Difference between revisions of "Team:SYSU-Software/Description"
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| − | <b>2. Teams are encouraged to “stand on the shoulder of the giants” while not to “re-invent the wheels”, but things goes not so smoothly.</b> Project descriptions are scattered in team wiki, and looking for a design is laborious. Further, different ways of representing designs in wiki makes them hard to understand. Worse still, without standardized repository of genetic design along with the wet-lab protocols, some of the constructs are not reproducible. [Click here for our experience in reproducing a construct in wet-lab.] | + | <b>2. Teams are encouraged to “stand on the shoulder of the giants” while not to “re-invent the wheels”, but things goes not so smoothly.</b> Project descriptions are scattered in team wiki, and looking for a design is laborious. Further, different ways of representing designs in wiki makes them hard to understand. Worse still, without standardized repository of genetic design along with the wet-lab protocols, some of the constructs are not reproducible. [Click <a href="https://2015.igem.org/Team:SYSU-Software/Validation"><b>here</b></a> for our experience in reproducing a construct in wet-lab.] |
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| − | A tool for genetic design that serves to closely connect the two parts mentioned | + | A tool for genetic design that serves to closely connect the two parts mentioned. Users can use the tool to <b>re-design</b> constructs and systems in the repositories, and also to <b>identify problems</b> or <b>improve functions in the constructs</b> presented by other teams in the open platform. |
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| − | The tool should provide an integrated solution to wet-lab: mathematical modeling using experimental results, plasmid design, experiment scheduling and protocol management. | + | The tool should provide an <b>integrated solution to wet-lab</b>: mathematical modeling using experimental results, plasmid design, experiment scheduling and protocol management. |
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| − | Designs that stand the test of time should be able to migrate from the crowdsourcing platform to the repository. | + | Designs that <b>stand the test of time</b> should be able to migrate from the crowdsourcing platform to the repository. |
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Our project consists of two inter-connected parts:<br><br> | Our project consists of two inter-connected parts:<br><br> | ||
| − | “Synbio Hub”: a proof-of-principle platform for collaborative construction and standardized repositories of genetic design. This part is further divided into two modules: CORE Bank, the repository, and Co-development, the crowdsourcing platform for collaborative design.<br><br> | + | <b>“Synbio Hub”</b>: a proof-of-principle platform for collaborative construction and standardized repositories of genetic design. This part is further divided into two modules: <b>CORE Bank</b>, the repository, and <b>Co-development</b>, the crowdsourcing platform for collaborative design.<br><br> |
| − | CORE Design: a well-designed tool for genetic design, mathematical modeling, plasmid design and experiment scheduling with protocol management. | + | <b>CORE Design</b>: a well-designed tool for genetic design, mathematical modeling, plasmid design and experiment scheduling with protocol management. |
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Revision as of 17:12, 17 September 2015
Description
Problems: Our Motivations
Software teams have an inborn connection to wet-lab teams’ needs.
1. Teams are encouraged to work together to tackle problems, but there is no platform that can supports collaborative building of genetic design in the community. Teams might collaborate to design constructs, but their collaborations are usually not open to the public. In fact, some hard nuts (like, complex network behavior) can be tackled with the help of collective intelligence in the Synbio community.
2. Teams are encouraged to “stand on the shoulder of the giants” while not to “re-invent the wheels”, but things goes not so smoothly. Project descriptions are scattered in team wiki, and looking for a design is laborious. Further, different ways of representing designs in wiki makes them hard to understand. Worse still, without standardized repository of genetic design along with the wet-lab protocols, some of the constructs are not reproducible. [Click here for our experience in reproducing a construct in wet-lab.]
3. Teams are busy working on experiments and in need of a integrated solutions to wet-lab, not only genetic design. Wet-lab teams need a better tool to manage their protocol and schedule their experiment, a tool for navigation of parts information in Registry, and more importantly and irreplaceably, a tool for mathematical modeling.
Solutions: Our Goals
A crowdsourcing platform that serves two inter-connected functions, to promote and facilitate communication and collaborations among iGEM teams, and to provide convenience to work on a genetic design, identify problems and characterise and improve the functions, collaboratively.
A standardized and centralized repository of projects of the past and future. This centralized repository could help improve transparency and reproducibility in iGEM by way of standard documentation of constructs and wet-lab protocols.
A tool for genetic design that serves to closely connect the two parts mentioned. Users can use the tool to re-design constructs and systems in the repositories, and also to identify problems or improve functions in the constructs presented by other teams in the open platform.
The tool should provide an integrated solution to wet-lab: mathematical modeling using experimental results, plasmid design, experiment scheduling and protocol management.
Designs that stand the test of time should be able to migrate from the crowdsourcing platform to the repository.
Our project: A glimpse
Our project consists of two inter-connected parts:
“Synbio Hub”: a proof-of-principle platform for collaborative construction and standardized repositories of genetic design. This part is further divided into two modules: CORE Bank, the repository, and Co-development, the crowdsourcing platform for collaborative design.
CORE Design: a well-designed tool for genetic design, mathematical modeling, plasmid design and experiment scheduling with protocol management.
“Synbio Hub”: a proof-of-principle platform for collaborative construction and standardized repositories of genetic design. This part is further divided into two modules: CORE Bank, the repository, and Co-development, the crowdsourcing platform for collaborative design.
CORE Design: a well-designed tool for genetic design, mathematical modeling, plasmid design and experiment scheduling with protocol management.