Taverna has been successfully applied to a number of bioinformatics problems:
The Manchester Centre for Integrative Systems Biology is in the process of measuring the kinetic and binding constants associated with enzyme reactions in metabolic pathways in the yeast, Saccharomyces cerevisiae. Quantitative models of these metabolic pathways are being integrated with transcriptomic, proteomic and metabolomic data by workflows that have been constructed and enacted using Taverna.
A poster by Peter Li describing the systems biology workflows was presented at the International Conference of Systems Biology 2006 and he has written several publications about the work.
Many of the workflows make use of Systems Biology Markup Language (SBML) as described in the paper Automated manipulation of systems biology models using libSBML within Taverna workflows by Li et al.
An example workflow using SBML is available on myExperiment.
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As part of the PLANET (A Network of European Plant Databases) project, URGI (Unité de Recherche Génomique-Info) developed BioFloWeb.
BioFloWeb is a stand-alone Web application processing Web services. A given user can choose among predefined workflows or define their own with Taverna. BioFloWeb has been demonstrated for retrieval of information about Arabidopsis genes from several European databases.
BioFloWeb makes extensive use of BioMoby services.
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A collaboration between Tom Oinn from the myGrid team and Anders Lanzen, Svenn Helge Grindhaug and Pal Puntervoll from the University of Bergen, Norway, has produced an interactive genome annotation pipeline.
Sequencing, characterising and annotating a genome are the first steps to understanding its function. Important stages in this include gene prediction, comparative genomics and function prediction of genes and gene products. With workflows all of these stages can be automate, requiring little human interaction. However, manual inspection can be required at certain points in the process.
Articles and papers about the success of Taverna for genome annotation are available on-line.
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