1 / 32

ERATO Systems Biology Workbench: Driving Collaboration and Simulation

ERATO Systems Biology Workbench aims to facilitate sharing of simulation software and collaboration among developers and modelers. Key features include multistate reactions, optimization, and network visualization. The platform integrates existing simulators and provides a common XML format for biochemical networks. The API offers access to various tools and supports integration with third-party simulators. The software infrastructure utilizes object-oriented, XML, and Java technologies.

sextond
Download Presentation

ERATO Systems Biology Workbench: Driving Collaboration and Simulation

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. 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

  2. Tool 7 Tool 6 Tool 5 Tool 2 Tool 4 Tool 1 Tool 3 Multistate reactions/stochastic Reaction/Diffusion Optimization Bifurcation analysis Visualization of networks Handle large systems Resource Sharing, Motivation Our goal: provide software infrastructure to enable sharing of simulation software (current and future) and collaboration between developers (and modelers!)

  3. Ligand binding Motion +ATT -ATT flagellar motor R +CH 3 MCPs MCPs CW Signal transduction W W P P -CH 3 Motor A A ~ ~ B Y ~ P Z ATP ADP ATP P P B Y i i Example Workbench application: bacterial chemotaxis

  4. Late signal from veg2 A-V model v10, April 4th, 2000 cb MVLbAS LiCl GSK-3 endomes  endomes mes  mes g frizzled mic  mic a2 late signal from ~ 7th cleavage micromeres veg1  veg2 mN nN nb a1 Maternal activator n1 mac / veg2  mic Endo-Mes-TXF Endo-only-TXF Zygotic Apical N Mes-TXF N-dependent-TXF Micromere id. factor Serrate Wnt8 A1 ? X t2 & & & & & OR & & & & OR & OR OTX Endo16 Mes Genes Endo- specific Genes Endo-mes Genes View from the genome, cb=cytoplasmic b, nb=nuclear b, mN=maternal N, nN=nuclear N, MVLbAS=maternal vegetally localised b catenin activating system

  5. ERATO Systems Biology Workbench: driving principles • Integrate, don’t 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

  6. 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/sbml.pdf • Proposed extensions due 2nd Quarter 2001

  7. 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

  8. 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

  9. 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

  10. 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

  11. Workbench Development Plan

More Related