Automated manipulation of systems biology models using libSBML within Taverna workflows

Area of Science:

• Computational biology
• Bioinformatics
• Systems biology

Background:

• Data manipulation tasks are frequently automated using programming libraries.
• Workflow systems facilitate automation and community sharing of computational processes.

Purpose of the Study:

• To extend the Taverna workflow system for invoking Java classes and methods.
• To enable seamless integration of existing Java code into Taverna workflows.

Main Methods:

• The Taverna workflow system was modified to support Java class and method invocation.
• The API Consumer application, a Java Doclet, selects Java components for workflow integration.
• Selected Java components are stored in an XML file for Taverna's use.

Main Results:

• Taverna can now execute Java code as workflow tasks.
• The API Consumer facilitates the selection and integration of Java libraries.
• A demonstration workflow mapped gene expression data to a metabolic pathway using libSBML.

Conclusions:

• The extended Taverna system effectively integrates Java code for automated data analysis.
• This approach enhances the reusability and shareability of computational methods in bioinformatics.
• The system facilitates complex data analysis tasks, such as mapping gene expression data onto biological pathway models.