CellDesigner2.5 supports simulation and parameter scan by an integration with SBML ODE Solver. Once you have installed CellDesigner2.5, you can browse and modify existing SBML models, simulate and view the dynamics through an intuitive graphical interface. The graphical notation scheme used in CellDesigner is based on a proposal by Kitano, et al. ("Using process diagrams for the graphical representation of biological networks",Nature Biotechnology 23(8), 961 - 966 (2005)).
By using CellDesigner, you can create your model with references to existing databases, simulate and analyze the dynamics.
Running Simulation with Control Panel
The “Control Panel” is designed to assist the users to simulate directly from CellDesigner controlling the amounts and parameters of the Species.
Calling SBML ODE Solver directly from CellDesigner, ControlPanel enables you to specify the details of parameters, changing amount, conducting parameter search, and interactive simulation with intuitive manner.
See also: "Running Simulation with Control Panel" (PDF version)
Database Connection - New Addition
On top of the existing connection to the databases, CellDesigner now support the connection to iHOP, which is a public service provided by the Protein Design Group.
National Center of Biotechnology (CNB), Spain.
- iHOP (Information Hyperlinked over Proteins)