Team:USTC-Software/Achieve/Medal

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           <li><a href="#main" class="button">Gold</a>
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           <li><a href="#Introduction" class="button">Bronze Medal</a></li>
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           <li><a href="#sliver" class="button">Silver</a>
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           <li><a href="#bronze" class="button">Bronze</a>  
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           <li><a href="#Software" class="button">Silver Medal</a></li>
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           <li><a href="#Methodology" class="button">Gold Medal</a></br>
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                <a href="#plus" class="button" id="subbutton">Plus</a>
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  <div id="Introduction">
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  <h2 align="justify"><img src="https://static.igem.org/mediawiki/2013/e/ee/USTC-Software_Bronze.png" width="52" height="52" align="absmiddle" />Bronze Medal</h2>
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  <p align="justify"><img src="https://static.igem.org/mediawiki/2013/7/72/USTC-Software-check_B.png" width="30" height="30" align="absmiddle" />Register the team, have a great summer, and have fun attending the Jamboree.</p>
 +
  <p><img src="https://static.igem.org/mediawiki/2013/7/72/USTC-Software-check_B.png" width="30" height="30" align="absmiddle" />Create and share a description of the team's project via the iGEM wiki.</p>
 +
  <p><img src="https://static.igem.org/mediawiki/2013/7/72/USTC-Software-check_B.png" width="30" height="30" align="absmiddle" />Present a Poster and Talk at the iGEM Jamboree.</p>
 +
  <p><img src="https://static.igem.org/mediawiki/2013/7/72/USTC-Software-check_B.png" width="30" height="30" align="absmiddle" />Develop and make available via the The Registry of Software Tools an open source software tool that supports synthetic biology based on BioBrick standard biological parts (remember, the iGEM judges will be looking for substantial team-based software projects).<a id="out"  href="https://github.com/igemsoftware/USTC-Software2013">read more</a></p>
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  <div id="Software">
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  <h2 align="justify"><img src="https://static.igem.org/mediawiki/2013/8/88/USTC-Software_Silver.png" width="52" height="52" align="absmiddle" />Silver Medal</h2>
 +
  <p align="justify"><img src="https://static.igem.org/mediawiki/2013/7/72/USTC-Software-check_B.png" width="30" height="30" align="absmiddle" />Provide a detailed, draft specification for the next version of your software tool<a id="out" href="https://2013.igem.org/Team:USTC-Software/Project/Preview">read more</a></p>
 +
  <p><img src="https://static.igem.org/mediawiki/2013/7/72/USTC-Software-check_B.png" width="30" height="30" align="absmiddle" />Provide a second, distinct (yet complementary) software tools project.<a id="out" href="https://2013.igem.org/Team:USTC-Software/Project/App_Clotho">read more</a></p>
 +
  <h3>Add</h3>
 +
  <p><img src="https://static.igem.org/mediawiki/2013/7/72/USTC-Software-check_B.png" width="30" height="30" align="absmiddle" />Provide a demonstration of their software either as a textual or video tutorial made available on their wiki. This tutorial should explain all the features of the tool as well as provide sample input and output as appropriate.<a id="out" href="https://2013.igem.org/Team:USTC-Software/Project/Software#Tutorial">read more</a></p> 
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  <div id="Methodology">
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  <h2 align="left"><img src="https://static.igem.org/mediawiki/2013/d/dc/USTC_Software_Gold.png" width="52" height="52" align="absmiddle" />Gold Medal</h2>
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  <p align="left"><img src="https://static.igem.org/mediawiki/2013/7/72/USTC-Software-check_B.png" width="30" height="30" align="absmiddle" />Have another team utilize the software developed by your team. You must clearly show how your software was used and the results that were obtained.<a id="out" href="https://2013.igem.org/Team:USTC-Software/collaboration">read more</a></p>
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  <div align="left"><br />
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  </div>
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  <p align="left"><img src="https://static.igem.org/mediawiki/2013/7/72/USTC-Software-check_B.png" width="30" height="30" align="absmiddle" />Outline and detail how your software effects Human Practices in Synthetic Biology. Such topics include: safety, security, ethics, or ownership, sharing, and innovation.
 +
<a id="out" href="https://2013.igem.org/Team:USTC-Software/Human_practice">read more</a></p>
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<div id="gold">
 
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        <p align="left" class="medal_title1"><img src="https://static.igem.org/mediawiki/2013/d/dc/USTC_Software_Gold.png" align="absmiddle"/> Gold Medal</p>
 
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        <div class="require_fulfill">
 
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          <div class="requirement">
 
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            <p align="left" class="requirement"><img src="https://static.igem.org/mediawiki/2013/1/1c/USTC-Software-check1.png" align="top"/>Have another team utilize the software developed by your team.</p>
 
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          <p align="left" class="fulfillment">In our presentation, we clearly declared that <a href="https://2012.igem.org/Team:USTC-China">USTC-China</a> has used our software RegulonLib, and how this software helped them designed their circuits.</p>
 
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        <div class="require_fulfill">
 
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          <div class="requirement">
 
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            <p align="left" class="requirement"><img src="https://static.igem.org/mediawiki/2013/1/1c/USTC-Software-check1.png" align="top"/>Outline and detail how your project effects Human Practice in Synthetic Biology.</p>
 
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          </div>
 
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          <p align="left" class="fulfillment">In the <a href="https://2012.igem.org/Team:USTC-Software/hp.html#safety_wrapper">safety section</a> on our wiki, we outlined our suggestions on safety issues in the future.</p>
 
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        <div class="require_fulfill">
 
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          <div class="requirement">
 
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            <p align="left" class="requirement"><img src="https://static.igem.org/mediawiki/2013/1/1c/USTC-Software-check1.png" align="top"/>A team may use SBOL in its software documentation.</p>
 
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          </div>
 
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          <p align="left" class="fulfillment">In our software, all operon information in the database have been stored in SBOL format. We build the database called RegulonLib that have all the regulation relationships in E. coli K-12, and all these Operons, promoters and genes are represented in SBOL files. We have shown that in our wiki and presentation. These SBOL files are included in every copy of our software that can be downloaded in the <a href="https://github.com/igemsoftware/USTC-Software_2012/tree/master/executables">repository</a>.</p>
 
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 +
  <h3 align="left">Or</h3>
 +
  <p align="left"><img src="https://static.igem.org/mediawiki/2013/7/72/USTC-Software-check_B.png" width="30" height="30" align="absmiddle" />In place of requirement two, a team may instead use SBOL in your software documentation.</p>
 +
 
 +
 
 +
  <p align="left" style="font-size:16px;">The gene information could be output in SBOL when clicking the button “SBOL it!”.
 +
The file whose name is same as the name of gene containing in.
 +
For example:
 +
This is a file named “gutM.xml”<br /><br /><img src="https://static.igem.org/mediawiki/igem.org/archive/2/23/20130924051624%21Starter.png"width="1000" height="436" /></p>
 +
 +
    <h3 align="left" id="plus">Plus</h3>
 +
    <h4 align="left">Develop and document a new technical standard that supports one of the following:</h4>
 +
    <p align="left"><img src="https://static.igem.org/mediawiki/2013/2/28/USTC-Software-checkbn.png" width="30" height="30" align="absmiddle" />design of BioBrick Parts or Devices</p>
 +
    <p align="left"><img src="https://static.igem.org/mediawiki/2013/2/28/USTC-Software-checkbn.png" width="30" height="30" align="absmiddle" />construction of BioBrick Parts or Devices</p>
 +
    <p align="left"><img src="https://static.igem.org/mediawiki/2013/2/28/USTC-Software-checkbn.png" width="30" height="30" align="absmiddle" />characterization of BioBrick Parts or Devices</p>
 +
    <p align="left"><img src="https://static.igem.org/mediawiki/2013/7/72/USTC-Software-check_B.png" width="30" height="30" align="absmiddle" />the analysis, modeling, and simulation of BioBrick Parts or Devices</p>
 +
    <p align="left" style="font-size:16px;">Actually, our software could model all parts in Biobrick Parts. So we choose two parts containing promoter and protein gene of LuxR which are used more than 1000 times.<br/><br />
 +
Biobrick Part 1:  <a id="content" href="http://parts.igem.org/Part:BBa_R0062">BBa_R0062</a>&nbsp;&nbsp;&nbsp;Promoter (luxR & HSL regulated -- lux pR)<br />
 +
Biobrick Part 2:  <a id="content" href="http://parts.igem.org/Part:BBa_C0062">BBa_C0062</a>&nbsp;&nbsp;&nbsp;luxR repressor/activator, (no LVA?) <br/>
 +
<br />
 +
Our software analyze the stability of the GRN after importing. Because those parts are multiple transcriptional regulator, the score of the stability is only two stars which means that after LuxR’s import the expression of each gene changed a lot.
 +
</p>
 +
   
 +
   
 +
    <p align="left"><img src="https://static.igem.org/mediawiki/2013/2/28/USTC-Software-checkbn.png" width="30" height="30" align="absmiddle" />the sharing of BioBrick Parts or Devices, either via physical DNA or as information via the internet.</p>
 +
    <h3 align="left">Or</h3>
 +
    <P align="left"><img src="https://static.igem.org/mediawiki/2013/2/28/USTC-Software-checkbn.png" width="30" height="30" align="absmiddle" />Build upon existing software from a previous iGEM competition found on the The Registry of Software Tools</P>
 +
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 +
     
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</div>
</div>
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<div id="sliver">
 
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        <p class="medal_title2"><img src="https://static.igem.org/mediawiki/2013/8/88/USTC-Software_Silver.png" align="absmiddle" /> Silver Medal</p>
 
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        <div class="require_fulfill">
 
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          <div class="requirement">
 
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            <p class="requirement"><img src="https://static.igem.org/mediawiki/2013/1/1c/USTC-Software-check1.png" align="top"/>Provide a detailed, draft specification for the next version of your software tool</p>
 
-
          </div>
 
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          <p class="fulfillment">For our software on The Registry of Software Tools, we provide detailed Future Work section for next version of the software, which is available via our <a href="https://github.com/igemsoftware/USTC-Software_2012">Wiki</a>.</p>
 
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        <div class="require_fulfill">
 
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          <div class="requirement">
 
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            <p class="requirement"><img src="https://static.igem.org/mediawiki/2013/1/1c/USTC-Software-check1.png" align="top"/>Provide a second, distinct (yet complementary) software tools project.</p>
 
-
          </div>
 
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          <p class="fulfillment">As said above, we made a second, distinct software called <a href="https://github.com/igemsoftware/USTC-Software-Clotho-App_2012">RegulonLib</a> in the Registry of Software Tools, check out our <a href="https://2012.igem.org/Team:USTC-Software/clotho.html">Wiki page</a> for more information about RegulonLib.</p>
 
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        <div class="require_fulfill">
 
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          <div class="requirement">
 
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            <p class="requirement"><img src="https://static.igem.org/mediawiki/2013/1/1c/USTC-Software-check1.png" align="top"/>Provide a demonstration of their software either as a textual or video tutorial made available on their wiki.</p>
 
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          </div>
 
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          <p class="fulfillment">Visit <a href="https://2012.igem.org/Team:USTC-Software/example.html">Example Page</a> for tutorial and demonstrations. We provide User Manual link available on the bottom of <a href="https://2012.igem.org/Team:USTC-Software/software.html">software wiki page</a>, which contains very detailed instruction for how to use our software. In addition, in the <a href="https://github.com/igemsoftware/USTC-Software_2012">repository</a> of our software, we also provide instruction on all to compile and use our software.</p>
 
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<div id="bronze">
 
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        <p class="medal_title3"><img src="https://static.igem.org/mediawiki/2013/e/ee/USTC-Software_Bronze.png" align="absmiddle" /> Bronze Medal</p>
 
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        <div class="require_fulfill">
 
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          <div class="requirement">
 
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            <p class="requirement"><img src="https://static.igem.org/mediawiki/2013/1/1c/USTC-Software-check1.png" align="top"/>Register the team, have a great summer, and have fun attending the Jamboree.</p>
 
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          </div>
 
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          <p class="fulfillment">It can be seen in <a href="https://igem.org/Team.cgi?id=742">Team Information</a> page that we have successfully registered.</p>
 
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        </div>
 
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        <div class="require_fulfill">
 
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          <div class="requirement">
 
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            <p class="requirement"><img src="https://static.igem.org/mediawiki/2013/1/1c/USTC-Software-check1.png" align="top"/>Create and share a description of the project of team via the iGEM wiki.</p>
 
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          </div>
 
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          <p class="fulfillment">This can be seen in the <a href="https://2012.igem.org/Team:USTC-Software/project.html#project_intro">project page</a> of our wiki.</p>
 
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        <div class="require_fulfill">
 
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          <div class="requirement">
 
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            <p class="requirement"><img src="https://static.igem.org/mediawiki/2013/1/1c/USTC-Software-check1.png" align="top"/>Present a Poster and Talk at the iGEM Jamboree.</p>
 
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          </div>
 
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          <p class="fulfillment">Download our Asia Jamboree <a href="https://2012.igem.org/files/presentation/USTC-Software.pdf">presentation</a> and <a href="https://2012.igem.org/files/poster/USTC-Software.pdf">poster</a>.</p>
 
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        <div class="require_fulfill">
 
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          <div class="requirement">
 
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            <p class="requirement"><img src="https://static.igem.org/mediawiki/2013/1/1c/USTC-Software-check1.png" align="top"/>Develop and make available via the The Registry of Software Tools an open source software tool that supports synthetic biology based on BioBrick standard biological parts.</p>
 
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          </div>
 
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          <p class="fulfillment">This year we made not one but two open source software tools in The Registry of Software Tools, including an all-in-one reverse engineering tool called <a href="https://github.com/igemsoftware/USTC-Software_2012">REBORN</a> and a Clotho App that finds all regulation relationships in E. coli K-12 called <a href="https://github.com/igemsoftware/USTC-Software-Clotho-App_2012">RegulonLib</a>.</p>
 
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Latest revision as of 02:52, 28 October 2013

Header2


Medal

Bronze Medal

Register the team, have a great summer, and have fun attending the Jamboree.

Create and share a description of the team's project via the iGEM wiki.

Present a Poster and Talk at the iGEM Jamboree.

Develop and make available via the The Registry of Software Tools an open source software tool that supports synthetic biology based on BioBrick standard biological parts (remember, the iGEM judges will be looking for substantial team-based software projects).read more

Silver Medal

Provide a detailed, draft specification for the next version of your software toolread more

Provide a second, distinct (yet complementary) software tools project.read more

Add

Provide a demonstration of their software either as a textual or video tutorial made available on their wiki. This tutorial should explain all the features of the tool as well as provide sample input and output as appropriate.read more

Gold Medal

Have another team utilize the software developed by your team. You must clearly show how your software was used and the results that were obtained.read more


Outline and detail how your software effects Human Practices in Synthetic Biology. Such topics include: safety, security, ethics, or ownership, sharing, and innovation. read more

Or

In place of requirement two, a team may instead use SBOL in your software documentation.

The gene information could be output in SBOL when clicking the button “SBOL it!”. The file whose name is same as the name of gene containing in. For example: This is a file named “gutM.xml”

Plus

Develop and document a new technical standard that supports one of the following:

design of BioBrick Parts or Devices

construction of BioBrick Parts or Devices

characterization of BioBrick Parts or Devices

the analysis, modeling, and simulation of BioBrick Parts or Devices

Actually, our software could model all parts in Biobrick Parts. So we choose two parts containing promoter and protein gene of LuxR which are used more than 1000 times.

Biobrick Part 1: BBa_R0062   Promoter (luxR & HSL regulated -- lux pR)
Biobrick Part 2: BBa_C0062   luxR repressor/activator, (no LVA?)

Our software analyze the stability of the GRN after importing. Because those parts are multiple transcriptional regulator, the score of the stability is only two stars which means that after LuxR’s import the expression of each gene changed a lot.

the sharing of BioBrick Parts or Devices, either via physical DNA or as information via the internet.

Or

Build upon existing software from a previous iGEM competition found on the The Registry of Software Tools

Retrieved from "http://2013.igem.org/Team:USTC-Software/Achieve/Medal"