{"id":"https://openalex.org/W2139035000","doi":"https://doi.org/10.1093/bioinformatics/btt641","title":"SBML and CellML translation in Antimony and JSim","display_name":"SBML and CellML translation in Antimony and JSim","publication_year":2013,"publication_date":"2013-11-08","ids":{"openalex":"https://openalex.org/W2139035000","doi":"https://doi.org/10.1093/bioinformatics/btt641","mag":"2139035000","pmid":"https://pubmed.ncbi.nlm.nih.gov/24215024"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btt641","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt641","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/30/7/903/48921333/bioinformatics_30_7_903.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/30/7/903/48921333/bioinformatics_30_7_903.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5067339679","display_name":"Lucian P. Smith","orcid":"https://orcid.org/0000-0001-7002-6386"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Lucian P. Smith","raw_affiliation_strings":["Department of Bioengineering, University of Washington, Seattle, WA, USA","Department of Bioengineering, University of Washington , Seattle, WA, USA"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of Washington, Seattle, WA, USA","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Department of Bioengineering, University of Washington , Seattle, WA, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090544172","display_name":"Erik Butterworth","orcid":null},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Erik Butterworth","raw_affiliation_strings":["Department of Bioengineering, University of Washington, Seattle, WA, USA","Department of Bioengineering, University of Washington , Seattle, WA, USA"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of Washington, Seattle, WA, USA","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Department of Bioengineering, University of Washington , Seattle, WA, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062325761","display_name":"James B. Bassingthwaighte","orcid":"https://orcid.org/0000-0001-8679-7257"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"James B. Bassingthwaighte","raw_affiliation_strings":["Department of Bioengineering, University of Washington, Seattle, WA, USA","Department of Bioengineering, University of Washington , Seattle, WA, USA"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of Washington, Seattle, WA, USA","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Department of Bioengineering, University of Washington , Seattle, WA, USA","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5044484291","display_name":"Herbert M. Sauro","orcid":"https://orcid.org/0000-0002-3659-6817"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Herbert M. Sauro","raw_affiliation_strings":["Department of Bioengineering, University of Washington, Seattle, WA, USA","Department of Bioengineering, University of Washington , Seattle, WA, USA"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of Washington, Seattle, WA, USA","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Department of Bioengineering, University of Washington , Seattle, WA, USA","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5067339679"],"corresponding_institution_ids":["https://openalex.org/I201448701"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.9465,"has_fulltext":true,"cited_by_count":18,"citation_normalized_percentile":{"value":0.86267974,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"30","issue":"7","first_page":"903","last_page":"907"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9995999932289124,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9995999932289124,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.9991000294685364,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.996399998664856,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/sbml","display_name":"SBML","score":0.965450644493103},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7050420045852661},{"id":"https://openalex.org/keywords/markup-language","display_name":"Markup language","score":0.6029431819915771},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.5538569092750549},{"id":"https://openalex.org/keywords/translation","display_name":"Translation (biology)","score":0.4829499125480652},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.3458753824234009},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3393177390098572},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.33873921632766724},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.2034527063369751},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1899622678756714},{"id":"https://openalex.org/keywords/xml","display_name":"XML","score":0.15868398547172546},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.06447732448577881}],"concepts":[{"id":"https://openalex.org/C87186988","wikidata":"https://www.wikidata.org/wiki/Q452197","display_name":"SBML","level":4,"score":0.965450644493103},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7050420045852661},{"id":"https://openalex.org/C45874996","wikidata":"https://www.wikidata.org/wiki/Q37045","display_name":"Markup language","level":3,"score":0.6029431819915771},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.5538569092750549},{"id":"https://openalex.org/C149364088","wikidata":"https://www.wikidata.org/wiki/Q185917","display_name":"Translation (biology)","level":4,"score":0.4829499125480652},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.3458753824234009},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3393177390098572},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.33873921632766724},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.2034527063369751},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1899622678756714},{"id":"https://openalex.org/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"score":0.15868398547172546},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.06447732448577881},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C105580179","wikidata":"https://www.wikidata.org/wiki/Q188928","display_name":"Messenger RNA","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btt641","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt641","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/30/7/903/48921333/bioinformatics_30_7_903.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:24215024","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24215024","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:europepmc.org:3342054","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3967103","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btt641","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt641","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/30/7/903/48921333/bioinformatics_30_7_903.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3611247453","display_name":null,"funder_award_id":"R01GM","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4330913702","display_name":null,"funder_award_id":"GM08107","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6066673208","display_name":null,"funder_award_id":"EB08407","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2139035000.pdf","grobid_xml":"https://content.openalex.org/works/W2139035000.grobid-xml"},"referenced_works_count":19,"referenced_works":["https://openalex.org/W1589685702","https://openalex.org/W1998125620","https://openalex.org/W2042880070","https://openalex.org/W2062744504","https://openalex.org/W2098851705","https://openalex.org/W2102653059","https://openalex.org/W2107062718","https://openalex.org/W2110699703","https://openalex.org/W2125615370","https://openalex.org/W2129299701","https://openalex.org/W2134221731","https://openalex.org/W2137128504","https://openalex.org/W2142659266","https://openalex.org/W2150908245","https://openalex.org/W2157239334","https://openalex.org/W2171458571","https://openalex.org/W2219090274","https://openalex.org/W6685016951","https://openalex.org/W6688645160"],"related_works":["https://openalex.org/W2082621456","https://openalex.org/W2150908245","https://openalex.org/W2981332207","https://openalex.org/W2211443823","https://openalex.org/W2100525485","https://openalex.org/W2040642413","https://openalex.org/W3048335229","https://openalex.org/W2146744007","https://openalex.org/W2890725831","https://openalex.org/W3041939341"],"abstract_inverted_index":{"lpsmith@u.washington.edu.":[0]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":6},{"year":2013,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}