Biology – Quantitative Biology – Molecular Networks
Scientific paper
2009-07-23
Biology
Quantitative Biology
Molecular Networks
23 pages, 20 figures
Scientific paper
Synthetic biology brings together concepts and techniques from engineering and biology. In this field, computer-aided design (CAD) is necessary in order to bridge the gap between computational modeling and biological data. An application named TinkerCell has been created in order to serve as a CAD tool for synthetic biology. TinkerCell is a visual modeling tool that supports a hierarchy of biological parts. Each part in this hierarchy consists of a set of attributes that define the part, such as sequence or rate constants. Models that are constructed using these parts can be analyzed using various C and Python programs that are hosted by TinkerCell via an extensive C and Python API. TinkerCell supports the notion of a module, which are networks with interfaces. Such modules can be connected to each other, forming larger modular networks. Because TinkerCell associates parameters and equations in a model with their respective part, parts can be loaded from databases along with their parameters and rate equations. The modular network design can be used to exchange modules as well as test the concept of modularity in biological systems. The flexible modeling framework along with the C and Python API allows TinkerCell to serve as a host to numerous third-party algorithms. TinkerCell is a free and open-source project under the Berkeley Software Distribution license. Downloads, documentation, and tutorials are available at www.tinkercell.com.
Bergmann Frank T.
Chandran Deepak
Sauro Herbert M.
No associations
LandOfFree
TinkerCell: Modular CAD Tool for Synthetic Biology does not yet have a rating. At this time, there are no reviews or comments for this scientific paper.
If you have personal experience with TinkerCell: Modular CAD Tool for Synthetic Biology, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and TinkerCell: Modular CAD Tool for Synthetic Biology will most certainly appreciate the feedback.
Profile ID: LFWR-SCP-O-354477