Team:Berkeley Software

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Revision as of 01:03, 1 August 2009

This is a template page. READ THESE INSTRUCTIONS.

You are provided with this team page template with which to start the iGEM season. You may choose to personalize it to fit your team but keep the same "look." Or you may choose to take your team wiki to a different level and design your own wiki. You can find some examples HERE.

You MUST have a team description page, a project abstract, a complete project description, and a lab notebook. PLEASE keep all of your pages within your teams namespace.

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 along with making the process easier, more standardized, and powerful. Our project attempts to address three key computational needs of 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 [Clotho] based framework.
Integrate formalized workflow capture 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.

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Home	The Team	The Project	Parts Submitted to the Registry	Modeling	Notebook

(Or you can choose different headings. But you must have a team page, a project page, and a notebook page.)

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 As synthetic biology continues to mature, it stands to reason that the computer aided design tools should grow as well along with making the process easier, more standardized, and powerful. Our project attempts to address three key computational needs of 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 [[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.
 # Integrate formalized workflow capture 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'''.