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. This selection is stored as an XML file which enables Taverna to present the subset of the API for use in the composition of 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 a 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 data and documentation are available from http://www.mcisb.org/software/taverna/libsbml/index.html