Team:UC Berkeley Tools

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Revision as of 10:43, 17 October 2008

[http://biocad-server.eecs.berkeley.edu/wiki/index.php/Clotho_Development#Downloads_and_Information The Alpha release is here.]

With >700 available parts and >2000 defined parts in the [http://partsregistry.org/Main_Page MIT Registry of Standard Biological Parts], and doubtless more parts local to the lab, synthetic biologists are now faced with the challenge of organizing, sorting, and editing these parts from an ever-growing collection of DNA. Due to this rapidly expanding collection, synthetic biology is reaching the point at which composite systems are becoming more and more prevalent. Computational tools are becoming increasingly needed to assist biologists to do the job, and it is no secret that many tools are indeed wheeling out into the community to help serve these needs.

Clotho is a toolset designed in a platform-based-design paradigm to consolidate all these tools into one working, integrated toolbox. Clotho is based on a core-and-hub system which manages multiple connections, each connection serving an independent purpose in an almost self-sufficient manner. Examples of connections include sequence viewers/editors, parts database managers, sequence alignment GUIs, and much more. Computer-savvy biologists can create new connections which will then be integrated into Clotho. In this tool-consolidation and customization it is hoped that, in the future, biologists need not look further for a program that provides the answer to their needs.

The Project

Contact Us

For emails regarding any bugs: clothobugs AT googlegroups DOT com

For emails regarding any desired features: clothofeatures AT googlegroups DOT com

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+With >700 available parts and >2000 defined parts in the [http://partsregistry.org/Main_Page MIT Registry of Standard Biological Parts], and doubtless more parts local to the lab, synthetic biologists are now faced with the challenge of organizing, sorting, and editing these parts from an ever-growing collection of DNA. Due to this rapidly expanding collection, synthetic biology is reaching the point at which composite systems are becoming more and more prevalent. Computational tools are becoming increasingly needed to assist biologists to do the job, and it is no secret that many tools are indeed wheeling out into the community to help serve these needs.
+Clotho is a toolset designed in a platform-based-design paradigm to consolidate all these tools into one working, integrated toolbox. Clotho is based on a core-and-hub system which manages multiple connections, each connection serving an independent purpose in an almost self-sufficient manner. Examples of connections include sequence viewers/editors, parts database managers, sequence alignment GUIs, and much more. Computer-savvy biologists can create new connections which will then be integrated into Clotho. In this tool-consolidation and customization it is hoped that, in the future, biologists need not look further for a program that provides the answer to their needs.
 ==The Project==
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-Genomics has reached the stage at which the amount of DNA sequence information in existing databases is quite large. Synthetic biology now is using these databases to catalog sequences according to their functionality and therefore creating standard biological parts which can be used to create large systems.
-As these databases grow, the need for integrated tools that perform complex operations, organize information, and automate regular processes is becoming increasingly obvious. The synthetic biology community could be better-served with the development of flexible tools which not only permit access and modification to that data but also allow one to perform meaningful manipulation and use of that information in an intelligent and efficient way. These tools need to be useful to biologists working in a laboratory environment while leveraging the experience of the larger CAD community.
-This project develops a toolset called "Clotho" which provides a variety of design views and tools to aid biologists to modify existing synthetic biological systems as well as create new ones. These tools differ from current offerings in this area in that they not only provide the needed tools to manipulate designs in one complete system but also provide unique ways in which to visualize the design as well as a number of connections to both local and global part repositories.
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