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InstitutionInstitute of Systems Biology Ltd.
Principal investigator Fedor Kolpakov

Email:Fedor Kolpakov

Country Russia
Beneficiary NumberP25
About usInstitute of Systems Biology, Ltd (ISB), Novosibirsk, Russia was founded in 2005 as a private

software company with the focus on systems biology and bioinformatics with the flagman product: BioUML workbench. The main focus of ISB research is microarray analysis, modelling and simulation of complex biological systems, biological data integration and visualisation. ISB was founded by a group of scientists lead by Fedor Kolpakov, one of the leader scientists in the field of systems biology. Several software packages were designed by Fedor Kolpakov: computer system MGL – Molecular Genetics Language - for database search, visualisation, and analysis of regulatory genomic sequences; computer system GeneNet for formal description and visualisation of gene networks; TRRD viewer – Java applet for visualisation of TRRD database content. He also participated in development of computer system FunSite for analysis of gene regulatory regions; computer system GeneExpress for study eukaryotic gene expression. Prior founding ISB this group of scientists has been involved in long standing cooperation with Russian and European scientists and organisations in the field of bioinformatics and systems biology. The main partners were: Biobase GmbH (Germany), Institute of Biomedical Technologies (Italy), Institute of Biomedical Chemistry (Moscow, Russia), Design-Technological Institute of Digital Techniques (Novosibirsk, Russia, Institute of Cytology and Genetics (Novosibirsk, Russia) and software development company First Software Corporation S.A. (trademark DevelopmentOnTheEdge - DOTE). These partners forms a consortium on performing an INTAS grant “INTAS ¹ 03-55-5218 “Building a comprehensive model of mammalian cellcycle regulatory network in normal and pathological states to predict potential anticancer pharmacological agents for key target molecules.”(2004-2007). ISB has built a powerful system biology platform by utilizing top technologies of software design, computational simulations and database development. One example of such technology is BeanExplorer™ which was developed by DOTE and was utilised by ISB team for designing systems biology software BioUML, specialised databases Biopath and Cyclonet. Software TRANSPLORERTM, developed jointly with BIOBASE (Germany), is also

made with use of BeanExplorer™ technology.
ContributionsThe ISB software packages (e.g. BioUML) will play in important role in the formal description

and visual modelling of the various biochemical pathways that will be integrated in LipidomicNet Knowledgebase. ISB thus contributes the necessary tools to allow efficient and

accurate capture and representation of the knowledge assembled in the project.
Member of TaskforcesTask Force I, Task Force VIII, and Task Force IX
Member of WorkpackagesWP7

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