Data Sources and Computational Approaches for Generating Models of Gene Regulatory Networks

Abstract

Whole-cell modeling platforms Ontology for modeling multi-scale and incomplete networks An ontology for cellular processes The PATIKA pathway ontology Extracting Models from Pathways Databases Pathway and Dynamic Analysis Tools for GRNs Global network properties Recurring network motifs Identifying pathway channels in networks: extreme pathway analysis Network stability analysis Predicting dynamics & bistability from network structure alone Concluding Remarks 3

From Pathways Databases to Network Models of Switching Behavior

“…Ultimately, these datasets have to be integrated into a framework that facilitates the study of the dynamics arising from networks of physico–chemical interactions orchestrating the physiology of a biological cell. The bioinformatics community is actively responding to this call for integration in terms of frameworks of pathways databases [ 1 , 2 ]. This paper addresses the use of these databases as sources of dynamical models for biological phenomena.…”