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BioUML integrated platform for building virtual cell and virtual physiological human

BioUML integrated platform for building virtual cell and virtual physiological human. Fedor Kolpakov Institute of Systems Biology Laboratory of Bioinformatics, Design Technological Institute of Digital Techniques Novosibirsk, Russia. BioUML platform.

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BioUML integrated platform for building virtual cell and virtual physiological human

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  1. BioUML integrated platform for building virtual cell and virtual physiological human Fedor Kolpakov Institute of Systems BiologyLaboratory of Bioinformatics,Design Technological Institute of Digital TechniquesNovosibirsk, Russia

  2. BioUML platform • BioUML is an open source integrated platform for systems biology that spans the comprehensive range of capabilities including access to databases with experimental data, tools for formalized description, visual modeling and analyses of complex biological systems. • Due to scripts (R, JavaScript) and workflow support it provides powerful possibilities for analyses of high-throughput data. • Plug-in based architecture (Eclipse run time from IBM is used) allows to add new functionality using plug-ins. BioUML platform consists from 3 parts: • BioUML server – provides access to biological databases; • BioUML workbench – standalone application. • BioUML web edition – web interface based on AJAX technology;

  3. BioUMLmain features • Supports access to main biological databases: • catalolgs: Ensembl, UniProt, ChEBI, GO… • pathways: KEGG, Reactome, EHMN, BioModels, SABIO-RK, TRANSPATH, EndoNet, BMOND… • Supports main standards used in systems biology: SBML, SBGN, CellML, BioPAX, OBO, PSI-MI… • database search: • full text search using Lucene engine • graph search • graph layout engine • visual modeling: • simulation engine supports (ODE, DAE, hybrid,1D PDE); • composite models; • agent based modeling; • parameters fitting; • genome browser (supports DAS protocol, tracks import/export); • data analyses and workflows – specialized plug-ins for microarray analysis, integration with R/Bioconductor, JavaScript support, interactive script console.

  4. BioUML workbench

  5. BioUML web edition

  6. BioUML web editiondedicated Amazon EC2 server: http://79.125.109.165/bioumlweb

  7. Text search:universal full text search engine based on Apache Lucene technology

  8. Metaphor: biological systems reconstruction as solitaire (patience) game Desk – BioUML editor Solitaire – biological pathway Cards – biological objects(genes, proteins, lipids, etc.) Pack of cards – different biological databases

  9. Graph layout

  10. Visual modeling

  11. Pane: simulation

  12. Reports (templates)

  13. Parameters fitting

  14. Parameters fitting: main features Experimental data – time courses or steady states expressed as exact or relative values of substance concentrations Different optimization methods for analysis Multi-experiments fitting Constraint optimization Local/global parameters Parameters optimization using java script

  15. Parameters fitting – user interface

  16. Comparison with COPASI(10,000 simulations)

  17. Genome browser

  18. Genome browser:main features • uses AJAX and HTML5 <canvas> technologies • interactive - dragging, semantic zoom • tracks support • Ensembl • DAS-servers • user-loaded BED/GFF/Wiggle files

  19. Data analyses:collaboration & reproducible research

  20. JavaScript host objects allows to merge R/Bioconductor and Java/BioUML worlds R world Java/BioUML world

  21. Analysis workflow

  22. Composite modelsPoster: Modular Approach To Modeling Of The Apoptosis MachineryAgent based modelingPoster:Agent based modelling – plug-in for BioUML platform

  23. Composite model of apoptosis (286 species, 684 reactions)

  24. CD95L moduleand results of fitting its dynamics to experimental data Bentele M, 2004 Neumann L, 2010

  25. Agent based model of arterial hypertension (blood pressure regulation)

  26. October 10: Tutorial3: BioUML – integrated platform for building virtual cell and virtual physiological human • October 12, 16.20-16.40, Parallel session:Fedor Kolpakov: Modular Approach To Modeling Of The Apoptosis Machinery • October 11-12, poster session • BioUML – Integrated Platform for Building Virtual Cell and Virtual Physiological Human • Modular Approach To Modeling Of The Apoptosis Machinery • The Optimization Plug-in For The BioUML Platform • Agent based modelling - plug-in for BioUML platform Numerical Analysis Of The Complex Model Of Human Cardio-Vascular System Using 1D Hemodynamic Model • Stand of geneXplain GmbH company

  27. Acknowledgements Part of this work was partially supported by the grant: European Committee grant №037590 “Net2Drug” European Committee grant №202272 “LipidomicNet” Integration and interdisciplinary grants №16, 91 of SB RAS. BioUML team Software developersBiologists Nikita TolstyhIlya KiselevRuslan Sharipov Tagir ValeevElena Kutumova Ivan Yevshin Anna Ryabova Alexey Shadrin

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