{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,30]],"date-time":"2026-03-30T21:34:15Z","timestamp":1774906455531,"version":"3.50.1"},"reference-count":15,"publisher":"Oxford University Press (OUP)","issue":"2","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2008,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>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.<\/jats:p>\n               <jats:p>Availability: Taverna and the API Consumer application can be freely downloaded from http:\/\/taverna.sourceforge.net<\/jats:p>\n               <jats:p>Contact: \u00a0peter.li@manchester.ac.uk<\/jats:p>\n               <jats:p>Supplementary information: Supplementary data and documentation are available from http:\/\/www.mcisb.org\/software\/taverna\/libsbml\/index.html<\/jats:p>","DOI":"10.1093\/bioinformatics\/btm578","type":"journal-article","created":{"date-parts":[[2007,12,2]],"date-time":"2007-12-02T01:14:36Z","timestamp":1196558076000},"page":"287-289","source":"Crossref","is-referenced-by-count":25,"title":["Automated manipulation of systems biology models using libSBML within Taverna workflows"],"prefix":"10.1093","volume":"24","author":[{"given":"Peter","family":"Li","sequence":"first","affiliation":[{"name":"1 School of Chemistry and Manchester Centre for Integrative Systems Biology, Manchester Interdisciplinary Biocentre, University of Manchester, M1 7DN, 2EMBL European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD and 3School of Computing Science, University of Manchester, M13 9PL, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tom","family":"Oinn","sequence":"additional","affiliation":[{"name":"1 School of Chemistry and Manchester Centre for Integrative Systems Biology, Manchester Interdisciplinary Biocentre, University of Manchester, M1 7DN, 2EMBL European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD and 3School of Computing Science, University of Manchester, M13 9PL, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Stian","family":"Soiland","sequence":"additional","affiliation":[{"name":"1 School of Chemistry and Manchester Centre for Integrative Systems Biology, Manchester Interdisciplinary Biocentre, University of Manchester, M1 7DN, 2EMBL European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD and 3School of Computing Science, University of Manchester, M13 9PL, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Douglas B.","family":"Kell","sequence":"additional","affiliation":[{"name":"1 School of Chemistry and Manchester Centre for Integrative Systems Biology, Manchester Interdisciplinary Biocentre, University of Manchester, M1 7DN, 2EMBL European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD and 3School of Computing Science, University of Manchester, M13 9PL, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2007,12,1]]},"reference":[{"key":"2023020209483761500_B1","doi-asserted-by":"crossref","first-page":"593","DOI":"10.1038\/nrg1922","article-title":"Standards for systems biology","volume":"7","author":"Brazma","year":"2006","journal-title":"Nat. Rev. Genet."},{"key":"2023020209483761500_B2","doi-asserted-by":"crossref","first-page":"W460","DOI":"10.1093\/nar\/gkh476","article-title":"ArrayXPath: mapping and visualizing microarray gene-expression data with integrated biological pathway resources using Scalable Vector Graphics","volume":"32","author":"Chung","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"2023020209483761500_B3","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1038\/ng0502-19","article-title":"GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways","volume":"31","author":"Dahlquist","year":"2002","journal-title":"Nat. Genet."},{"key":"2023020209483761500_B4","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1016\/S1478-5382(03)02370-9","article-title":"CellDesigner: a process diagram editor for gene-regulatory and biochemical networks","volume":"1","author":"Funahashi","year":"2003","journal-title":"BIOSILICO"},{"key":"2023020209483761500_B5","doi-asserted-by":"crossref","first-page":"264","DOI":"10.1186\/1471-2105-6-264","article-title":"maxdLoad2 and maxdBrowse: standards-compliant tools for microarray experimental annotation, data management and dissemination","volume":"6","author":"Hancock","year":"2005","journal-title":"BMC Bioinformatics"},{"key":"2023020209483761500_B6","doi-asserted-by":"crossref","first-page":"524","DOI":"10.1093\/bioinformatics\/btg015","article-title":"The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models","volume":"19","author":"Hucka","year":"2003","journal-title":"Bioinformatics"},{"key":"2023020209483761500_B7","doi-asserted-by":"crossref","first-page":"W729","DOI":"10.1093\/nar\/gkl320","article-title":"Taverna: a tool for building and running workflows of services","volume":"34","author":"Hull","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"2023020209483761500_B8","doi-asserted-by":"crossref","first-page":"873","DOI":"10.1111\/j.1742-4658.2006.05136.x","article-title":"Metabolomics, modelling and machine learning in systems biology: towards an understanding of the languages of cells. The 2005 Theodor B\u00fccher lecture","volume":"273","author":"Kell","year":"2006","journal-title":"FEBS J."},{"key":"2023020209483761500_B9","doi-asserted-by":"crossref","first-page":"1085","DOI":"10.1016\/j.drudis.2006.10.004","article-title":"Systems biology, metabolic modelling and metabolomics in drug discovery and development","volume":"11","author":"Kell","year":"2006","journal-title":"Drug Discov. Today"},{"key":"2023020209483761500_B10","doi-asserted-by":"crossref","first-page":"689","DOI":"10.1080\/15216540701694252","article-title":"The virtual human: towards a global systems biology of multiscale, distributed biochemical network models","volume":"59","author":"Kell","year":"2007","journal-title":"IUBMB Life"},{"key":"2023020209483761500_B11","doi-asserted-by":"crossref","first-page":"3045","DOI":"10.1093\/bioinformatics\/bth361","article-title":"Taverna: a tool for the composition and enactment of bioinformatics workflows","volume":"20","author":"Oinn","year":"2004","journal-title":"Bioinformatics"},{"key":"2023020209483761500_B12","doi-asserted-by":"crossref","first-page":"1067","DOI":"10.1002\/cpe.993","article-title":"Taverna: lessons in creating a workflow environment for the life sciences","volume":"18","author":"Oinn","year":"2006","journal-title":"Concurrency Comput. Pract. Exper."},{"key":"2023020209483761500_B13","doi-asserted-by":"crossref","first-page":"300","DOI":"10.1007\/978-1-84628-757-2_19","article-title":"Taverna\/myGrid: aligning a workflow system with the life sciences community","volume-title":"Workflows for e-Science: Scientific Workflows for Grids","author":"Oinn","year":"2007"},{"key":"2023020209483761500_B14","doi-asserted-by":"crossref","first-page":"493","DOI":"10.1021\/ci025584y","article-title":"The Chemistry Development Kit (CDK): an open-source java library for chemo- and bioinformatics","volume":"43","author":"Steinbeck","year":"2003","journal-title":"J. Chem. Inf. Comput. Sci."},{"key":"2023020209483761500_B15","doi-asserted-by":"crossref","first-page":"857","DOI":"10.1002\/pmic.200600438","article-title":"A review of standards for data exchange within systems biology","volume":"7","author":"Str\u00f6mb\u00e4ck","year":"2007","journal-title":"Proteomics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/24\/2\/287\/49044509\/bioinformatics_24_2_287.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/24\/2\/287\/49044509\/bioinformatics_24_2_287.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T10:27:37Z","timestamp":1675333657000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/24\/2\/287\/228424"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2007,12,1]]},"references-count":15,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2008,1,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btm578","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2008,1,15]]},"published":{"date-parts":[[2007,12,1]]}}}