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Revision as of 16:37, 17 October 2018
Project
Welcome to CO-RAD!
The complexity of genetic circuits has made it difficult for synthetic biologists to design the artificial
biological systems. In our project, we developed CO-RAD, a Collaborative
Optimization platform with multiple functions including Recommendation,
Analysis and Design. With the help of CO-RAD, users can design genetic circuits easily and cooperate
with remote partners in real time.
More importantly, the search & recommendation system in CO-RAD were developed to
inspire users with some previous projects and optimize their design with evolutionary
algorithm. Moreover, <a href="javascript:void(0)" goto="Simulation-Circuits"> a
novel numerical simulation algorithm </a>
for circuit）applied in CO-RAD was developed to predict the expression level of genetic circuits in no time.
Through in addition, we incorporated self-designed <a href="javascript:void(0)" goto="Validation">
wet-lab validation </a> into
our project to validate the new results designed by our CO-RAD platform. In conclusion, by assisting in
collaboration and inspiration, CO-RAD makes complex biological systems accessible to researchers who want
rapid, intuitive, and high-quality
accomplish their designs. Click here to design in <a href="http://www.sysu-corad.com/">CO-RAD</a> way.
<img src="" />
Background
Groupwork is the bread and butter of biological system & circuit design, due to the complexity of this research
field. In consequence of the complexity of biological systems, genetic circuit design and the limited personal
experience, it is very difficult for individuals to design a viable circuit alone.This raises the demand of
effective collaboration methods. It would be better if the biologists can work face to face, in which way they
can exchange ideas with absolute ease. However, in many cases we can't even make sure everyone works on the
same continent, let alone in the same room, so we need appropriate ways for tele-cooperation. Sadly,
traditional online tools don't satisfy biologists' needs. For example, genetic circuits and experimental
protocols cannot be precisely represented via Google Doc. Local designing software such as SBOLDesigner don't
let scientists edit online cooperatively, which brings down efficiency a lot. Besides, creative ideas and
valuable suggestions are also important in collaboration, which will have a great influence in the final result
of users' co-design.
<img src="" />
Figure 1: Percentage of multientity publications, 2000–2009
<img src="" />
Figure 2: The percentage of multiinstitutional publications in 22 ESI fields
Therefore, we're here to solve the following problems:
- How to make tele-cooperation as convenient as face-to-face collaboration?
- How to encourage users to think of and share more creative ideas while cooperating?
Solution
Help users come up with more creative ideas
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Search & recommendation
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Analysis & simulation
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Guide the design
Search & recommendaion
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Given the experience of previous achievements provides valuable inspiration while cooperating, we
developed this function to help users quickly find the project they need.
Analysis & simulation
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Deeper understanding of the circuit design can help users make more hypothetical opinions. Our software
analyzes circuits and gives values for CG and CAI, and builds mathematical simulation models to predict
expression levels.
Guide the design
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Through an algorithm that simulates evolution, users can get optimal kinetic parameters for circuits,
which can assist users in modifying their circuits to reach the expected behavior.
Solve the inconvenience of remote collaboration and communication
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Real-time collaboration
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Synchronization sketchpad
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SBOL support
Real-time collaboration
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A real-time genetic circuit design platform where multiple users can edit one file at the same time,
just like (and even better than!) working on the same computer.
Synchronization sketchpad
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A tool that simulates pen and paper, users can express their opinions by labeling or drawing during the
communication process.
SBOL support
<img src="
Our system is compatible with SBOL, the most common data format in the field of synthetic biology,
which means circuits edited on other software can be quickly imported into our software without
re-editing.
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