Team:USTC-Software

From 2012.igem.org

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<p/>The project starts from using experimental data to generate proper ordinary differential equations (ODEs) that describe the behavior of the given data. With ODEs, we can abstract the possible GRNs and use the Parts available in registry to generate plasmid models that can be used in experiments. In this way, we combine mathematics, biology and experiments, the three main areas supporting a complete iGEM project, in a single software.  
<p/>The project starts from using experimental data to generate proper ordinary differential equations (ODEs) that describe the behavior of the given data. With ODEs, we can abstract the possible GRNs and use the Parts available in registry to generate plasmid models that can be used in experiments. In this way, we combine mathematics, biology and experiments, the three main areas supporting a complete iGEM project, in a single software.  
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<div id="safety_title">Safety</div>
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<p>This century saw the increasing popularity of synthetic biology, which is a combination of biology, chemistry, physics, mathematics, computer science, etc. Greater importance comes with greater concern about the safety and security issues. As a software team, we are not facing the same issues that may caused by bacteria, chemicals and contaminating materials. Still, we are concerned with the possibility of safety problems maybe in or caused our project. We have listed the answers to the safety questions as follows.</p>
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<p class="question">1.Q: Would any of your project ideas raise safety issues in terms of : </p>
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<p class="question">Researcher safety,</p>
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<p class="question">Public safety, or</p>
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<p class="question">Environmental safety?</p>
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<p class="answer">A: No. Our project serves to help researchers design the feasible biological circuits with certain behavior, and thus relieve them from heavy experimental work in the lab. And any parts that we suggest are coming from natural E. Coli that have been fully sequenced and understood. So plans generated from our software simulate the behavior researchers want with things that can be found in nature. Therefore, our project will not raise safety issues in terms of researchers, public and environments.</p>
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<p class="question">2.Q: Do any of the new BioBrick parts (or devices) that you made this year raise any safety issues? If yes,</p>
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<p class="question">did you document these issues in the Registry?</p>
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<p class="question">how did you manage to handle the safety issue?</p>
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<p class="question">How could other teams learn from your experience?</p>
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<p class="answer">A: No. As a software team, we will not submit any BioBrick parts or devices. The parts we use in this project encodes non-hazardous genes and the data are from the registry and other databases that are widely recognized.</p>
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<p class="question">3.Q: Is there a local biosafety group, committee, or review board at your institution?</p>
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<p class="question">If yes, what does your local biosafety group think about your project?</p>
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<p class="question">If no, which specific biosafety rules or guidelines do you have to consider in your country?</p>
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<p class="answer">A: Yes. The project in under the instruction of School of Life Sciences in University of Science and Technology of China. And with the supervision of our instructors and advisors, we are sure that our software development project will not raise any kind of issues in terms of researcher safety, public safety and environmental safety.</p>
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<p class="question">4.Q: Do you have any other ideas how to deal with safety issues that could be useful for future iGEM competitions? How could parts, devices and systems be made even safer through biosafety engineering?</p>
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<p class="answer">A: Yes. (1) We suggest the registry of standard biological parts should have a dedicated safety page of every part to ensure that users would not raise any safety issue when using them. (2) In addition to safety usage of single part, a database should be setup to store the possible safety issue when using several parts together. (3) With the safety page and database, team of the software development track can write softwares that help researchers search safety issues that may be caused by their experiments.</p>
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Revision as of 10:29, 7 September 2012

Project Description

Project Description
USTC-Software 2012

This summer, USTC-Software team is going to combine experiment data, genetic circuits and mathematical models into a single software, one that not only enables us to better understand Genetic Regulatory Networks (GRNs), but also provide researchers with complete workflows.

Genetic Regulatory Network (GRN) has been a major subject in recent researches of synthetic biology, and the modulation of a GRN gives rise to a variety of exciting works among iGEM programs as well as softwares assisting synthetic biology researches. Traditionally, researches of GRNs have been focused on either connecting GRNs with real parts on a plasmid or with experimental data, but complete work that combines the three factors have not been paid enough attention to. Here we propose a project that aims to fully connect them with a software that enables us to study GRNs in a much more efficient way.

The project starts from using experimental data to generate proper ordinary differential equations (ODEs) that describe the behavior of the given data. With ODEs, we can abstract the possible GRNs and use the Parts available in registry to generate plasmid models that can be used in experiments. In this way, we combine mathematics, biology and experiments, the three main areas supporting a complete iGEM project, in a single software.

Safety

This century saw the increasing popularity of synthetic biology, which is a combination of biology, chemistry, physics, mathematics, computer science, etc. Greater importance comes with greater concern about the safety and security issues. As a software team, we are not facing the same issues that may caused by bacteria, chemicals and contaminating materials. Still, we are concerned with the possibility of safety problems maybe in or caused our project. We have listed the answers to the safety questions as follows.

1.Q: Would any of your project ideas raise safety issues in terms of :

Researcher safety,

Public safety, or

Environmental safety?

A: No. Our project serves to help researchers design the feasible biological circuits with certain behavior, and thus relieve them from heavy experimental work in the lab. And any parts that we suggest are coming from natural E. Coli that have been fully sequenced and understood. So plans generated from our software simulate the behavior researchers want with things that can be found in nature. Therefore, our project will not raise safety issues in terms of researchers, public and environments.

2.Q: Do any of the new BioBrick parts (or devices) that you made this year raise any safety issues? If yes,

did you document these issues in the Registry?

how did you manage to handle the safety issue?

How could other teams learn from your experience?

A: No. As a software team, we will not submit any BioBrick parts or devices. The parts we use in this project encodes non-hazardous genes and the data are from the registry and other databases that are widely recognized.

3.Q: Is there a local biosafety group, committee, or review board at your institution?

If yes, what does your local biosafety group think about your project?

If no, which specific biosafety rules or guidelines do you have to consider in your country?

A: Yes. The project in under the instruction of School of Life Sciences in University of Science and Technology of China. And with the supervision of our instructors and advisors, we are sure that our software development project will not raise any kind of issues in terms of researcher safety, public safety and environmental safety.

4.Q: Do you have any other ideas how to deal with safety issues that could be useful for future iGEM competitions? How could parts, devices and systems be made even safer through biosafety engineering?

A: Yes. (1) We suggest the registry of standard biological parts should have a dedicated safety page of every part to ensure that users would not raise any safety issue when using them. (2) In addition to safety usage of single part, a database should be setup to store the possible safety issue when using several parts together. (3) With the safety page and database, team of the software development track can write softwares that help researchers search safety issues that may be caused by their experiments.

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