GeneNet in 2005

The GeneNet system is designed for collection and analysis of the data on gene and metabolic networks, signal transduction pathways and kinetic characteristics of elementary processes. In the past 2 years, the GeneNet structure was considerably improved: (i) the current version of the database is now implemented using ORACLE9i; (ii) the capacities to describe the structure of the protein complexes and the interactions between the units are increased; (iii) two tables with kinetic constants and more detailed descriptions of certain reactions were added; and (iv) a module for kinetic modeling was supplemented. The current SRS release of the GeneNet database contains 37 graphical maps of gene networks, as well as descriptions of 1766 proteins, 1006 genes, 241 small molecules and 3254 relationships between gene network units, and 552 kinetic constants. Information distributed between 16 interlinked tables was obtained by annotating 1980 journal publications. SRS release of the GeneNet database, the graphical viewer and the modeling section are available at http://wwwmgs.bionet.nsc.ru/mgs/gnw/genenet/

Chapter # AN INTEGRATION OF THE DESCRIPTIONS OF GENE NETWORKS AND THEIR MODELS PRESENTED IN SIGMOID (CELLERATOR) AND GENENET

Motivation: The problems that arise when modeling complex molecular genetic systems at the cell level are so large-scale that they require integrated efforts of many research teams. Therefore, it is a topical problem to integrate the technologies applied to description of gene networks and their models developed at the ICG (Russia) and UCI (USA) with the aim to provide a tight cooperation in the field of systems biology. Results: A software for conversion of gene networks and the models of gene network dynamics represented in the GeneNet system into a format suitable for loading to the SIGMOID database and Cellerator system was developed