Team:HFUT CHINA/Overview.html

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<h1><a href="https://2014.igem.org/Team:HFUT_CHINA"><img src="https://static.igem.org/mediawiki/2014/0/0e/Hfut-Logo.png" alt=""></a></h1>
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                         <li><a href="./details2.html">Overview</a></li>
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                         <li><a href="https://2014.igem.org/Team:HFUT_CHINA/Overview.html">Overview</a></li>
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                         <li><a href="./details8.html">Examples</a></li>
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                         <li><a href="https://2014.igem.org/Team:HFUT_CHINA/Examples.html">Examples</a></li>
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                         <li><a href="./details5.html">Future Work</a></li>
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                         <li><a href="https://2014.igem.org/Team:HFUT_CHINA/Future_Work.html">Future Work</a></li>
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                         <li><a href="./detailsdownload.html">Download</a></li>
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                         <li><a href="https://2014.igem.org/Team:HFUT_CHINA/Download.html">Download</a></li>
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                         <li><a href="./details1.html">Database & Algorithm</a></li>
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                         <li><a href="https://2014.igem.org/Team:HFUT_CHINA/Database&Algorithm.html">Database & Algorithm</a></li>
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                         <li><a href="./details3.html">Tutorial</a></li>
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                         <li><a href="https://2014.igem.org/Team:HFUT_CHINA/Tutorial.html">Tutorial</a></li>
                        
                        
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                         <li><a href="https://2014.igem.org/Team:HFUT_CHINA/Safety.html">Safety</a></li>
                        
                        
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                 <li><a>Human Practice</a>
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                         <li><a href="https://2014.igem.org/Team:HFUT_CHINA/Communication.html">Communication</a>
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                         <li><a href="./about.html">Join Us</a></li>
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                         <li><a href="https://2014.igem.org/Team:HFUT_CHINA/Contact_us.html">Contact us</a></li>
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                        <li><a href="./contact_7.html">Contact us</a></li>
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      <h2 class="wrapper"><font class="font_1">Medal</font></h2>
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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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          </tr>
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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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Jamboree.</p>
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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 align="center" class="STYLE10">&nbsp;</p>
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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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            <td width="916"><p align="justify">Present a Poster and Talk at the Giant Jamboree.</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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3.  By the link between parts to recommend (recommended homologous part).<br>
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To meet the need  of the analysis and recommendation, our team innovatively improved most of  algorithms and methods to make the simulation more accurate and more efficient.</p>
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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 2500 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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            <td width="184"><p align="center"><strong>Silver Medal: </strong></p>
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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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            <td width="916"><p align="justify">Provide a comprehensive and well-designed User Guide.    (Be creative! An instructional
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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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            <td width="916"><p align="justify">Demonstrate that you followed best practises in    software development so that other
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            <td width="184"><p align="center"><strong>Gold Medal: </strong></p>
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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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            <td width="916"><p align="justify">Make your software interact / interface with the    Registry.</p>
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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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            <td width="916"><p align="justify">Develop a well documented library or API for other    developers (rather than only a
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            <td width="916"><p align="justify">Support and use the SBOL and / or SBOLv standard.</p>
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Revision as of 09:04, 17 October 2014

HFUT_CHINA

overview

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.


3. By the link between parts to recommend (recommended homologous part).


To meet the need of the analysis and recommendation, our team innovatively improved most of algorithms and methods to make the simulation more accurate and more efficient.

 

DATABASE

In order to support Biodesigner, we build a database that contains the systems designed by the teams of previous years. About 2500 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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