The ERATO Systems Biology Workbench

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The ERATO Systems Biology Workbench
Hamid Bolouri ERATO Kitano Systems Biology
Project California Institute of Technology
University of Hertfordshire, UK Project PIs
Hiroaki Kitano and John Doyle Software
development team Andrew Finney, Michael Hucka,
Herbert Sauro Collaborators Adam Arkin
(BioSpice), Dennis Bray (StochSim), Igor Goryanin
(DBsolve), Les Loew (VirtualCell), Pedro Mendes
(Gepasi), Masaru Tomita (Ecell) Acknowledgements
Mark Borisuk, Eric Mjolsness, Tau-Mu Yi
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Resource Sharing, Motivation
Our goal provide software infrastructure to
enable sharing of simulation software (current
and future) and collaboration between developers
(and modelers!)
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Example Workbench application bacterial
chemotaxis
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ERATO Systems Biology Workbench driving
principles

• Integrate, dont reinvent!
• integrate existing simulators
• use standard application integration methods
• object oriented, XML, Java and related
  technologies
• Accommodate future tools
• minimize need for ad hoc solutions
• object oriented, XML, Java and related
  technologies
• XML API standards for future contributors
• Make sure contributors benefit
• symmetric plug-in infrastructure
• open source code infrastructure software
• widen user-base, but protect IPR of contributors

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Systems Biology Markup Language SBML

• A common XML format for biochemical networks
• Enables exchange of models between simulators
• Developed in collaboration with
• BioSpice, DBsolve, Gepasi, Jarnac, Ecell,
  StochSim, VirtualCell
• Available for public review since Sept 2000 at
  ftp//ftp.cds.caltech.edu/pub/caltech-erato/sbml/s
  bml.pdf
• Proposed extensions due 2nd Quarter 2001

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Example workbench plug-in modules

• Data filtering and preparation
• e.g. image processing, regression, clustering
• Database support
• e.g. web searching, storage management,
  translators, conflict resolution
• Model description tools
• scripts, languages, schematic tools
• Model preprocessing
• e.g. conserved quantities, redundancy removal
• Maths language / maths description support
• Equation solvers
• e.g. ODE, DAE, PDE, stochastic
• Analysis tools
• e.g. 2/3/4D graphing, bifurcation, MCA
• Optimization and parameter searching

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Example potential plug-ins from DBsolve

• Data filtering and preparation
• regression to implicit and explicit algebraic
  equations
• Database support
• direct data import from WITT, MPW, KEGG
• Model description tools
• stoichiometric matrix
• Model preprocessing
• conserved quantities redundancy removal
• Maths language / maths description support
• maths editor
• Equation solvers
• mixed ODE NAE, LSODE
• Analysis tools
• 2D graphing, bifurcation, continuation, all
  steady states
• Optimization and parameter searching
• Hooke Jeeves, Levenburg-Marquardt

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Systems Biology Workbench - APIs

• APIs provided by the Workbench for simulators
• Will provide access to a spectrum of current
  tools
• Integration into 3rd party simulators will
  require
• SBML output
• One menu item associated with one external
  library call
• Available Q1 2001
• Lower level APIs for optimization, bifurcation,
  time-based simulation and data display will
  follow, Q2 2001
• APIs provided by simulators to plug into
  Workbench
• Existing collaborators
• no API conformance, we will interface to given
  APIs
• The minimum requirement
• Either parse SBML, parse equivalent documented
  format or provide a model construction API
• Output some documented numeric format or
  structure
• Future contributors to SBW
• Standard API for independent development
  available Q2 2001

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Systems Biology Workbench - APIs

• APIs provided by the Workbench for simulators
• Will provide access to a spectrum of current
  tools
• Integration into 3rd party simulators will
  require
• SBML output
• One menu item associated with one external
  library call
• Available Q1 2001
• Lower level APIs for optimization, bifurcation,
  time-based simulation and data display will
  follow, Q2 2001
• APIs provided by simulators to plug into
  Workbench
• Existing collaborators
• no API conformance, we will interface to given
  APIs
• The minimum requirement
• Either parse SBML, parse equivalent documented
  format or provide a model construction API
• Output some documented numeric format or
  structure
• Future contributors to SBW
• Standard API for independent development
  available Q2 2001

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Workbench Development Plan
Task Nov Dec Jan Feb Mar Apr May
Design
GUI and Simulation Engine (Sauro)
Stochastic Simulation (Gibson)
Bifurcation analysis (Goryanin)
Param. optimization (Mendes)
Multi-representation simulation
Linux Port
QA, Install etc