Celldesigner: A Modeling Tool for Biochemical Networks

Akira Funahashi, Yukiko Matsuoka, Akiya Jouraku, Hiroaki Kitano, Norihiro Kikuchi
2006 Proceedings of the 2006 Winter Simulation Conference  
Understanding of logic and dynamics of gene-regulatory and biochemical networks is a major challenge of systems biology. To facilitate this research topic, we have developed CellDesigner, a modeling tool of gene-regulatory and biochemical networks. CellDesigner supports users to easily create such networks using solidly defined and comprehensive graphical representation (SBGN: Systems Biology Graphical Notation). CellDesigner is SBML compliant, and is SBW-enabled software so that it can
more » ... xport SBML described documents and can integrate with other SBW-enabled simulation/analysis software packages. CellDesigner also supports simulation and parameter search, which is supported by integration with SBML ODE Solver, enabling us to simulate through our sophisticated graphical user interface. We could also browse and modify existing SBML models with references to existing databases. CellDesigner is implemented in Java, thus it runs on various platforms such as Windows, Linux, and MacOS X. CellDesigner is freely available via the Web.
doi:10.1109/wsc.2006.322946 dblp:conf/wsc/FunahashiMJKK06 fatcat:j7xm46qjlzhxndwfxmos5zjue4