Automated manipulation of systems biology models using libSBML within Taverna workflows

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 syst...

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Bibliographic Details
Published in:Bioinformatics Vol. 24; no. 2; pp. 287 - 289
Main Authors: Li, Peter, Oinn, Tom, Soiland, Stian, Kell, Douglas B.
Format: Journal Article
Language:English
Published: Oxford Oxford University Press 15.01.2008
Oxford Publishing Limited (England)
Subjects:
Algorithms
Biological and medical sciences
Computer Simulation
Database Management Systems
Databases, Factual
Fundamental and applied biological sciences. Psychology
General aspects
Information Storage and Retrieval - methods
Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects)
Models, Biological
Software
Systems Biology - methods
User-Computer Interface
Automation
Biology
Models
Method
Bioinformatics
ISSN:1367-4803, 1367-4811, 1460-2059, 1367-4811
Online Access:Get full text
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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
Bibliography:To whom correspondence should be addressed.
istex:EAAF67BE6CCD1FA5E1BD46D3889F0F862C09AADC
ark:/67375/HXZ-7R50BW0W-X
Associate Editor: Chris Stoeckert
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ISSN:1367-4803
1367-4811
1460-2059
1367-4811
DOI:10.1093/bioinformatics/btm578