Team:Shenzhen BGIC 0101/Criteria

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<h1>Medal Fulfillment</h1>
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<h2>Bronze Medal</h2>
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<img src="https://static.igem.org/mediawiki/2013/1/1b/Zhengque.png" width="20px" height="20px"/>1.Register the team, have a great summer, and have fun attending the Jamboree.
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<div id="post-1815" class="post-1815 post type-post status-publish format-standard hentry category-evolution" style="background: transparent;color: #E6E6E6;">
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<br/><h2>Bronze Medal</h2><br/>
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<p class="ach">
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<img src="https://static.igem.org/mediawiki/2012/4/41/USTC-Software-check.png" width="20px" height="20px"/>Register the team, have a great summer, and have fun attending the Jamboree.
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<img src="https://static.igem.org/mediawiki/2012/4/41/USTC-Software-check.png" width="20px" height="20px"/>Create and share a description of the team's project via the iGEM wiki.
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<img src="https://static.igem.org/mediawiki/2013/1/1b/Zhengque.png" width="20px" height="20px"/>2.Create and share a description of the team's project via the iGEM wiki.
</p>
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<p class="ans"><a href="https://2013.igem.org/Team:Shenzhen_BGIC_0101/Software">Overview of project</a></p>
<p class="ans"><a href="https://2013.igem.org/Team:Shenzhen_BGIC_0101/Software">Overview of project</a></p>
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<img src="https://static.igem.org/mediawiki/2012/4/41/USTC-Software-check.png" width="20px" height="20px"/>Present a Poster and Talk at the iGEM Jamboree.
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<img src="https://static.igem.org/mediawiki/2013/1/1b/Zhengque.png" width="20px" height="20px"/>3.Present a Poster and Talk at the iGEM Jamboree.
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<img src="https://static.igem.org/mediawiki/2012/4/41/USTC-Software-check.png" width="20px" height="20px"/>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  
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<img src="https://static.igem.org/mediawiki/2013/1/1b/Zhengque.png" width="20px" height="20px"/>4.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>
</p>
<p class="ans">Our software in <a href="https://github.com/igemsoftware/Shenzhen_BGIC_0101_2013">Github</a>.<br/>
<p class="ans">Our software in <a href="https://github.com/igemsoftware/Shenzhen_BGIC_0101_2013">Github</a>.<br/>
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Our giant software aims at operating Biobrick of device level based on synthesized DNA fragments.<br/>But for biobrick level, the second module can also assist users to design genes, such as deletion of EcorI, XbaI, SpeI, PstI, Not I in the CDS, codon optimization and repeat smash.  
Our giant software aims at operating Biobrick of device level based on synthesized DNA fragments.<br/>But for biobrick level, the second module can also assist users to design genes, such as deletion of EcorI, XbaI, SpeI, PstI, Not I in the CDS, codon optimization and repeat smash.  
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<br/><h2>Silver Medal</h2><br/>
<br/><h2>Silver Medal</h2><br/>
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<img src="https://static.igem.org/mediawiki/2012/4/41/USTC-Software-check.png" width="20px" height="20px"/>A. Provide a detailed, draft specification for the next version of your software tool. As our project is so large and extensible greatly, at least 5 ideas can’t be realized due to time limitation.
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<img src="https://static.igem.org/mediawiki/2013/1/1b/Zhengque.png" width="20px" height="20px"/>1A. Provide a detailed, draft specification for the next version of your software tool. </br> As our project is so large and <a href="https://2013.igem.org/Team:Shenzhen_BGIC_0101/Next_version">extensible greatly</a>, at least 5 ideas can’t be realized due to time limitation.
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<img src="https://static.igem.org/mediawiki/2012/4/41/USTC-Software-check.png" width="20px" height="20px"/>B. Provide a second, distinct (yet complementary) software tools project. For the third module SegmMan, we have a complementary design & synthesis method OLS chip synthesis, so that Genovo is compatible for both synthesizer and chip.
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<img src="https://static.igem.org/mediawiki/2013/1/1b/Zhengque.png" width="20px" height="20px"/>1B. Provide a second, distinct (yet complementary) software tools project. </br> Genovo consists of 4 different modules perform functions independently, <a href="https://2013.igem.org/Team:Shenzhen_BGIC_0101/Modules">NeoChr, NecleoMod, SegmMan, OLSdesigner</a>. Expecially, for the third module SegmMan, we have a complementary design & synthesis method <a href="https://2013.igem.org/Team:Shenzhen_BGIC_0101/Tutorial/olsdesigner">OLS chip synthesis</a>, so that Genovo is compatible for both synthesis company customer and chip synthesis customer.
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<img src="https://static.igem.org/mediawiki/2012/4/41/USTC-Software-check.png" width="20px" height="20px"/>Provide a demonstration of their software either as a textual or video tutorial made available on their wiki.
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<img src="https://static.igem.org/mediawiki/2013/1/1b/Zhengque.png" width="20px" height="20px"/>2.Provide a demonstration of their software either as a textual or video tutorial made available on their wiki.
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<p class="ans">Textual <a href="https://2013.igem.org/Team:Shenzhen_BGIC_0101/Tutorial">tutorial</a></p>
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<p class="ans"><a href="https://2013.igem.org/Team:Shenzhen_BGIC_0101/Tutorial">Textual Tutorial</a> about how to use Genovo in command line </p>
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<p class="ans"><a href="https://2013.igem.org/Team:Shenzhen_BGIC_0101/Tutorial/videoturorial">Video Tutorial</a> about how to use Genovo in JBrowse GUI </p>
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<br/><h2>Gold Medal</h2><br/>
<br/><h2>Gold Medal</h2><br/>
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<img src="https://static.igem.org/mediawiki/2012/4/41/USTC-Software-check.png" width="20px" height="20px"/>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.
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<img src="https://static.igem.org/mediawiki/2013/1/1b/Zhengque.png" width="20px" height="20px"/>1.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.
</p>
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<p class="ans">We have software team Shenzhen_BGIC_ATCG to use the second module to design their genes. SC2.0 project also try out SegmMan module on chrVII’s segmentation.</p>
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<p class="ans">We have software team Shenzhen_BGIC_ATCG to use the second module to design their genes. SC2.0 project also try out SegmMan module on chrVII’s segmentation.
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<p class="ach">
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<a href="https://2013.igem.org/Team:Shenzhen_BGIC_0101/Requirements#Collaboration">See here</a>.</p>
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<img src="https://static.igem.org/mediawiki/2012/4/41/USTC-Software-check.png" width="20px" height="20px"/>A. Outline and detail how your software effects Human Practices in Synthetic Biology.
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<img src="https://static.igem.org/mediawiki/2013/1/1b/Zhengque.png" width="20px" height="20px"/>2A. Outline and detail how your software effects Human Practices in Synthetic Biology.
</p>
</p>
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<p class="ans">Share:<br/>
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<p class="ans">Share:</p>
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Web-based server for public to use Software assessment and comparison with Biostudio.<br/>
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<p><a href="https://2013.igem.org/Team:Shenzhen_BGIC_0101/Web-based_trial">Web-based server</a> for public to use Software assessment and comparison with Biostudio.<br/>
Innovation:<br/>
Innovation:<br/>
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We interview with core leader, Dr. Patrick Yizhi Cai and talk about Genovo’s design and application.<br/>
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We <a href="https://2013.igem.org/Team:Shenzhen_BGIC_0101/Requirements#HumanPractices">interview</a> with core leader, Dr. Patrick Yizhi Cai and talk about Genovo’s design and application.<br/>
Advertisement:<br/>
Advertisement:<br/>
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We tried to sell our team shirts to people from BGI.<br/>
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We tried to <a href="https://docs.google.com/forms/d/1v8vvGN4TRq1yzLuKNed43mgl1KEyaWpOjh9VJfyNZqM/viewform">sell</a> our team shirts to people from BGI.<br/>
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<img src="https://static.igem.org/mediawiki/2012/4/41/USTC-Software-check.png" width="20px" height="20px"/>B. Use SBOL in your software documentation.
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<img src="https://static.igem.org/mediawiki/2013/1/1b/Zhengque.png" width="20px" height="20px"/>2B. Use SBOL in your software documentation.
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<p class="ans">We use SBOL as one of the output of first module to describe the genes in new created pathway.</p>
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<p class="ans">We use <a href="https://2013.igem.org/Team:Shenzhen_BGIC_0101/Compatibility">SBOL</a> as one of the output of first module to describe the genes in new created pathway.</p>
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<p>
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<img src="https://static.igem.org/mediawiki/2012/4/41/USTC-Software-check.png" width="20px" height="20px"/>A. Develop and document a new technical standard that supports one of the following:
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<img src="https://static.igem.org/mediawiki/2013/1/1b/Zhengque.png" width="20px" height="20px"/>3A. Develop and document <a href="https://2013.igem.org/Team:Shenzhen_BGIC_0101/NewStandard">a new technical standard</a> that supports one of the following:
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<p class="ans">a. Design of BioBrick Parts or Devices<br/>
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<p class="ans">
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Chromosome Design Standard<br/>
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1. Construction of BioBrick Parts or Devices<br/>
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Design Operation Standard<br/>
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<a href="https://2013.igem.org/Team:Shenzhen_BGIC_0101/NewStandard">Assembly Strategy Standard</a><br/>
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b. Construction of BioBrick Parts or Devices<br/>
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2. Design of BioBrick Parts or Devices<br/>
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Assembly Strategy Standard
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<a href="https://2013.igem.org/Team:Shenzhen_BGIC_0101/NewStandard">Chromosome Design Standard</a><br/>
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<a href="https://2013.igem.org/Team:Shenzhen_BGIC_0101/NewStandard">Design Operation Standard</a><br/>
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<br/><h2>Special Awards</h2><br/>
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<img src="https://static.igem.org/mediawiki/2012/4/41/USTC-Software-check.png" width="20px" height="20px"/>test
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<p>*  3B. Build upon existing software from a previous iGEM competition found on the The Registry of Software Tools.</br>
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No. But Genovo's UI is better, it's mainly developed on well known synthetic biology tool <a href="http://54.235.254.95/gd/">GeneDesign</a>, <a href="https://bitbucket.org/notadoctor/biostudio-dev">BioStudio</a>,
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<a href="http://www.gmod.org/wiki/JBrowse">JBrowse</a>.</p>
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<h3>contact us</h3>
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<p>BGI-Shenzhen, Beishan Industrial Zone<br />
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Yantian District, Shenzhen, 518083, China</p>
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<p> <span>email:</span><br />
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<a href="mailto:gongjianhui@genomics.com">gongjianhui@genomics.com</a></p>
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<h3>sponsor</h3>
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<p>BGIC<br/></p>
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Latest revision as of 20:40, 28 October 2013




Medal Fulfillment


Bronze Medal


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

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

Overview of project

3.Present a Poster and Talk at the iGEM Jamboree.

4.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

Our software in Github.
Note:
Our giant software aims at operating Biobrick of device level based on synthesized DNA fragments.
But for biobrick level, the second module can also assist users to design genes, such as deletion of EcorI, XbaI, SpeI, PstI, Not I in the CDS, codon optimization and repeat smash.


Silver Medal


1A. Provide a detailed, draft specification for the next version of your software tool.
As our project is so large and extensible greatly, at least 5 ideas can’t be realized due to time limitation.

1B. Provide a second, distinct (yet complementary) software tools project.
Genovo consists of 4 different modules perform functions independently, NeoChr, NecleoMod, SegmMan, OLSdesigner. Expecially, for the third module SegmMan, we have a complementary design & synthesis method OLS chip synthesis, so that Genovo is compatible for both synthesis company customer and chip synthesis customer.

2.Provide a demonstration of their software either as a textual or video tutorial made available on their wiki.

Textual Tutorial about how to use Genovo in command line

Video Tutorial about how to use Genovo in JBrowse GUI


Gold Medal


1.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.

We have software team Shenzhen_BGIC_ATCG to use the second module to design their genes. SC2.0 project also try out SegmMan module on chrVII’s segmentation. See here.

2A. Outline and detail how your software effects Human Practices in Synthetic Biology.

Share:

Web-based server for public to use Software assessment and comparison with Biostudio.
Innovation:
We interview with core leader, Dr. Patrick Yizhi Cai and talk about Genovo’s design and application.
Advertisement:
We tried to sell our team shirts to people from BGI.

2B. Use SBOL in your software documentation.

We use SBOL as one of the output of first module to describe the genes in new created pathway.

3A. Develop and document a new technical standard that supports one of the following:

1. Construction of BioBrick Parts or Devices
Assembly Strategy Standard
2. Design of BioBrick Parts or Devices
Chromosome Design Standard
Design Operation Standard

* 3B. Build upon existing software from a previous iGEM competition found on the The Registry of Software Tools.
No. But Genovo's UI is better, it's mainly developed on well known synthetic biology tool GeneDesign, BioStudio, JBrowse.


Retrieved from "http://2013.igem.org/Team:Shenzhen_BGIC_0101/Criteria"