Conference publications

Abstracts

XX conference

KINET – A New web database on kinetics data and parameters for E.coli

Ermak Т.V., Akberdin I.R.¹, Timonov V.S., Khlebodarova T.M.¹, Likhoshvai V.A.¹

Siberian State University of Telecommunications and Infomation Sciences , Novosibirsk, Russia

¹Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia

1 pp. (accepted)

Motivation and Aim: One of the main challenge of the systems biology is a development of in silico cell. The cell is a theoretical platform (fundament) for performance of computational experiments and for verification of generated theoretical hypothesis on basis of the mathematical modeling. To reach this aim it demands development of robust mathematical models describing whole complex gene network of the prokaryote cell’s functioning, for example. In turn, it requires accumulation and analysis of published information and data in web-warehouses on operation of the cell as an integrated system.

Previously, the Kinet database was developed in the ICG SB RAS [1]. The Kinet is a database of kinetics data and parameters of biochemical processes for E.coli. The database accumulates unique published data collected in the Institute over seven years. But the web access to the Kinet was unavailable for wide range of scientists.

Methods and Algorithms: Web application is developing on Java platform using Vaadin toolkit (http://vaadin.com).

Results: To solve the problem with availability to the Kinet we have developed the web application that has user friendly interface and easy access to unique data.

Conclusion: We have presented unique kinetics data of biochemical reactions (conditions of experiments, values of kinetics parameters, concentrations of key metabolites, cell enzymes and other) as the web-source. Researchers from all over the world can decrease time needed for development of mathematical modeling of biochemical processes, analyzing, selecting and other tasks related with kinetics data using the Kinet database. The Kinet will be helpful in carrying out of large-scale in silico studies. Also the database can be useful as information source.

Availability: Available upon request.

Acknowledgements: This study was partially supported by the Scientific school № 5278.2012.4 and Program of the RAS “Molecular and cell biology”….

References:

Khlebodarova T.M et al., Information sources for modeling Escherichia coli metabolic pathways// Proc. of the 5th BGRS International Conference, Vol. 2, pp. 19-24.

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