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Cyclonet


NAR Molecular Biology Database Collection entry number 794
Kolpakov F.1,2, Poroikov V.3, Sharipov R.1,2,4, Kondrakhin Y1,2, Zakharov A.3, Lagunin A.3, Milanesi L.5, and Kel A.6
1Institute of Systems Biology, 15, Detskiy proezd, Novosibirsk, 630090, Russia
2Design Technological Institute of Digital Techniques, Siberian Branch of Rus. Acad. Sci., 6, Institutskaya, Novosibirsk, 630090, Russia
3Institute of Biomedical Chemistry of Rus. Acad. Med. Sci., 10, Pogodinskaya Str., Moscow, 119121, Russia
4Institute of Cytology and Genetics, Siberian Branch of Rus. Acad. Sci., 10, Lavrentyev aven., Novosibirsk, 630090, Russia
5Institute of Biomedical Technologies, 93, Via Fratelli Cervi, Segrate (MI), 20090, Italy
6BIOBASE GmbH, 33, Halchtersche Strasse, Wolfenbuettel, 38304, Germany

Database Description

Computational modelling of mammalian cell cycle regulation is a challenging task, which requires comprehensive knowledge on many interrelated processes in the cell. We have developed a web-based integrated database on cell cycle regulation in mammals in normal and pathological states (Cyclonet database, http://cyclonet.biouml.org/). It integrates data obtained by "omics" sciences and chemoinformatics on the basis of systems biology approach. Cyclonet is a specialized resource, which enables researchers working in the field of anticancer drug discovery to analyze the wealth of currently available information in a systematic way. Cyclonet contains information on relevant genes and molecules; diagrams and models of cell cycle regulation and results of their simulation; microarray data on cell cycle and on various types of cancer, information on drug targets and their ligands, as well as extensive bibliography on modelling of cell cycle and cancer related gene expression data. Cyclonet database is also accessible through BioUML workbench, which allows flexible querying, analyzing and editing the data by means of visual modelling. Cyclonet aims to predict promising anticancer targets and their agents by application of PASS (Prediction of Activity Spectra for Substances).

The main goal of the Cyclonet database is to integrate information from genomics, proteomics, chemoinformatics and systems biology on mammalian cell cycle regulation in normal and pathological states. This will help molecular biologists working in the field of anticancer drug development to analyze systematically all these data and generate experimentally testable hypothesis.
Cyclonet incorporates data on various carcinogenesis related topics, such as: cell cycle control in mammals, cell survival programs (e.g., NF-κB pathway), regulation of nucleosome compactisation and chromatin remodelling in cell cycle, DNA methylation and other epigenetic mechanisms of cell growth and differentiation. Biological pathways, computer models of cell cycle, microarray data coming from studies of cell cycle and analysis of cancer-related materials are also systematically collected in this database [1].
Cyclonet supports discovery of novel drug targets and development of effective anticancer therapies by collecting all available data related to the control of cell cycle in normal and pathological states and providing a system biology platform for knowledge-based anticancer drug discovery.
Novel software technologies were used for the database development:
  • BioUML workbench (http://www.biouml.org, [2]) was used for formal description and visual modelling of biological pathways and processes related to the cell cycle regulation and cancer. It also allows to simulate the described systems behaviour using Java or MATLAB simulation engines;
  • BeanExplorer Enterprise Edition (http://www.beanexplorer.com) was used to develop web interface for Cyclonet database.

Recent Developments

Now we are developing a set of plug-ins in BioUML workbench for visual modelling of integration between the biological pathways and microarray data that will provide: coloring of diagrams for biological pathways to display data on gene expression levels, reconstruction of gene networks and fitting the model parameters in accordance with the microarray data. Also, a new information arising from both "omic"-sciences and chemoinformatics is added periodically to the Cyclonet database, to update its content.

Acknowledgements

This work was supported by INTAS grant no.8470; 03-51-5218, MIUR-FIRB grant no. 8470; RBLA0332RH Laboratory for Interdisciplinary Technologies in Bioinformatics, by European Commission under FP6 - "Life sciences, genomics and biotechnology for health" contract LSHGCT-2004-503568 "COMBIO", and under "Marie Curie research training networks" contract MRTN-CT-2004-512285 "TRANSISTOR" and BIOINFOGRID no. 8470; 026808.

References

1. Kolpakov F., Poroikov V., Sharipov R., Kondrakhin Y., Zakharov A., Lagunin A., Milanesi L. and Kel A. (2007) Cyclonet - an integrated database on cell cycle regulation and carcinogenesis. Nucleic Acids Res. 35: in press
2. Kolpakov,F., Puzanov,M., Koshukov,A. (2006) BioUML: visual modeling, automated code generation and simulation of biological systems. Proceedings of BGRS'2006, v.3, 281-285.


Go to the abstract in the NAR 2007 Database Issue.
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