Difference between revisions of "Team:SYSU-Software/Description"

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        For long designs in synthetic biology has been hindered by the lack of logical methods; on the contrary, many mature and useful principles have been applied to engineering disciplines. These principles are promising guidelines in pushing forward the field of synthetic biology. However, it is hard for synthetic biologists to master both experimental techniques and engineering methods.
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          <h1 class = "juzhong">Description</h1>
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              <h2 class = "juzhong">Problems: Our Motivations</h2>
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              <p class = "wenzi juzhong">Software teams have an inborn connection to wet-lab teams’ needs.</p>
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            Our project aims at realizing the potential of computer-aided design in synthetic biology. According to their needs, users define the functions of a system, and then use our software to find the functional component for assembly. The software makes use of the ordinary differential equations to connect each component, leading step by step to a synthetic system with the defined function.
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                      <b>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.</b> 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.
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            To this end, we base our software on the analysis of existing devices and systems. Utilization of ordinary differential equations helps to resolve the existing design into basic units of different levels (i.e., devices or systems). Now we can endow the original system with new functions using this basic units.
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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.]
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                  <b>3. Teams are busy working on experiments and in need of a integrated solutions to wet-lab, not only genetic design.</b> 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.
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              <h2 class = "juzhong">Solutions: Our Goals</h2>
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                      A <b>crowdsourcing platform</b> that serves two inter-connected functions, to promote and facilitate <b>communication and collaborations</b> among iGEM teams, and to provide convenience to <b>work on a genetic design</b>, <b>identify problems</b> and <b>characterise and improve the functions</b>, collaboratively.
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                      A <b>standardized</b> and <b>centralized</b> 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.
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                      A tool for genetic design that serves to closely connect the two parts mentioned above. 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.
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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.
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                      Designs that stand the test of time should be able to migrate from the crowdsourcing platform to the repository.
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              <h2 class = "juzhong">Our project: A glimpse</h2>
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                      Our project consists of two inter-connected parts:<br><br>
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                      “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>
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                      CORE Design: a well-designed tool for genetic design, mathematical modeling, plasmid design and experiment scheduling with protocol management.
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Revision as of 13:13, 17 September 2015

SYSU-SOFTWARE IGEM 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 above. 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.