IN SILICO CELL II. INFORMATION SOURCES FOR MODELING ESCHERICHIA COLI METABOLIC PATHWAYS

SUMMARY Motivation: Development of an in silico cell, a computer resource for modeling and analysis of physiological processes is an urgent task of systems biology and computational biology. This field of inquiry demands development of software for accumulation and analysis of information on operation of the cell as an integrated system. Results: We developed three information sources for computer modeling of manifold processes of E. coli: 1) EcoTRRD database designed for description of structure and function of regulatory regions of E. coli genes; 2) EcoGeneNet database was developed for description of metabolic networks in E. coli; 3) EcoKiNET database allows to accumulate the quantitative information about the dynamics on biosynthesis of amino acids, nucleotides, and sugars in E. coli. Availability: The diagrams of E. coli metabolic networks are available through the GeneNet viewer at http://wwwmgs.bionet.nsc.ru/mgs/gnw/genenet/viewer/; the EcoKiNET database is available an authorized access to the web recourse is provided or the data exported into XML files may be granted on the basis of collaboration; the EcoTRRD database is available as a flat-file that could be accessible on the basis of collaboration via kol@bionet.nsc.ru.