Team:Berkeley Software

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As synthetic biology continues to mature, it stands to reason that the computer aided design tools should grow as well thus making the design process easier, standardized, collaborative, and powerful. Our project attempts to address three key computational needs in the synthetic biology community:
As synthetic biology continues to mature, it stands to reason that the computer aided design tools should grow as well thus making the design process easier, standardized, collaborative, and 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.
# 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.
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# Integrate formalized workflow capture programs with synthetic biology assembly protocols. This is accomplished by extending the [https://kepler-project.org '''Kepler Workflow Management System'''].
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# Integrate formalized workflow design programs with synthetic biology assembly protocols. This is accomplished by extending the [https://kepler-project.org '''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'''.
# 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'''.
|[[Image:Team.png|right|frame|Your team picture]]
|[[Image:Team.png|right|frame|Your team picture]]

Revision as of 01:13, 1 August 2009


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Welcome to the UC Berkeley computational iGEM team wiki.
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As synthetic biology continues to mature, it stands to reason that the computer aided design tools should grow as well thus making the design process easier, standardized, collaborative, and powerful. Our project attempts to address three key computational needs in the synthetic biology community:

  1. 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.
  2. Integrate formalized workflow design programs with synthetic biology assembly protocols. This is accomplished by extending the Kepler Workflow Management System.
  3. 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.
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