[ description ]

SigPath is a collaborative project of the Institute for Computational Biomedicine and the Department of Physiology and Biophysics at the Weill Medical College of Cornell University, and the Department of Pharmacology & Biological Chemistry at Mount Sinai School of Medicine.

SigPath is an information system designed to support quantitative studies on the signaling pathways and networks of the cell. The current version of SigPath is a prototype that shows how we address the management of the primary types of biochemical information needed to study cellular signaling (protein-protein interactions, protein-small molecule interactions, elementary chemical reactions and enzymatic reactions). We plan to extend this prototype to other types of information, such as mRNA, lipids and sugars, by following the same approach that we used for the current prototype.

A primary emphasis of SigPath is that biochemical information is stored with the details required to make possible quantitative modeling of specific aspects of the cellular machinery. A second emphasis of the system is that SigPath provides user-friendly ways to submit information. For this purpose, we designed and implemented BioWizards which guide the user through the submission process. BioWizards rely extensively on background information imported from primary databases (SwissProt plus mammalian Trembl for proteins, nciopen for small molecules)

A number of advances has been made in the simulation of components of signaling pathways of the cell. Simulation methods are key approaches in obtaining a better description of the specific programs that govern cellular functions. A challenge in appying these methods to integrate biological information into a quantitative model is that current sources of information, such as the primary literature, are not searchable with a computer in a way that would allow the setup of a precise model. We are designing SigPath as an information system where both qualitative and quantitative informations can be stored. This will make possible to add kinetic rate constants to reactions which have been entered previously in SigPath. Return to the project page