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At present time bioinformatics may be considered as one of the most dynamically upcoming discipline in the sphere of biological sciences. Popular expressions “who possesses the information that possesses the world” entirely relate henceforward to scientific researches. The demand on bioinformational products grows steadily, it confirm not only their increasing mass but also the number of companies, playing on this market. It is possible to say that their number grows by leaps and bounds, and does not intend to stop. Our group may be regarded as old resident in this field, because we have been carrying out such kind of work and researches more than five years and have achieved positive success on this field. Besides of software development our Institute is working on database formation and development of electronic encyclopedias.
Encyclopedia of Stem Cells

thumb_new-1In the connection with computer and IT technologies development increasingly more books are moving from the paper to the hard data. It concerns the scientific, technical and juridical literature in the first turn, where serious demands are made not only from content but also from information structuring. Thinking over, any database may become e-book. It should meet at least two requirements for it: firstly, information keeping in database has to be interesting for one or another reader’s category, secondly, its interface should be sufficiently attractive and convenient, and meet a number of special requirements, peculiar to given category of readers. The list of such requirements is own for every defined discipline, and e-books creators should take it into account. Leaning on the experience in the research of complex biochemical systems we have managed to collect detailed lists for some pharmacological and medical directions that allow starting creations of several e-books. Below you can get to know about results of work on one dedicated to stem cells.
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EKMD – Enzyme Kinetic Mechanism Database

EnzBaze_2Everyone, who some time was engaged in the kinetic modeling of biochemical systems, knows that the lion’s share of time takes routine spade-work – search of articles and extraction of useful information from them. In order to develop kinetic model with high prediction power it is necessary not only to describe in detail the mechanism of action for every enzyme in the pathway but also bind the model to the ceiling amount of various kinds of experimental data. Frequently for kinetic model of enzyme work development there is a need to have analyzed several tens of scientific articles, having sifted out the main art of information (up to 80 - 90%). There is no prize for guessing, that it extends time being required for model development, because it should not be forgotten that in the pathway into consideration may be quite a few enzymes. It is essentially to mark out that demand for such information on the bioinformational market is high enough and continues to increase. It connects with the fact that increasingly more scientific groups and laboratories apply kinetic modeling for their researches.
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Stem cells database

It may be appeared that database development is auxiliary and not very important task during e-book creation. However it is far from true. The meaning of database in this project is difficult to overestimate, as exactly thanks to it the interactive connection of all the informational elements is realized, i.e. the processes of search, processing and perception of information are significantly simplified.

Database is defined know-how in the field of stem cells study, as there were no analogical products on the bioinformatics market before. That is why we have created the separate project on the basis of it and continue the process of its filling.
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KMD - Kinetic Models Database

KMD_statAIM OF THE PROJECT: To develop database of automatically generated kinetic models corresponding to all pathways displayed in KEGG database.

RESULTS

  • KMD consisting of about 19000 models has been developed.
  • Rate equations of all models are in accordance to mass action law. All kinetic parameters are in the physiological range.
  • Each model has stable steady state.
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Institute for Systems Biology SPb

Moscow, Leninskie Gory, 1, build.75G, office. 613, Science park, 119992

+7(495)930-8407,   +7(495)930-8407, +7(495)783-8718

insysbio@insysbio.ru   insysbio@insysbio.ru

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