Synthetic Biology:ToolsWishlist

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This is a quick dump. I will pretty it up soon.
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This page discusses some ideas for software tools that might be useful to synthetic biologists. Feel free to contribute.
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Tools ought to be designed like an extensible integrated development environment ([http://en.wikipedia.org/wiki/Integrated_development_environment IDE]) such as [http://www.eclipse.org Eclipse]. Usability should be a primary design gaol. The tools should make work more productive for synthetic biologists from a variety of backgrounds. Tools should work together, sharing a common representation for biological parts, devices, systems, and strains. New functionality ought to be easy to add via a plug-in API, and should be able to take advantage of a common framework for displaying and manipulating DNA sequences, parts, devices, systems, and strains.
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From the beginning tools should be designed as a usable [http://en.wikipedia.org/wiki/Integrated_development_environment IDE] (Integrated Development Environment) like Eclipse or NetBeans. Should be accessible to users with a variety of backgrounds. Tools (or subtools) should work together, seamlessly sharing a common representation for parts, devices, systems, and strains. New functionality should be easy to add via a plug-in interface, and should be able to take advantage of a common framework for displaying and manipulating DNA sequences, parts, devices, systems, and strains.
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==Specific tools==
==Specific tools==

Revision as of 19:10, 22 February 2008

This page discusses some ideas for software tools that might be useful to synthetic biologists. Feel free to contribute.

Tools ought to be designed like an extensible integrated development environment (IDE) such as Eclipse. Usability should be a primary design gaol. The tools should make work more productive for synthetic biologists from a variety of backgrounds. Tools should work together, sharing a common representation for biological parts, devices, systems, and strains. New functionality ought to be easy to add via a plug-in API, and should be able to take advantage of a common framework for displaying and manipulating DNA sequences, parts, devices, systems, and strains.

Contents

Specific tools

Project management tool

Design tool

Assembly tool

Simulation tool

Personal tools