Tav4SB project
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.
Resources
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.
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 (
.bshfiles) 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.
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.
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.