Difference between revisions of "Team:UESTC-software/Medal requirements"
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<h2 id="Bronze">Bronze</h2> | <h2 id="Bronze">Bronze</h2> | ||
<p class="img-p" style="font-size:13px;"><img class="small-img" src="https://static.igem.org/mediawiki/igem.org/0/03/Uestc_software-medal1.png" /></p> | <p class="img-p" style="font-size:13px;"><img class="small-img" src="https://static.igem.org/mediawiki/igem.org/0/03/Uestc_software-medal1.png" /></p> | ||
| − | <strong>1. Register for iGEM, have a great summer, and attend the Giant Jamboree.</strong> | + | <strong><B style="color:#3dbec6;">√ &nbps;</B>1. Register for iGEM, have a great summer, and attend the Giant Jamboree.</strong> |
| − | <p> | + | <p>We have signed up for the collegiate category of the iGEM competition as a "software" track team. Certainly we had a great summer for our joint effort and are going to attend the Giant Jamboree.</p> |
| − | <strong>2. Meet all deliverables on the Requirements page (section 3), except those that specifically mention parts. </strong> | + | <strong><B style="color:#3dbec6;">√ &nbps;</B>2. Meet all deliverables on the Requirements page (section 3), except those that specifically mention parts. </strong> |
| − | <p>Our team | + | <p>Our team have completed all the deliverables in time, including team wiki, poster, presentation, project attribution, safety forms and judging forms. We have submitted our codes to iGEM Github Repository by the wiki freezing time. </p> |
| − | <strong>3. Create a page on your team wiki with clear attribution of each aspect of your project. This page must clearly attribute work done by the students and distinguish it from work done by others, including host labs, advisors, instructors, sponsors, professional website designers, artists, and commercial services.</strong> | + | <strong><B style="color:#3dbec6;">√ &nbps;</B>3.Create a page on your team wiki with clear attribution of each aspect of your project. This page must clearly attribute work done by the students and distinguish it from work done by others, including host labs, advisors, instructors, sponsors, professional website designers, artists, and commercial services.</strong> |
| − | <p> | + | <p>Yes, we did. Please see our <a href="https://2016.igem.org/Team:UESTC-software/Attributions" style="color: #3dbec6;>Attributions</a>.</p> |
| − | <strong>4. Document at least one new substantial contribution to the iGEM community that showcases a project made with BioBricks. This contribution should be equivalent in difficulty to making and submitting a BioBrick part.</strong> | + | <strong><B style="color:#3dbec6;">√ &nbps;</B>4. Document at least one new substantial contribution to the iGEM community that showcases a project made with BioBricks. This contribution should be equivalent in difficulty to making and submitting a BioBrick part.</strong> |
| − | <p> | + | <p>Our software is able to provide a BioBrick part with the function for sgRNA expressing cassette which can be used with a CRISPR/Cas9 system to degrade a target DNA fragment. The part is for the DNA file editing purpose and is provided in the SBOL format. The sequence includes a pBAD promoter, target DNA specific sequence, a Cas9 handle sequence and a S. Pyogenes terminator. Please see the <a href="https://2016.igem.org/Team:UESTC-software/Project?id=0" style="color:#3dbec6;">Project</a> page for more details. </p> |
<h2 id="Sliver">Sliver</h2> | <h2 id="Sliver">Sliver</h2> | ||
<p class="img-p"><img class="small-img" src="https://static.igem.org/mediawiki/igem.org/c/cf/Uestc_software-medal2.png" /></p> | <p class="img-p"><img class="small-img" src="https://static.igem.org/mediawiki/igem.org/c/cf/Uestc_software-medal2.png" /></p> | ||
| − | <strong>1. Validate that something you created (art & design, hardware, software, etc) performs its intended function. Provide thorough documentation of this validation on your team wiki. </strong> | + | <strong><B style="color:#3dbec6;">√ &nbps;</B>1. Validate that something you created (art & design, hardware, software, etc) performs its intended function. Provide thorough documentation of this validation on your team wiki. </strong> |
| − | <p> | + | <p>A series of tests have been carried out to validate the usability and robustness of our software. All the initial design goals have been achieved. Please see the <a href="https://2016.igem.org/Team:UESTC-software/Proof" style="color:#3dbec6;">Proof</a> page for details.</p> |
| − | <strong>2. Convince the judges you have helped any registered iGEM team from high school, a different track, another university, or another institution in a significant way by, for example, mentoring a new team, characterizing a part, debugging a construct, modeling/simulating their system or helping validate a software/hardware solution to a synbio problem | + | <strong><B style="color:#3dbec6;">√ &nbps;</B>2. Convince the judges you have helped any registered iGEM team from high school, a different track, another university, or another institution in a significant way by, for example, mentoring a new team, characterizing a part, debugging a construct, modeling/simulating their system or helping validate a software/hardware solution to a synbio problem.</strong> |
| − | <p> | + | <p>We interacted with five other iGEM teams in a variety of activities! Our key contributions to the research of other teams are as follows. </p> |
| − | <ul> | + | <ul> |
| − | <li>(1) | + | <li>(1) In collaboration with TMMU_China, we helped them build <a href="http://bio101.uestc.edu.cn/tmmu/" style="color:#3dbec6;">“Protein Calculator”</a>, a web app to predict the experiment result based on their modeling method. The web app cut enormous workload for them so that they could focus on their web-lab experiments.</li> |
| − | <li>(2) | + | <li>(2) In collaboration with UESTC-China, we helped them build a tool for analyzing a large amount of experimental data, saving them from the hassle of statistical analysis work.</li> |
| − | < | + | </ul> |
| − | + | <p>Please see the <a href="https://2016.igem.org/Team:UESTC-software/Collaborations" style="color:#3dbec6;">Collaborations</a> page for more details. </p> | |
| − | <strong>3. iGEM projects involve important questions beyond the lab bench, for example relating to (but not limited to) ethics, sustainability, social justice, safety, security, and intellectual property rights. Demonstrate how your team has identified, investigated, and addressed one or more of these issues in the context of your project. Your activity could center around education, public engagement, public policy issues, public perception, or other activities (see the human practices hub for more information and examples of previous teams | + | <strong><B style="color:#3dbec6;">√ &nbps;</B>3. iGEM projects involve important questions beyond the lab bench, for example relating to (but not limited to) ethics, sustainability, social justice, safety, security, and intellectual property rights. Demonstrate how your team has identified, investigated, and addressed one or more of these issues in the context of your project. Your activity could center around education, public engagement, public policy issues, public perception, or other activities (see the human practices hub for more information and examples of previous teams's exemplary work).</strong> |
| − | < | + | <ul> |
| − | + | <li>(1) We developed an edutainment video game, Bio2048, for young children to learn biological hierarch concepts. </li> | |
| + | <li>(2) We gave a popular science lecture to students from Puyang Middle School to promote their interests in the science behind DNA information storage technology and synthetic biology in general.</li> | ||
| + | <li>(3) We organized an open-lab day event for primary school students. Seventeen families attend the event to discuss the DNA information storage technology and other aspects of synthetic biology.</li> | ||
| + | <li>(4) On the 60<sup>th</sup> anniversary of our university, we presented a poster on our project to hundreds of students, alumni and guests. </li> | ||
| + | <li>(5) We carried out street interviews, poster presentations, Sina microblog platform and other activities to promote the public’s awareness on synthetic biology. </li> | ||
| + | </ul> | ||
| + | <p>Please see the <a href="https://2016.igem.org/Team:UESTC-software/HP/Silver" style="color:#3dbec6;">Human Practices</a> page for more details.</p> | ||
<h2 id="GOLD">GOLD</h2> | <h2 id="GOLD">GOLD</h2> | ||
<p class="img-p"><img class="small-img" src="https://static.igem.org/mediawiki/igem.org/9/93/Uestc_software-medal3.png" /></p> | <p class="img-p"><img class="small-img" src="https://static.igem.org/mediawiki/igem.org/9/93/Uestc_software-medal3.png" /></p> | ||
| − | <strong>1. Expand on your silver medal activity by demonstrating how you have integrated the investigated issues into the design and/or execution of your project.</strong> | + | <strong><B style="color:#3dbec6;">√ &nbps;</B>1. Expand on your silver medal activity by demonstrating how you have integrated the investigated issues into the design and/or execution of your project.</strong> |
| − | <p> | + | <p>We collected feedback from public on the idea of DNA information storage. The comments and advices are vital input to our final design of Bio101. </p> |
| − | <p> | + | <p>For the edutainment video game, Bio2048, was modified according to the feedback from target students, young students and educators. It received 5-star evaluation on the Tencent’s app store.</p> |
| − | < | + | Please see the <a href="https://2016.igem.org/Team:UESTC-software/HP/Gold" style="color:#3dbec6;">Human Practices</a> page for more details.</p> |
| − | + | <strong><B style="color:#3dbec6;">√ &nbps;</B>2. Improve the function OR characterization of an existing iGEM project (that your team did not originally create) and display your achievement on your wiki. </strong> | |
| − | <strong>2. Improve the function OR characterization of an existing iGEM project (that your team did not originally create) and display your achievement on your wiki. </strong> | + | <p>DNA information storage is a promising direction of Synthetic Biology, there were some scientists and iGEM teams that had opened the way for us. One was CUHK’s project<a href="https://2010.igem.org/Team:Hong_Kong-CUHK" style="color:#3dbec6;"> (https://2010.igem.org/Team:Hong_Kong-CUHK )</a>in 2010. Their system aims to store text information into DNA. We appreciate their achievements, but there are some limitations in their solutions.</p> |
| − | <p> | + | <ul> |
| − | < | + | <li> (1) It can only transform text files.</li> |
| − | + | <li> (2) There are too many homopolymers (i.e., repeated consecutive bases or repeated bases fragment, such as AAAAAA or TACTTACTTACT) in the encoded DNA sequences.</li> | |
| − | + | <li> (3) It does not provide an appropriate error correction component in their system. If a small part of the encoded DNA sequences goes wrong, its influence is deadly for the whole system.</li> | |
| − | + | </ul> | |
| − | <p> | + | <p>Our system solved these problems. The comparison between the two projects are given in Table 1. In addition, we proposed a DNA editing protocol based on the CRISPR/Cas9 system.</p> |
| − | <p> | + | <p>Please see the <a href="https://2016.igem.org/Team:UESTC-software/Features" style="color:#3dbec6;">Features </a>page for more details.</p> |
| − | + | ||
| − | + | <strong><B style="color:#3dbec6;">√ &nbps;</B>3.Demonstrate a functional proof of concept of your project (biological materials may not be taken outside the lab).</strong> | |
| − | <strong>3. Demonstrate a functional proof of concept of your project (biological materials may not be taken outside the lab ). | + | <p><a href="http://bio101.uestc.edu.cn/transform/ style="color:#3dbec6;">Bio101 </a>has been tested internally and externally. We and our collaborators carried out a series software tests from its usability and stability and the results were documented in a detailed testing report. The distributions of A, G, C, T and higher-order combinations of the nucleotides are similar and homopolymers are rare. We also use massive data to test limit of homopolymers the max number eleven and the most of the longest competitive bases between eight to ten. To identify fault tolerance capacity, we damage artificially the encoded sequences by deletion, insertion, and replacement. But we can still recover the information successfully. </p> |
| − | <p> | + | <p>In addition, we went through the whole process of DNA information storage. We used our software to encode a file and the DNA sequences were synthesized by a specialized company (General Biosystems Company, Anhui, China). After a few weeks’ storage and cultivation, we extracted the DNA samples and they were sequenced by a specialized company (Qingkezixi Biotechnology Company, Chengdu, China). Finally, Bio101 was used to decode the DNA sequences. As a result, we recovered our original file. </p> |
| − | + | <p>Please see the <a href="https://2016.igem.org/Team:UESTC-software/Proof" style="color:#3dbec6;">Proof</a> page for more details.</p> | |
| − | <p>( | + | <strong><B style="color:#3dbec6;">√ &nbps;</B>4.Bring your prototype or other work to the Giant Jamboree and demonstrate it to iGEMers and judges in your track showcase (biological materials may not be taken outside the lab).</strong> |
| − | <strong>4. Bring your prototype or other work to the Giant Jamboree and demonstrate it to iGEMers and judges in your track showcase (biological materials may not be taken outside the lab).We will | + | <p> We will demonstrate how Bio101 and Bio2048 work at the Giant Jamboree!</p> |
| + | <p>Please see the <a href="https://2016.igem.org/Team:UESTC-software/Demonstrate" style="color:#3dbec6;">Results</a> page for more details.</p> | ||
</div> | </div> | ||
Revision as of 17:11, 19 October 2016
Medal Requirements
Bronze
We have signed up for the collegiate category of the iGEM competition as a "software" track team. Certainly we had a great summer for our joint effort and are going to attend the Giant Jamboree.
√ &nbps;2. Meet all deliverables on the Requirements page (section 3), except those that specifically mention parts.Our team have completed all the deliverables in time, including team wiki, poster, presentation, project attribution, safety forms and judging forms. We have submitted our codes to iGEM Github Repository by the wiki freezing time.
√ &nbps;3.Create a page on your team wiki with clear attribution of each aspect of your project. This page must clearly attribute work done by the students and distinguish it from work done by others, including host labs, advisors, instructors, sponsors, professional website designers, artists, and commercial services.Yes, we did. Please see our √ &nbps;4. Document at least one new substantial contribution to the iGEM community that showcases a project made with BioBricks. This contribution should be equivalent in difficulty to making and submitting a BioBrick part.
Our software is able to provide a BioBrick part with the function for sgRNA expressing cassette which can be used with a CRISPR/Cas9 system to degrade a target DNA fragment. The part is for the DNA file editing purpose and is provided in the SBOL format. The sequence includes a pBAD promoter, target DNA specific sequence, a Cas9 handle sequence and a S. Pyogenes terminator. Please see the Project page for more details. A series of tests have been carried out to validate the usability and robustness of our software. All the initial design goals have been achieved. Please see the Proof page for details. We interacted with five other iGEM teams in a variety of activities! Our key contributions to the research of other teams are as follows. Please see the Collaborations page for more details. Please see the Human Practices page for more details. We collected feedback from public on the idea of DNA information storage. The comments and advices are vital input to our final design of Bio101. For the edutainment video game, Bio2048, was modified according to the feedback from target students, young students and educators. It received 5-star evaluation on the Tencent’s app store.Sliver
GOLD
DNA information storage is a promising direction of Synthetic Biology, there were some scientists and iGEM teams that had opened the way for us. One was CUHK’s project (https://2010.igem.org/Team:Hong_Kong-CUHK )in 2010. Their system aims to store text information into DNA. We appreciate their achievements, but there are some limitations in their solutions.
- (1) It can only transform text files.
- (2) There are too many homopolymers (i.e., repeated consecutive bases or repeated bases fragment, such as AAAAAA or TACTTACTTACT) in the encoded DNA sequences.
- (3) It does not provide an appropriate error correction component in their system. If a small part of the encoded DNA sequences goes wrong, its influence is deadly for the whole system.
Our system solved these problems. The comparison between the two projects are given in Table 1. In addition, we proposed a DNA editing protocol based on the CRISPR/Cas9 system.
Please see the Features page for more details.
√ &nbps;3.Demonstrate a functional proof of concept of your project (biological materials may not be taken outside the lab).Bio101 has been tested internally and externally. We and our collaborators carried out a series software tests from its usability and stability and the results were documented in a detailed testing report. The distributions of A, G, C, T and higher-order combinations of the nucleotides are similar and homopolymers are rare. We also use massive data to test limit of homopolymers the max number eleven and the most of the longest competitive bases between eight to ten. To identify fault tolerance capacity, we damage artificially the encoded sequences by deletion, insertion, and replacement. But we can still recover the information successfully.
In addition, we went through the whole process of DNA information storage. We used our software to encode a file and the DNA sequences were synthesized by a specialized company (General Biosystems Company, Anhui, China). After a few weeks’ storage and cultivation, we extracted the DNA samples and they were sequenced by a specialized company (Qingkezixi Biotechnology Company, Chengdu, China). Finally, Bio101 was used to decode the DNA sequences. As a result, we recovered our original file.
Please see the Proof page for more details.
√ &nbps;4.Bring your prototype or other work to the Giant Jamboree and demonstrate it to iGEMers and judges in your track showcase (biological materials may not be taken outside the lab).We will demonstrate how Bio101 and Bio2048 work at the Giant Jamboree!
Please see the Results page for more details.
CATALOGUE