Computer system of modules integration for automatic construction and numerical analysis of molecular genetic systems

I. R. Akberdin ; F. V. Kazantsev ; V. A. Likhoshvai ; S. I. Fadeev ; I. A. Gainova ; V. K. Korolev ; A. E. Medvedev

Sibirskie èlektronnye matematičeskie izvestiâ, Tome 6 (2009), pp. 440-456.

Résumé

At the turn of the 20th and 21th centuries there was such meaningful scientific progress in molecular biology as mapping of the human genome. This event is a start of the new period in development of the life science often called as post genome era. At the same time there were also qualitative changes in computer technology that multiply increase possibilities of computer's technology using for processing and storage of the huge information data. The intensive increased volume of experimental data generating by methods of the modern system biology stimulates a development of computer data bases for information processing and storage from literature and also stimulates a development of software for analysis and studying of complex models from these data base. The existing variety of computer tools solving the system biology tasks and modeling of the molecular genetic systems (MGS) in particular allows us to use the different approaches for solving of the assigned tasks. At the same time there is necessary to face the challenges under selection of the definite software. There are specificity of the model formats in this software and doubling of his functionality in other computer systems. In the judgment of specialists the decision of the compatibility problems of different specialized systems and development of free and open formats on data presentation are key in the achievement of purpose to develop the integrative systems supporting technologies of complex model analysis. We have represented the integrative computer system that oriented on construction and numerical analysis of models describing dynamics of the MGS functioning in pro- and eukaryotes. The system consists from the next program modules: module MGSgenerator and module STEP+. Module MGSgenerator is an intermediate unit in generation process of the mathematical models on basis of the gene networks reconstructed in GeneNet. Module STEP+ allows us to realize the numerical analysis of the model representing by autonomous system of ordinary differential equations. The mathematical model converts from our specialized format SBML in input STEP+ format by MGSgenerator module. We have tested the integrative computer system on basis of the MGS model describing intracellular auxin metabolism in a plant cell.

Détail

Keywords: integrative computer system, gene network, molecular genetic systems, intracellular auxin metabolism in a plant cell.

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