{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,6,1]],"date-time":"2024-06-01T04:39:21Z","timestamp":1717216761003},"reference-count":15,"publisher":"Oxford University Press (OUP)","issue":"17","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: GRN2SBML automatically encodes gene regulatory networks derived from several inference tools in systems biology markup language. Providing a graphical user interface, the networks can be annotated via the simple object access protocol (SOAP)-based application programming interface of BioMart Central Portal and minimum information required in the annotation of models registry. Additionally, we provide an R-package, which processes the output of supported inference algorithms and automatically passes all required parameters to GRN2SBML. Therefore, GRN2SBML closes a gap in the processing pipeline between the inference of gene regulatory networks and their subsequent analysis, visualization and storage.<\/jats:p>\n               <jats:p>Availability: GRN2SBML is freely available under the GNU Public License version 3 and can be downloaded from http:\/\/www.hki-jena.de\/index.php\/0\/2\/490.<\/jats:p>\n               <jats:p>Supplementary information: General information on GRN2SBML, examples and tutorials are available at the tool\u2019s web page.<\/jats:p>\n               <jats:p>Contact: \u00a0Sebastian.Vlaic@hki-jena.de or andraeger@eng.ucsd.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt370","type":"journal-article","created":{"date-parts":[[2013,6,27]],"date-time":"2013-06-27T00:32:39Z","timestamp":1372293159000},"page":"2216-2217","source":"Crossref","is-referenced-by-count":4,"title":["GRN2SBML: automated encoding and annotation of inferred gene regulatory networks complying with SBML"],"prefix":"10.1093","volume":"29","author":[{"given":"Sebastian","family":"Vlaic","sequence":"first","affiliation":[{"name":"1 Leibnitz Institute for Natural Product Research and Infection Biology - Hans-Kn\u00f6ll-Institute, Beutenbergstr. 11a, D-07745 Jena, Germany, 2Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, Sand 1, 72076 T\u00fcbingen, Germany and 3University of California, San Diego, 417 Powell-Focht Bioengineering Hall 9500, Gilman Drive, La Jolla, CA 92093-0412, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bianca","family":"Hoffmann","sequence":"additional","affiliation":[{"name":"1 Leibnitz Institute for Natural Product Research and Infection Biology - Hans-Kn\u00f6ll-Institute, Beutenbergstr. 11a, D-07745 Jena, Germany, 2Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, Sand 1, 72076 T\u00fcbingen, Germany and 3University of California, San Diego, 417 Powell-Focht Bioengineering Hall 9500, Gilman Drive, La Jolla, CA 92093-0412, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Peter","family":"Kupfer","sequence":"additional","affiliation":[{"name":"1 Leibnitz Institute for Natural Product Research and Infection Biology - Hans-Kn\u00f6ll-Institute, Beutenbergstr. 11a, D-07745 Jena, Germany, 2Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, Sand 1, 72076 T\u00fcbingen, Germany and 3University of California, San Diego, 417 Powell-Focht Bioengineering Hall 9500, Gilman Drive, La Jolla, CA 92093-0412, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael","family":"Weber","sequence":"additional","affiliation":[{"name":"1 Leibnitz Institute for Natural Product Research and Infection Biology - Hans-Kn\u00f6ll-Institute, Beutenbergstr. 11a, D-07745 Jena, Germany, 2Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, Sand 1, 72076 T\u00fcbingen, Germany and 3University of California, San Diego, 417 Powell-Focht Bioengineering Hall 9500, Gilman Drive, La Jolla, CA 92093-0412, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andreas","family":"Dr\u00e4ger","sequence":"additional","affiliation":[{"name":"1 Leibnitz Institute for Natural Product Research and Infection Biology - Hans-Kn\u00f6ll-Institute, Beutenbergstr. 11a, D-07745 Jena, Germany, 2Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, Sand 1, 72076 T\u00fcbingen, Germany and 3University of California, San Diego, 417 Powell-Focht Bioengineering Hall 9500, Gilman Drive, La Jolla, CA 92093-0412, USA"},{"name":"1 Leibnitz Institute for Natural Product Research and Infection Biology - Hans-Kn\u00f6ll-Institute, Beutenbergstr. 11a, D-07745 Jena, Germany, 2Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, Sand 1, 72076 T\u00fcbingen, Germany and 3University of California, San Diego, 417 Powell-Focht Bioengineering Hall 9500, Gilman Drive, La Jolla, CA 92093-0412, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2013,6,26]]},"reference":[{"key":"2023012810455593700_btt370-B1","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/75556","article-title":"Gene ontology: tool for the unification of biology. The Gene Ontology Consortium","volume":"25","author":"Ashburner","year":"2000","journal-title":"Nat Genet"},{"key":"2023012810455593700_btt370-B2","article-title":"Qualitative models","author":"Chaouiya","year":"2013"},{"key":"2023012810455593700_btt370-B3","doi-asserted-by":"crossref","first-page":"543","DOI":"10.1038\/msb.2011.77","article-title":"Controlled vocabularies and semantics in systems biology","volume":"7","author":"Courtot","year":"2013","journal-title":"Mol. Syst. Biol."},{"key":"2023012810455593700_btt370-B4","doi-asserted-by":"crossref","first-page":"2167","DOI":"10.1093\/bioinformatics\/btr361","article-title":"JSBML: a flexible Java library for working with SBML","volume":"27","author":"Dr\u00e4ger","year":"2011","journal-title":"Bioinformatics"},{"key":"2023012810455593700_btt370-B5","doi-asserted-by":"crossref","first-page":"1879","DOI":"10.1093\/bioinformatics\/btl195","article-title":"A model diagram layout extension for SBML","volume":"22","author":"Gauges","year":"2006","journal-title":"Bioinformatics"},{"key":"2023012810455593700_btt370-B6","doi-asserted-by":"crossref","first-page":"bar041","DOI":"10.1093\/database\/bar041","article-title":"BioMart Central Portal: an open database network for the biological community","volume":"2011","author":"Guberman","year":"2011","journal-title":"Database"},{"key":"2023012810455593700_btt370-B7","doi-asserted-by":"crossref","first-page":"86","DOI":"10.1016\/j.biosystems.2008.12.004","article-title":"Gene regulatory network inference: data integration in dynamic models-a review","volume":"96","author":"Hecker","year":"2009","journal-title":"Biosystems"},{"key":"2023012810455593700_btt370-B8","doi-asserted-by":"crossref","first-page":"262","DOI":"10.1186\/1471-2105-10-262","article-title":"Integrative modeling of transcriptional regulation in response to antirheumatic therapy","volume":"10","author":"Hecker","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"2023012810455593700_btt370-B9","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":"2023012810455593700_btt370-B10","doi-asserted-by":"crossref","first-page":"D580","DOI":"10.1093\/nar\/gkr1097","article-title":"Identifiers.org and MIRIAM Registry: community resources to provide persistent identification","volume":"40","author":"Juty","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"2023012810455593700_btt370-B15","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1186\/1752-0509-7-55","article-title":"The systems biology simulation core algorithm","volume":"7","author":"Keller","year":"2013","journal-title":"BMC Systems Biology"},{"key":"2023012810455593700_btt370-B11","doi-asserted-by":"crossref","first-page":"1509","DOI":"10.1038\/nbt1156","article-title":"Minimum information requested in the annotation of biochemical models (MIRIAM)","volume":"23","author":"Le Nov\u00e8re","year":"2005","journal-title":"Nat. Biotechnol."},{"key":"2023012810455593700_btt370-B12","doi-asserted-by":"crossref","first-page":"2498","DOI":"10.1101\/gr.1239303","article-title":"Cytoscape: a software environment for integrated models of biomolecular interaction networks","volume":"13","author":"Shannon","year":"2003","journal-title":"Genome Res."},{"key":"2023012810455593700_btt370-B13","doi-asserted-by":"crossref","first-page":"147","DOI":"10.1186\/1752-0509-6-147","article-title":"The extended TILAR approach: a novel tool for dynamic modeling of the transcription factor network regulating the adaption to in vitro cultivation of murine hepatocytes","volume":"6","author":"Vlaic","year":"2012","journal-title":"BMC Syst. Biol."},{"key":"2023012810455593700_btt370-B14","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1752-0509-7-1","article-title":"Inference of dynamical gene-regulatory networks based on time-resolved multi-stimuli multi-experiment data applying NetGenerator V2.0","volume":"7","author":"Weber","year":"2013","journal-title":"BMC Syst. Biol."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/29\/17\/2216\/48888179\/bioinformatics_29_17_2216.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/29\/17\/2216\/48888179\/bioinformatics_29_17_2216.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,28]],"date-time":"2023-01-28T12:31:40Z","timestamp":1674909100000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/29\/17\/2216\/244842"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,6,26]]},"references-count":15,"journal-issue":{"issue":"17","published-print":{"date-parts":[[2013,9,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btt370","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2013,9,1]]},"published":{"date-parts":[[2013,6,26]]}}}