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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.

Contents

Tav4SB home

• 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

Acknowledgments/funding

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

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 European Social Fund and state budget.

Tav4SB

Taverna services for(4) Systems Biology

Tav4SB project is a simple grid environment providing 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. Tav4SB is an open source project.

Overview

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 memory each) and 1 Mathematica worker. Hardware base will be extended to the computational cluster maintained by the Center of Excellence BioExploratorium and, in the near future, to servers of the Bioinformatics Lab at Mossakowski Medical Research Centre, PAS.

Client installation

Taverna Workbench client is just one option to use the Tav4SB WS operations (see the docs in BioCatalogue); for example, you can use WSs directly in Python or, virtually, any other programming language of your choice. However, to run exemplary experiments you'll need the Taverna Workbench client, so if you want to do that:

1. Download and install or unpack the most recent Taverna Workbench client (at least the 2.3.0 version).
   Note: for Tav4SB WS operations and for most of the provided workflows you can find the Taverna Workbench 1 version (in SCUFL format), if you prefer, but beware - those have more bugs and may be not up to date.
2. If you're unfamiliar with the Taverna Workbench, please, first look through Taverna docs - the Quick start guide should be fine for the beginning.
3. (optional) For some of the workflows to work you will need additional Java libraries, available as JARs. You can download them all now and unpack them to a Taverna's library folder, or you can copy selected libraries later, when and if needed.

That's it! You're ready to run our exemplary experiments. Don't forget to check out a comprehensive list of available resources.

Exemplary experiments

Note: when running workflows ignore Taverna 2 workflow validation warnings, i.e. when asked if to proceed despite warnings, choose "Yes".

1. Simulate SBML-derived ODEs
2. Probabilistic model checking (PMC) of SBML stochastic model
3. Multi-parameter sensitivity analysis (MPSA) of a deterministic and stochastic SBML models.

Resources

1. Web service

   WSDL file is located at

   http://bioputer.mimuw.edu.pl/tav4sb/services/wsdl
               

   Tav4SB WS API is fully-documented at BioCatalogue, a curated catalogue of life sciences Web services. See also Web service operations wrappers and exemplary experiments workflows for docs and examples on how to use the Tav4SB WS API from the Taverna Workbench.

2. Workflows

   • WS operations wrappers

     • odeSolver @{localhost, myExperiment};
     • prism @{localhost, myExperiment};
     • asyncPrism @{localhost, myExperiment};
     • sbml2Prism @{localhost, myExperiment};
     • mathPlot @{localhost, myExperiment};
     • sampleDistribution @{localhost, myExperiment};
     • sampleParams @{localhost };
     • calcSensitivity @{localhost };

   • Exemplary experiments

     • Simulate SBML-derived ODEs workflow @{localhost, myExperiment};
     • Probabilistic model checking of SBML stochastic model workflow: compute @{localhost, myExperiment}, plot @{localhost, myExperiment}.
     • Multi-parameter sensitivity analysis (MPSA) of the deterministic SBML model @{localhost, myExperiment} and stochastic SBML model @{localhost, myExperiment} as well as plotting of the error surface @{localhost, myExperiment}.

   • Helpers

     Workflows folder contains also:
     • nested workflows used in experiments, e.g. workflow converting time points (XML) to list of data series (XML) for plotting function,
     • BeanShell scripts (.bsh files) sourced in Taverna's Beanshell processors, e.g. script setting parameters values in SBML with help of the JSBML library.
     • XSLT files used by the Taverna's local Transform XSL processor.

3. Models

   • The enzymatic reaction deterministic model (SBML) with names and parameters values from the Cho et al. (2003) paper;
   • stochastic version of the enzymatic reaction model (SBML), together with the additional PRISM reward and PRISM formula for the translated model version.

4. JAR libraries

   Some of the BeanShell scripts require additional Java libraries to be copied to a Taverna's library folder. Currently we use:
   • JSBML 0.8-b2 @{localhost, SourceForge} for client-side manipulation of the SBML models.
   You can download them in a zipped pack.

Source code

Source code is available under the GNU AGPL license.

Release package

Currently, no source code repository is available, you can only download the latest release package:

Tav4SB 0.2.2 @{localhost}

Old releases:

• Tav4SB 0.2.1 @{localhost};
  In case you can't find it, here's also a source code for the version 3.3.1 of PRISM available under the GNU GPLv2 license.
• Tav4SB 0.2 @{localhost};

Release notes

Release notes are available in the recent release. You can also find them here.

Installation instructions

Installation instructions are available in the recent release. You can also find them here.

Citing

If you want to refer to this work, use the following citation:

1. Rybiński, M. et al., 2012, Tav4SB: integrating tools for analysis of kinetic models of biological systems, BMC Systems Biology, 6(1), p.25.

   If you want to read this article, for now, we recommend our preprint. The provisional PDF published at the journal's site contains many formatting bugs, mainly in equations.

Other Tav4SB-related articles are:

1. Rybiński, M. et al., 2011, Tav4SB: grid environment for analysis of kinetic models of biological systems, ISBRA 2011 Short Abstracts, pp. 92-95.

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