Biopath (BMOND)

1
BioUML integrated platform for building virtual
cell and virtual physiological human
Fedor Kolpakov1,2, Nikita Tolstykh1,2, Elena
Kutumova1,2, Ilya Kiselev1,2,Aleksey Shadrin1,2,
Tagir Valeev1,3, Anna Ryabova1,3 1Institute of
Systems Biology, Novosibirsk, Russia 2Design
Technological Institute of Digital Techniques SB
RAS, Novosibirsk, Russia3A.P. Ershov Institute
of Invormatics Systems SB RAS, Novosibirsk,
Russia Contacts fedor_at_biouml.org
Main features

• Motivation
• Reconstruction of complex biological systems and
  consequent building of virtual cell and virtual
  physiological human requires integrated platform
  that provides
• integration with a wide range of biological
  databases
• integration with omics data
• powerful search capabilities
• decomposition of complex biological systems into
  blocks and modules
• visual modeling, multi-scale modeling, agent
  based modeling
• multi-experiment parameters fitting
• powerful data analyses capabilities
• support of reproducible research
• client-server architecture for team work.

• supports main standards in systems biology  
• SBML - Systems Biology Markup Language. BioUML
  supports SBML Level 1 version 1-2 Level 2
  versions 1-4 Level 3 version 1. BioUML is the
  only simulator that have passed all tests from
  SBML test suite version 2.0  
• SBGN - Systems Biology Graphic Notation. BioUML
  supports Process Diagrams as they are defined by
  SBGN version 1.0.  
• BioPAX - Biological Pathway Exchange. BioUML can
  import data in BioPAX 2.0 format. Imported data
  can be stored as native BioPAX file, SQL or text
  database.  
• PSI-MI - The Proteomics Standards Initiative
  Molecular Interaction XML format.  
• OBO - Ontology Flat File Format. BioUML can
  import ontology in OBO 1.2 format. Imported data
  can be presented as semantic networks.  
• CellML - Cell Markup Language . BioUML can read
  and simulated biochemical models presented in
  CellML 1.0 format.
• supports main biological databases
• catalolgs Ensembl, UniProt, ChEBI, GO
• pathways KEGG, Reactome, EHMN, BioModels,
  TRANSPATH, EndoNet, BMOND
• powerful search possibilities
• full text search (Apache Lucene is used)
• graph search - finds related pathway components
  and presents results as an editable graph
• reports, templates
• different templates for representing data element
  info
• model reports
• Overview
• Reactions
• Parameters

• 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 usage of scripting langauges (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 data and
  analyses methods installed on the server side for
  BioUML clients (workbench and web edition) via
  the Internet.
• BioUML workbench - Java application that can work
  standalone or as "thick" client for BioUML
  server.
• BioUML web edition - "thin" client for BioUML
  server (you just need to start web browser) that
  provides most of functionality of BioUML
  workbench. It uses AJAX and HTML5 ltcanvasgt
  technology for visual modeling and interactive
  data editing.

Mitochondrion module in SBGN notation
Genome browser
Acknowledgements This work was supported by FP6
grant 037590 Net2Drug, FP7 grant 090107
"LipidomicNet" and interdisciplinary project 46
of SB RAS.
Availability http//www.biouml.org
Workflow