Sunday, October 12, 2008


Welcome to the TinkerCell Blog.

TinkerCell is a free and open-source project for Synthetic Biology. The intent behind TinkerCell is to make it into a community-driven project. Adding new functionalities to TinkerCell is kept very simple for this reason. 

TinkerCell is designed to serve as a visual interface that brings together information from databases and analyses programs written in C (or C based languages like Python, Ruby, R, etc.). This is how it is achieved:
  1. All items in TinkerCell have "data" associated with them. For example, a binding reaction will have the dissociation constant, or a ribosome binding site will have some sort of "efficiency" value. The list of attributes for each item is customizable. If a database contains information such as these, then TinkerCell models can be linked with the database(s) in order to fill all the details of the model.
  2. TinkerCell provides a list of functions that allow C programs to directly interact with TinkerCell, thus allowing existing powerful packages such numerical analyses or linear algebra libraries to be directly incorporated into TinkerCell. This also benefits from the speed of C programs. Since languages such as Python can be embedded in C, such C-based programs can also be used to add functions to TinkerCell
  3. Users can construct networks and use the C programs to analyze their network through the visual interface. 

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