BioUML integrated platform for building virtual cell and virtual physiological human 0100100010011101 ISB 0100100010011101 ISB Fedor Kolpakov Institute of Systems Biology Laboratory of Bioinformatics, Design Technological Institute of Digital Techniques Novosibirsk, Russia
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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. - PowerPoint PPT Presentation
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BioUML integrated platform for building
virtual cell and virtual physiological human
0100100010011101
ISB0100100010011101
ISB
Fedor Kolpakov
Institute of Systems Biology
Laboratory of Bioinformatics,Design Technological Institute of Digital Techniques
Novosibirsk, Russia
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;
BioUML main features• Supports access to main biological databases:
JavaScript host objects allowsto merge R/Bioconductor and Java/BioUML worlds
Analysis workflow
Composite modelsPoster:
Modular Approach To Modeling Of The Apoptosis Machinery
Agent based modelingPoster:
Agent based modelling – plug-in for BioUML platform
Composite model of apoptosis (286 species, 684 reactions)
Bentele M, 2004
Neumann L, 2010
CD95L module and results of fitting its dynamics to
experimental data
Agent based model of arterial hypertension (blood pressure regulation)
October 10: Tutorial 3: 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
AcknowledgementsPart 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 developers BiologistsNikita Tolstyh Ilya Kiselev Ruslan Sharipov Tagir Valeev Elena Kutumova Ivan YevshinAnna Ryabova Alexey Shadrin