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Team:USTC-Software/achievements
From 2012.igem.org
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<div class="require_fulfill"> | <div class="require_fulfill"> | ||
<div class="requirement"> | <div class="requirement"> | ||
| - | <img src="https://static.igem.org/mediawiki/2012/4/41/USTC-Software-check.png" alt="Checked" width="30px" height="30px" / | + | |
| - | + | <p class="requirement"><img src="https://static.igem.org/mediawiki/2012/4/41/USTC-Software-check.png" alt="Checked" width="30px" height="30px" />Outline and detail how your project effects Human Practice in Synthetic Biology.</p> | |
</div> | </div> | ||
<p class="fulfillment">In the safety section on our wiki(https://2012.igem.org/Team:USTC-Software/hp.html#safety_wrapper), we outlined our suggestions on safety issues in the future.</p> | <p class="fulfillment">In the safety section on our wiki(https://2012.igem.org/Team:USTC-Software/hp.html#safety_wrapper), we outlined our suggestions on safety issues in the future.</p> | ||
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<div class="require_fulfill"> | <div class="require_fulfill"> | ||
<div class="requirement"> | <div class="requirement"> | ||
| - | <img src="https://static.igem.org/mediawiki/2012/4/41/USTC-Software-check.png" alt="Checked" width="30px" height="30px" / | + | |
| - | + | <p class="requirement"><img src="https://static.igem.org/mediawiki/2012/4/41/USTC-Software-check.png" alt="Checked" width="30px" height="30px" />In place of developing a new standard, a team may instead use SBOL in its software documentation.</p> | |
</div> | </div> | ||
<p 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 repository(https://github.com/igemsoftware/USTC-Software_2012/tree/master/executables).</p> | <p 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 repository(https://github.com/igemsoftware/USTC-Software_2012/tree/master/executables).</p> | ||
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<div class="require_fulfill"> | <div class="require_fulfill"> | ||
<div class="requirement"> | <div class="requirement"> | ||
| - | <img src="https://static.igem.org/mediawiki/2012/4/41/USTC-Software-check.png" alt="Checked" width="30px" height="30px" / | + | |
| - | + | <p class="requirement"><img src="https://static.igem.org/mediawiki/2012/4/41/USTC-Software-check.png" alt="Checked" width="30px" height="30px" />Provide a detailed, draft specification for the next version of your software tool</p> | |
</div> | </div> | ||
<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 Wiki.(https://github.com/igemsoftware/USTC-Software_2012)</p> | <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 Wiki.(https://github.com/igemsoftware/USTC-Software_2012)</p> | ||
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<div class="require_fulfill"> | <div class="require_fulfill"> | ||
<div class="requirement"> | <div class="requirement"> | ||
| - | <img src="https://static.igem.org/mediawiki/2012/4/41/USTC-Software-check.png" alt="Checked" width="30px" height="30px" / | + | |
| - | + | <p class="requirement"><img src="https://static.igem.org/mediawiki/2012/4/41/USTC-Software-check.png" alt="Checked" width="30px" height="30px" />Provide a second, distinct (yet complementary) software tools project.</p> | |
</div> | </div> | ||
<p class="fulfillment">As said above, we made a second, distinct software called RegulonLib in the Registry of Software Tools (https://github.com/igemsoftware/USTC-Software-Clotho-App_2012), it also can be seen in our wiki(https://2012.igem.org/Team:USTC-Software/software.html#clotho_group)</p> | <p class="fulfillment">As said above, we made a second, distinct software called RegulonLib in the Registry of Software Tools (https://github.com/igemsoftware/USTC-Software-Clotho-App_2012), it also can be seen in our wiki(https://2012.igem.org/Team:USTC-Software/software.html#clotho_group)</p> | ||
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<div class="require_fulfill"> | <div class="require_fulfill"> | ||
<div class="requirement"> | <div class="requirement"> | ||
| - | <img src="https://static.igem.org/mediawiki/2012/4/41/USTC-Software-check.png" alt="Checked" width="30px" height="30px" / | + | |
| - | + | <p class="requirement"><img src="https://static.igem.org/mediawiki/2012/4/41/USTC-Software-check.png" alt="Checked" width="30px" height="30px" />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.</p> | |
</div> | </div> | ||
<p class="fulfillment">We provide User Manual link available on the bottom of software wiki page(https://2012.igem.org/Team:USTC-Software/software.html), which contains very detailed instruction for how to use our software. In addition, in the repository of our software, we also provide instruction on all to compile and use our software(https://github.com/igemsoftware/USTC-Software_2012).</p> | <p class="fulfillment">We provide User Manual link available on the bottom of software wiki page(https://2012.igem.org/Team:USTC-Software/software.html), which contains very detailed instruction for how to use our software. In addition, in the repository of our software, we also provide instruction on all to compile and use our software(https://github.com/igemsoftware/USTC-Software_2012).</p> | ||
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<div class="require_fulfill"> | <div class="require_fulfill"> | ||
<div class="requirement"> | <div class="requirement"> | ||
| - | <img src="https://static.igem.org/mediawiki/2012/4/41/USTC-Software-check.png" alt="Checked" width="30px" height="30px" / | + | |
| - | + | <p class="requirement"><img src="https://static.igem.org/mediawiki/2012/4/41/USTC-Software-check.png" alt="Checked" width="30px" height="30px" />Register the team, have a great summer, and have fun attending the Jamboree.</p> | |
</div> | </div> | ||
<p class="fulfillment">It can be seen in Team Information page(https://igem.org/Team.cgi?id=742) that we have successfully registered.</p> | <p class="fulfillment">It can be seen in Team Information page(https://igem.org/Team.cgi?id=742) that we have successfully registered.</p> | ||
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<div class="require_fulfill"> | <div class="require_fulfill"> | ||
<div class="requirement"> | <div class="requirement"> | ||
| - | <img src="https://static.igem.org/mediawiki/2012/4/41/USTC-Software-check.png" alt="Checked" width="30px" height="30px" / | + | |
| - | + | <p class="requirement"><img src="https://static.igem.org/mediawiki/2012/4/41/USTC-Software-check.png" alt="Checked" width="30px" height="30px" />Create and share a description of the team's project via the iGEM wiki.</p> | |
</div> | </div> | ||
<p class="fulfillment">This can be seen in the project page of our wiki(https://2012.igem.org/Team:USTC-Software/project.html#project_intro).</p> | <p class="fulfillment">This can be seen in the project page of our wiki(https://2012.igem.org/Team:USTC-Software/project.html#project_intro).</p> | ||
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<div class="require_fulfill"> | <div class="require_fulfill"> | ||
<div class="requirement"> | <div class="requirement"> | ||
| - | <img src="https://static.igem.org/mediawiki/2012/4/41/USTC-Software-check.png" alt="Checked" width="30px" height="30px" / | + | |
| - | + | <p class="requirement"><img src="https://static.igem.org/mediawiki/2012/4/41/USTC-Software-check.png" alt="Checked" width="30px" height="30px" />Present a Poster and Talk at the iGEM Jamboree.</p> | |
</div> | </div> | ||
<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> | <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"> | <div class="require_fulfill"> | ||
<div class="requirement"> | <div class="requirement"> | ||
| - | <img src="https://static.igem.org/mediawiki/2012/4/41/USTC-Software-check.png" alt="Checked" width="30px" height="30px" / | + | |
| - | + | <p class="requirement"><img src="https://static.igem.org/mediawiki/2012/4/41/USTC-Software-check.png" alt="Checked" width="30px" height="30px" />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).</p> | |
</div> | </div> | ||
<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 REBORN (https://github.com/igemsoftware/USTC-Software_2012) and a Clotho App that finds all regulation relationships in E. coli K-12 called RegulonLib (https://github.com/igemsoftware/USTC-Software-Clotho-App_2012). The first tool, REBORN, uses BioBrick standard biological parts to automatically rebuild the biological systems. And the second tool, RegulonLib, helps find regulation relationships based on standard biological parts and the regulation information available on Regulon Databank. Therefore, we have fulfilled this requirement by developing and making available two software tools based on BioBrick standard biological parts in The Registry of Software Tools.</p> | <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 REBORN (https://github.com/igemsoftware/USTC-Software_2012) and a Clotho App that finds all regulation relationships in E. coli K-12 called RegulonLib (https://github.com/igemsoftware/USTC-Software-Clotho-App_2012). The first tool, REBORN, uses BioBrick standard biological parts to automatically rebuild the biological systems. And the second tool, RegulonLib, helps find regulation relationships based on standard biological parts and the regulation information available on Regulon Databank. Therefore, we have fulfilled this requirement by developing and making available two software tools based on BioBrick standard biological parts in The Registry of Software Tools.</p> | ||
Revision as of 13:34, 24 October 2012
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.
In our presentation, we clearly declared that USTC-China has used our software RegulonLib, and how this software helped them designed their circuits.
Outline and detail how your project effects Human Practice in Synthetic Biology.
In the safety section on our wiki(https://2012.igem.org/Team:USTC-Software/hp.html#safety_wrapper), we outlined our suggestions on safety issues in the future.
In place of developing a new standard, a team may instead use SBOL in its software documentation.
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 repository(https://github.com/igemsoftware/USTC-Software_2012/tree/master/executables).
Silver Medal
Provide a detailed, draft specification for the next version of your software tool
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 Wiki.(https://github.com/igemsoftware/USTC-Software_2012)
Provide a second, distinct (yet complementary) software tools project.
As said above, we made a second, distinct software called RegulonLib in the Registry of Software Tools (https://github.com/igemsoftware/USTC-Software-Clotho-App_2012), it also can be seen in our wiki(https://2012.igem.org/Team:USTC-Software/software.html#clotho_group)
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.
We provide User Manual link available on the bottom of software wiki page(https://2012.igem.org/Team:USTC-Software/software.html), which contains very detailed instruction for how to use our software. In addition, in the repository of our software, we also provide instruction on all to compile and use our software(https://github.com/igemsoftware/USTC-Software_2012).
Bronze Medal
Register the team, have a great summer, and have fun attending the Jamboree.
It can be seen in Team Information page(https://igem.org/Team.cgi?id=742) that we have successfully registered.
Create and share a description of the team's project via the iGEM wiki.
This can be seen in the project page of our wiki(https://2012.igem.org/Team:USTC-Software/project.html#project_intro).
Present a Poster and Talk at the iGEM Jamboree.
Download our Asia Jamboree presentation and poster.
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).
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 REBORN (https://github.com/igemsoftware/USTC-Software_2012) and a Clotho App that finds all regulation relationships in E. coli K-12 called RegulonLib (https://github.com/igemsoftware/USTC-Software-Clotho-App_2012). The first tool, REBORN, uses BioBrick standard biological parts to automatically rebuild the biological systems. And the second tool, RegulonLib, helps find regulation relationships based on standard biological parts and the regulation information available on Regulon Databank. Therefore, we have fulfilled this requirement by developing and making available two software tools based on BioBrick standard biological parts in The Registry of Software Tools.
