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Team:Berkeley Software
From 2009.igem.org
Welcome to the Berkeley Software team's wiki. Our wiki is currently under construction. We apologize for its temporarily disorganized state.
Welcome to the UC Berkeley computational iGEM team wiki.
As synthetic biology continues to mature, it stands to reason that the computer aided design tools should grow as well. If done properly this will make the design process easier, standardized, collaborative, and ultimately much more powerful. Our project attempts to address three key computational needs in the synthetic biology community:
- Create a robust set of application programming interfaces (APIs) which create a common framework so that individual independent software tools can communicate with each other as well as communicate with data repositories. This is accomplished with a completely revamped [http://www.clothocad.com Clotho] based framework.
- Integrate formalized workflow design programs with synthetic biology assembly protocols. This is accomplished by extending the Kepler Workflow Management System.
- Raise the level of abstraction by which designs are specified, shared, and visualized. This is accomplished by the design of a domain specific language called Eugene and a design tool called Spectacles.
In addition to these goals our project really attempts to build an inter-university/industry approach by collaborating with researchers at Stanford, the University of Minnesota, Davidson, Washington, and Microsoft Research India.
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