Taverna services for Systems Biology

Contents

Contact

If you have any questions, comments or seek help with our WS or any other resource, please contact us via tav4sb discussion group or directly at tav4sb@mimuw.edu.pl.

Overview

The Taverna services for Systems Biology (Tav4SB) project is a simple grid environment providing a set of Web service (WS) operations, together with bundling them workflows, prepared for the Taverna Workbench. Target application area is the System Biology field, in particular, analysis of kinetic models of biological systems.

Our service supports Systems Biology Markup Language (SBML) format (level 2, version 1 is safe to use). Currently, they include:

  • deterministic SBML ODE Solver (SOSlib; version 1.6) simulations,
  • PRISM (version 4.0.2) model checking of SBML models,
  • Mathematica (version 7.0) data points plotting for visualization of ODE simulations or model checking results and for sampling from probabilistic distributions.

Grid environment is currently deployed on servers of the Computational Biology Group at Faculty of Mathematics, Informatics and Mechanics, University of Warsaw. There are 16 SOSlib workers, 36 PRISM workers (3GB of RAM each) and 1 Mathematica worker. In the near future hardware base will be extended to computational servers in the Bioinformatics Lab at the Mossakowski Medical Research Centre, PAS.

Tav4SB is an open source software project.