Team:HFUT CHINA/Overview.html

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                 <li><a>Human Practice</a>
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            <td width="184" valign="top"><p align="center"><strong> Bronze Medal:</strong> </p></td>
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            <td width="916" valign="top"><p align="left">&nbsp;</p></td>
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            <td width="916"><p align="justify">Register the team, have a great summer, and have fun    attending the Giant
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<p align="center" class="STYLE10">INTRODUCTION</p>
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              <p align="justify">&nbsp;</p></td>
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  <p class="STYLE9">Synthetic Biology is to create the new species by building parts and biobricks through the Genetic Engineering. iGEM is a worldwide synthetic biology competition. Till now, more than one thousand teams have participated in iGEM, resulting in a large number of synthetic devices designed. However, not many analyses are done on these devices. Are these existing devices could provide useful information for new participators to design new devices? In order to answer this question, we aim to developing a  software to help designing devices.     </p>
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  <p>&nbsp;</p>
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            <td width="916"><p align="justify">Create and share a description of the team's project    via the iGEM wiki.</p>
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  <p class="STYLE9">The main function of our software “BioDesigner” is to recommend biobricks for participators when they are designing new devices.  By collecting the information of existing devices and making analysis on these devices, Biodesigner will recommend biobricks based on the users’ habits or the biobricks users have been used.  </p>
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            <td width="916"><p align="justify">Develop and make available via The Registry of Software    Tools, an open source
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<div align="justify"><span class="STYLE9">To our best known, BioDesigner is the first recommendation software based on the analysis of existing devices. Besides, we also establish a database containing the information of existing devices to support BioDesigner. BioDesigner would be a good assistant for your design.  Using it would make your design easier and smarter.  </span> </div>
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  <p align="center" class="STYLE10">SOFTWARE </p>
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  <p align="center" class="STYLE10">&nbsp;</p>
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  <p align="justify" class="STYLE9">BioDesigner contains two parts, server part and client part. The codes for server part are written in java programming language and the codes for client part are written in C++ programming language. The GUI is designed with Qt which is based on C++. As a result, all of them can be compiled across various platforms. The program has been built on Windows, Linux and Mac operating systems.<br>
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  <p align="justify" class="STYLE9"> The server part is used to build the database that contains the information of existing devices, and make analysis on these information. The client part consists of GUI and analysis of users input. Users input there information through GUI, and client codes deal with the input and send requirements to the server. Server receives the requirements from client, and makes analysis based on the database. Then, it returns information to client. Client deals with the information and visualizes it.  <br>
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  <p align="justify" class="STYLE9">OThe database is stored in server, which would simplify the installation. Since the server is more powerful, the algorithms for recommendation are executed on server, which will reduce the analysis time.</p>
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  <p align="justify" class="STYLE10">&nbsp;</p>
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  <p align="center" class="STYLE10">METHODOLOGY</p>
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  <p align="justify" class="STYLE9">In order to accomplish the function of BioDesigner, such as  recommending biobricks, we adapt various recommendation algorithms to achieve the goal. These algorithms include Collaborative filtering and Association rules.<br>
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1.  Collaborative filtering: <br>
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a. The collaborative filtering based on the content:  Given a biobrick, Biodesigner finds a similar biobrick to recommend according to the sequence of biobrick.<br>
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b. The collaborative filtering based on the user: By storing the biobricks users have been used, Biodesigner statistics users’ habit to recommend the higher frequency biobrick.<br>
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2. Association rules: Based on existing device chains, implied relationship, including relationship between two successive biobricks, three successive biobricks, four successive biobirkcs and five successive biobricks, are obtained. Biodesigner uses these relationships to recommend the biobrick over the minimum confidence.<br>
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  <p align="justify" class="STYLE10">&nbsp;</p>
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  <p align="center" class="STYLE10">DATABASE</p>
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  <p align="justify" class="STYLE9">In order to support Biodesigner, we build a database that contains the systems designed by the teams of previous years. About 3600 device chains are collected and stored in our database. We also download the biobrick information contained by these chains from Registry of Standard Biological Parts and stored these information in our database.  </p>
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  <p align="justify" class="STYLE9">&nbsp;</p>
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      <p>The database used in BioDesigner is flexible. The users can add or delete data freely. We use the Restlet and Hibernate to build the database framework. When the client sends a request, a respond will be sent from the serve.
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software tool that supports Synthetic Biology based on    Standard Parts.</p>
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              <p align="justify">&nbsp;</p></td>
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            <td width="184"><p align="center"><strong>Silver Medal: </strong></p>
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              <p align="left">&nbsp;</p></td>
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            <td width="184" valign="top"><p align="center"><img src="images/a.png" width="18" height="18"></p></td>
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            <td width="916"><p align="justify">Demonstrate the relevance of your development for    Synthetic Biology based on
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standard Parts. </p>
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              <p align="justify">&nbsp; </p>              </td>
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            <td width="184" valign="top"><p align="center"><img src="images/a.png" width="18" height="18"></p></td>
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            <td width="916"><p align="justify">Provide a comprehensive and well-designed User Guide.    (Be creative! An instructional
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video may work as well.)</p>
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              <p align="justify">&nbsp;</p></td>
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            <td width="184" valign="top"><p align="center"><img src="images/a.png" width="18" height="18"></p></td>
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            <td width="916"><p align="justify">Provide detailed API documentation, preferably,    automatically built from source code
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documentation (use tools like doxygen,    yard, rdoc, naturaldocs, etc).</p>
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              <p align="justify">&nbsp;</p></td>
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            <td width="184" valign="top"><p align="center"><img src="images/a.png" width="18" height="18"></p></td>
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            <td width="916"><p align="justify">Demonstrate that you followed best practises in    software development so that other
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developers can modify, use and reuse your    code. Provide more than one realistic test case. Examples of best practices    are
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automated unit testing and documentation of test coverage, bug tracking    facilities, documentation of releases and changes between
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releases.</p>              </td>
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            <td width="184"><p align="center"><strong>Gold Medal: </strong></p>
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              <p align="left">&nbsp;</p></td>
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            <td width="916"><div align="justify"></div></td>
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            <td width="184" valign="top"><div align="center"><img src="images/a.png" width="18" height="18"></div></td>
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            <td width="916"><p align="justify">Provide a convincing validation, testing the    performance of the development --
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experimentally (can be outsourced) or by    other teams and users. Note, even if the algorithm or tool turns out not to    work that
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well, the Gold requirement is fulfilled if the test is good and the    analysis convincing. Validation may include: preferably
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experiments,    informatics analysis (complexity, run time) of an algorithm, or user studies.</p>
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              <p align="justify">&nbsp;</p></td>
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            <td width="184" valign="top"><p align="center"><img src="images/a.png" width="18" height="18"></p></td>
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            <td width="916"><p align="justify">Make your software interact / interface with the    Registry.</p>
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              <p align="justify">&nbsp;</p></td>
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            <td width="184" valign="top"><p align="center"><img src="images/b.png" width="18" height="18"></p></td>
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            <td width="916"><p align="justify">Re-use and further develop previous iGEM software    projects (or parts thereof) or use
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and/or improvement of existing synthetic    biology tools or frameworks.</p>
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              <p align="justify">&nbsp;</p></td>
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            <td width="184" valign="top"><p align="center"><img src="images/a.png" width="18" height="18"></p></td>
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            <td width="916"><p align="justify">Develop a well documented library or API for other    developers (rather than only a
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+
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stand-alone app for end users.)</p>
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              <p align="justify">&nbsp;</p></td>
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            <td width="184" valign="top"><p align="center"><img src="images/a.png" width="18" height="18"></p></td>
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            <td width="916"><p align="justify">Support and use the SBOL and / or SBOLv standard.</p>
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              <p align="justify">&nbsp;</p></td>
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            <td width="916"><p align="justify">iGEM projects involve important questions beyond the    bench, for example relating to
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(but not limited to) ethics, sustainability,    social justice, safety, security, or intellectual property rights. Describe    an
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approach that your team used to address at least one of these questions.    Evaluate your approach, including whether it allowed you
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to answer your    question(s), how it influenced the team's scientific project, and how it    might be adapted for others to use
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(within and beyond iGEM). We encourage    thoughtful and creative approaches, and those that draw on past Policy &amp;    Practice
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(formerly Human Practices) activities.</p>              </td>
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Latest revision as of 03:26, 18 October 2014

HFUT_CHINA

overview

butterflies-are-gross
pig-head-pozole
canadian-thanksgiving-in-texas
weisswurst-pretzels-and-beer-for-breakfast
cow-head-barbacoa
cooking-with-dr-pepper
hatch-chile-feast
greece-eating-our-way-through-the-mainland

INTRODUCTION

 

Synthetic Biology is to create the new species by building parts and biobricks through the Genetic Engineering. iGEM is a worldwide synthetic biology competition. Till now, more than one thousand teams have participated in iGEM, resulting in a large number of synthetic devices designed. However, not many analyses are done on these devices. Are these existing devices could provide useful information for new participators to design new devices? In order to answer this question, we aim to developing a software to help designing devices.

 


The main function of our software “BioDesigner” is to recommend biobricks for participators when they are designing new devices. By collecting the information of existing devices and making analysis on these devices, Biodesigner will recommend biobricks based on the users’ habits or the biobricks users have been used.

 


To our best known, BioDesigner is the first recommendation software based on the analysis of existing devices. Besides, we also establish a database containing the information of existing devices to support BioDesigner. BioDesigner would be a good assistant for your design. Using it would make your design easier and smarter.

SOFTWARE

 

BioDesigner contains two parts, server part and client part. The codes for server part are written in java programming language and the codes for client part are written in C++ programming language. The GUI is designed with Qt which is based on C++. As a result, all of them can be compiled across various platforms. The program has been built on Windows, Linux and Mac operating systems.


The server part is used to build the database that contains the information of existing devices, and make analysis on these information. The client part consists of GUI and analysis of users input. Users input there information through GUI, and client codes deal with the input and send requirements to the server. Server receives the requirements from client, and makes analysis based on the database. Then, it returns information to client. Client deals with the information and visualizes it.


OThe database is stored in server, which would simplify the installation. Since the server is more powerful, the algorithms for recommendation are executed on server, which will reduce the analysis time.

 

METHODOLOGY

In order to accomplish the function of BioDesigner, such as recommending biobricks, we adapt various recommendation algorithms to achieve the goal. These algorithms include Collaborative filtering and Association rules.

1. Collaborative filtering:


a. The collaborative filtering based on the content: Given a biobrick, Biodesigner finds a similar biobrick to recommend according to the sequence of biobrick.


b. The collaborative filtering based on the user: By storing the biobricks users have been used, Biodesigner statistics users’ habit to recommend the higher frequency biobrick.


2. Association rules: Based on existing device chains, implied relationship, including relationship between two successive biobricks, three successive biobricks, four successive biobirkcs and five successive biobricks, are obtained. Biodesigner uses these relationships to recommend the biobrick over the minimum confidence.


 

DATABASE

In order to support Biodesigner, we build a database that contains the systems designed by the teams of previous years. About 3600 device chains are collected and stored in our database. We also download the biobrick information contained by these chains from Registry of Standard Biological Parts and stored these information in our database.

 


The database used in BioDesigner is flexible. The users can add or delete data freely. We use the Restlet and Hibernate to build the database framework. When the client sends a request, a respond will be sent from the serve.

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