This work is partially supported by the Biocentrum Ochota project (POIG.02.03.00-00-003/09) and was partially supported by the Polish government grant (N N206 356036).

Mikołaj Rybiński is a scholar within Sub-measure 8.2.2 Regional Innovation Strategies, Measure 8.2 Transfer of knowledge, Priority VIII Regional human resources for the economy, Human Capital Operational Programme co-financed by EU and state budget.

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Tav4SB project

Contents

• Overview
• Client installation
• Exemplary experiments
  1. Simulate ODEs
  2. PMC
  3. MPSA
• Resources
  1. Web service
  2. Workflows
  3. Models
  4. JAR libraries
• Source code
  1. Release package
  2. Release notes
  3. Installation instruction
• Citing

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.

Tav4SB is an open source software project.

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