Automated manipulation of systems biology models using libSBML within Taverna workflows.

@article{citeulike:2072539, abstract = {SUMMARY: Many data manipulation processes involve the use of programming libraries. These processes may beneficially be automated due to their repeated use. A convenient type of automation is in the form of workflows that also allow such processes to be shared amongst the community. The Taverna workflow system has been extended to enable it to use and invoke Java classes and methods as tasks within Taverna workflows. These classes and methods are selected for use during workflow construction by a Java Doclet application called the API Consumer. The API Consumer generates an XML file that enables Taverna to select a subset of Java classes and methods for use in the composition of Taverna workflows. The ability of Taverna to invoke Java classes and methods is demonstrated by a workflow in which we use libSBML to map gene expression data onto a metabolic pathway represented as an SBML model. AVAILABILITY: Taverna and the API Consumer application can be freely downloaded from http://taverna.sourceforge.net. CONTACT: peter.li@manchester.ac.uk SUPPLEMENTARY INFORMATION: Supplementary material and documentation are available from http://www.mcisb.org/software/taverna/libsbml/index.html.}, address = {School of Chemistry and Manchester Centre for Integrative Systems Biology, Manchester Interdisciplinary Biocentre, University of Manchester, M1 7DN, UK, EMBL European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK, School of Computing Science, University of Manchester, M13 9PL, UK.}, author = {Li, Peter and Oinn, Tom and Soiland, Stian and Kell, Douglas B B. }, citeulike-article-id = {2072539}, doi = {http://dx.doi.org/10.1093/bioinformatics/btm578}, issn = {1460-2059}, journal = {Bioinformatics}, month = {December}, posted-at = {2008-05-03 21:03:41}, priority = {0}, title = {Automated manipulation of systems biology models using libSBML within Taverna workflows.}, url = {http://dx.doi.org/10.1093/bioinformatics/btm578}, year = {2007} }

TY - JOUR ID - citeulike:2072539 L3 - citeulike-article-id:2072539 TI - Automated manipulation of systems biology models using libSBML within Taverna workflows. JF - Bioinformatics AD - School of Chemistry and Manchester Centre for Integrative Systems Biology, Manchester Interdisciplinary Biocentre, University of Manchester, M1 7DN, UK, EMBL European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK, School of Computing Science, University of Manchester, M13 9PL, UK. SN - 1460-2059 N2 - SUMMARY: Many data manipulation processes involve the use of programming libraries. These processes may beneficially be automated due to their repeated use. A convenient type of automation is in the form of workflows that also allow such processes to be shared amongst the community. The Taverna workflow system has been extended to enable it to use and invoke Java classes and methods as tasks within Taverna workflows. These classes and methods are selected for use during workflow construction by a Java Doclet application called the API Consumer. The API Consumer generates an XML file that enables Taverna to select a subset of Java classes and methods for use in the composition of Taverna workflows. The ability of Taverna to invoke Java classes and methods is demonstrated by a workflow in which we use libSBML to map gene expression data onto a metabolic pathway represented as an SBML model. AVAILABILITY: Taverna and the API Consumer application can be freely downloaded from http://taverna.sourceforge.net. CONTACT: peter.li@manchester.ac.uk SUPPLEMENTARY INFORMATION: Supplementary material and documentation are available from http://www.mcisb.org/software/taverna/libsbml/index.html. AU - Li, Peter AU - Oinn, Tom AU - Soiland, Stian AU - Kell, Douglas B PY - 2007/12/01/ UR - http://dx.doi.org/10.1093/bioinformatics/btm578 ER -