{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,4,13]],"date-time":"2023-04-13T13:33:55Z","timestamp":1681392835697},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"11","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: GetBonNie is a web-based application for building, analyzing and sharing rule-based models encoded in the BioNetGen language (BNGL). Tools accessible within the GetBonNie environment include (i) an applet for drawing graphs that correspond to BNGL code; (ii) a network-generation engine for translating a set of rules into a chemical reaction network; (iii) simulation engines that implement generate-first, on-the-fly and network-free methods for simulating rule-based models; and (iv) a database for sharing models, parameter values, annotations, simulation tasks and results.<\/jats:p>\n               <jats:p>Availability: GetBonNie is free at http:\/\/getbonnie.org.<\/jats:p>\n               <jats:p>Contact: \u00a0getbonnie@cs.unm.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp173","type":"journal-article","created":{"date-parts":[[2009,3,26]],"date-time":"2009-03-26T01:54:27Z","timestamp":1238032467000},"page":"1457-1460","source":"Crossref","is-referenced-by-count":13,"title":["GetBonNie for building, analyzing and sharing rule-based models"],"prefix":"10.1093","volume":"25","author":[{"given":"Bin","family":"Hu","sequence":"first","affiliation":[{"name":"1 Department of Biology, University of New Mexico, Albuquerque, NM 87131, 2Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, 3Department of Computer Science, University of New Mexico, Albuquerque, NM 87131, 4Department of Computational Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, 5Computational Biology Division, Translational Genomics Research Institute, Phoenix, AZ 85004 and 6Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87545, USA"},{"name":"1 Department of Biology, University of New Mexico, Albuquerque, NM 87131, 2Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, 3Department of Computer Science, University of New Mexico, Albuquerque, NM 87131, 4Department of Computational Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, 5Computational Biology Division, Translational Genomics Research Institute, Phoenix, AZ 85004 and 6Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87545, USA"}]},{"given":"G.","family":"Matthew Fricke","sequence":"additional","affiliation":[{"name":"1 Department of Biology, University of New Mexico, Albuquerque, NM 87131, 2Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, 3Department of Computer Science, University of New Mexico, Albuquerque, NM 87131, 4Department of Computational Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, 5Computational Biology Division, Translational Genomics Research Institute, Phoenix, AZ 85004 and 6Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87545, USA"}]},{"given":"James R.","family":"Faeder","sequence":"additional","affiliation":[{"name":"1 Department of Biology, University of New Mexico, Albuquerque, NM 87131, 2Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, 3Department of Computer Science, University of New Mexico, Albuquerque, NM 87131, 4Department of Computational Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, 5Computational Biology Division, Translational Genomics Research Institute, Phoenix, AZ 85004 and 6Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87545, USA"}]},{"given":"Richard G.","family":"Posner","sequence":"additional","affiliation":[{"name":"1 Department of Biology, University of New Mexico, Albuquerque, NM 87131, 2Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, 3Department of Computer Science, University of New Mexico, Albuquerque, NM 87131, 4Department of Computational Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, 5Computational Biology Division, Translational Genomics Research Institute, Phoenix, AZ 85004 and 6Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87545, USA"}]},{"given":"William S.","family":"Hlavacek","sequence":"additional","affiliation":[{"name":"1 Department of Biology, University of New Mexico, Albuquerque, NM 87131, 2Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, 3Department of Computer Science, University of New Mexico, Albuquerque, NM 87131, 4Department of Computational Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, 5Computational Biology Division, Translational Genomics Research Institute, Phoenix, AZ 85004 and 6Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87545, USA"},{"name":"1 Department of Biology, University of New Mexico, Albuquerque, NM 87131, 2Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, 3Department of Computer Science, University of New Mexico, Albuquerque, NM 87131, 4Department of Computational Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, 5Computational Biology Division, Translational Genomics Research Institute, Phoenix, AZ 85004 and 6Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87545, USA"},{"name":"1 Department of Biology, University of New Mexico, Albuquerque, NM 87131, 2Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, 3Department of Computer Science, University of New Mexico, Albuquerque, NM 87131, 4Department of Computational Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, 5Computational Biology Division, Translational Genomics Research 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