Cyclonet
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.
Webpage:
http://cyclonet.biouml.org/
Tags:
metabolic and signaling pathways protein-protein interactions
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