Assembling and exporting a quantitative model

The SigPath prototype has been designed to promote the use of quantitative models to study cell signaling pathways and networks. To support this goal, SigPath provides features that make it possible to generate simple quantitative models from pre-submitted quantitative information. Several modeling environments have been developed and can be used to construct and simulate quantitative models (such as JSIM and Kinetikit). Similarly, a number of databases, knowledge bases and information systems are available to store (mostly qualitative) information about signaling components and pathways. However, to our knowledge, SigPath is the first system that makes possible an efficient transfer of information between a source of cell signaling information and the tools needed to model and simulate the systems described by this information.

The current support for this feature is limited in our prototype. Most notably, SigPath only supports mass-action law and Michaelis-Menten kinetics, in one compartment systems. This excludes the modeling of channels, transporters, receptors that require multiple compartments and specialized kinetic parameters. To support these important signaling components, SigPath will need to be extended with data representations suitable for the qualitative and quantitative description of these components, with BioWizards for information entering, and with enhanced model export features.

Models (and other SigPath entities such as reaction and molecules) can also be exported in XML format.

Assembling and exporting a quantitative model from information stored in SigPath is illustrated in the following tutorials:

Assembling a model

Exporting a model to JSIM

Exporting a model to Kinetikit

Exporting a model in XML format

[Note: To view the animated tutorials you need a Macromedia Flash Player. If your browser does not have a flash player plugin you can download it from the Macromedia web site]