{"id":"https://openalex.org/W2117792713","doi":"https://doi.org/10.1093/bioinformatics/btk042","title":"Tools for the SBML Community","display_name":"Tools for the SBML Community","publication_year":2006,"publication_date":"2006-01-12","ids":{"openalex":"https://openalex.org/W2117792713","doi":"https://doi.org/10.1093/bioinformatics/btk042","mag":"2117792713","pmid":"https://pubmed.ncbi.nlm.nih.gov/16410323"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btk042","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btk042","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/22/5/628/48840093/bioinformatics_22_5_628.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":null,"license_id":null,"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":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/22/5/628/48840093/bioinformatics_22_5_628.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5003647740","display_name":"Colin S. Gillespie","orcid":"https://orcid.org/0000-0003-1787-0275"},"institutions":[{"id":"https://openalex.org/I84884186","display_name":"Newcastle University","ror":"https://ror.org/01kj2bm70","country_code":"GB","type":"education","lineage":["https://openalex.org/I84884186"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Colin S. Gillespie","raw_affiliation_strings":["School of Mathematics and Statistics, University of Newcastle 1 \u00a0 1 \u00a0 \u00a0 Newcastle upon Tyne, NE1 7RU, UK"],"affiliations":[{"raw_affiliation_string":"School of Mathematics and Statistics, University of Newcastle 1 \u00a0 1 \u00a0 \u00a0 Newcastle upon Tyne, NE1 7RU, UK","institution_ids":["https://openalex.org/I84884186"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011926448","display_name":"Darren J. Wilkinson","orcid":"https://orcid.org/0000-0003-0736-802X"},"institutions":[{"id":"https://openalex.org/I84884186","display_name":"Newcastle University","ror":"https://ror.org/01kj2bm70","country_code":"GB","type":"education","lineage":["https://openalex.org/I84884186"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Darren J. Wilkinson","raw_affiliation_strings":["School of Mathematics and Statistics, University of Newcastle 1 \u00a0 1 \u00a0 \u00a0 Newcastle upon Tyne, NE1 7RU, UK"],"affiliations":[{"raw_affiliation_string":"School of Mathematics and Statistics, University of Newcastle 1 \u00a0 1 \u00a0 \u00a0 Newcastle upon Tyne, NE1 7RU, UK","institution_ids":["https://openalex.org/I84884186"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001280057","display_name":"Carole J. Proctor","orcid":"https://orcid.org/0000-0002-1366-1399"},"institutions":[{"id":"https://openalex.org/I84884186","display_name":"Newcastle University","ror":"https://ror.org/01kj2bm70","country_code":"GB","type":"education","lineage":["https://openalex.org/I84884186"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Carole J. Proctor","raw_affiliation_strings":["Henry Wellcome Laboratory for Biogerontology Research, School of Clinical and Medical Sciences, Gerontology, University of Newcastle 2 \u00a0 2 \u00a0 \u00a0 Newcastle upon Tyne, NE4 6BE, UK"],"affiliations":[{"raw_affiliation_string":"Henry Wellcome Laboratory for Biogerontology Research, School of Clinical and Medical Sciences, Gerontology, University of Newcastle 2 \u00a0 2 \u00a0 \u00a0 Newcastle upon Tyne, NE4 6BE, UK","institution_ids":["https://openalex.org/I84884186"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029338507","display_name":"Daryl P. Shanley","orcid":"https://orcid.org/0000-0003-3096-6386"},"institutions":[{"id":"https://openalex.org/I84884186","display_name":"Newcastle University","ror":"https://ror.org/01kj2bm70","country_code":"GB","type":"education","lineage":["https://openalex.org/I84884186"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Daryl P. Shanley","raw_affiliation_strings":["Henry Wellcome Laboratory for Biogerontology Research, School of Clinical and Medical Sciences, Gerontology, University of Newcastle 2 \u00a0 2 \u00a0 \u00a0 Newcastle upon Tyne, NE4 6BE, UK"],"affiliations":[{"raw_affiliation_string":"Henry Wellcome Laboratory for Biogerontology Research, School of Clinical and Medical Sciences, Gerontology, University of Newcastle 2 \u00a0 2 \u00a0 \u00a0 Newcastle upon Tyne, NE4 6BE, UK","institution_ids":["https://openalex.org/I84884186"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5109566704","display_name":"Richard J. Boys","orcid":null},"institutions":[{"id":"https://openalex.org/I84884186","display_name":"Newcastle University","ror":"https://ror.org/01kj2bm70","country_code":"GB","type":"education","lineage":["https://openalex.org/I84884186"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Richard J. Boys","raw_affiliation_strings":["School of Mathematics and Statistics, University of Newcastle 1 \u00a0 1 \u00a0 \u00a0 Newcastle upon Tyne, NE1 7RU, UK"],"affiliations":[{"raw_affiliation_string":"School of Mathematics and Statistics, University of Newcastle 1 \u00a0 1 \u00a0 \u00a0 Newcastle upon Tyne, NE1 7RU, UK","institution_ids":["https://openalex.org/I84884186"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5037656057","display_name":"Thomas B. L. Kirkwood","orcid":"https://orcid.org/0000-0002-6675-8944"},"institutions":[{"id":"https://openalex.org/I84884186","display_name":"Newcastle University","ror":"https://ror.org/01kj2bm70","country_code":"GB","type":"education","lineage":["https://openalex.org/I84884186"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Thomas B. L. Kirkwood","raw_affiliation_strings":["Henry Wellcome Laboratory for Biogerontology Research, School of Clinical and Medical Sciences, Gerontology, University of Newcastle 2 \u00a0 2 \u00a0 \u00a0 Newcastle upon Tyne, NE4 6BE, UK"],"affiliations":[{"raw_affiliation_string":"Henry Wellcome Laboratory for Biogerontology Research, School of Clinical and Medical Sciences, Gerontology, University of Newcastle 2 \u00a0 2 \u00a0 \u00a0 Newcastle upon Tyne, NE4 6BE, UK","institution_ids":["https://openalex.org/I84884186"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5003647740"],"corresponding_institution_ids":["https://openalex.org/I84884186"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.5895,"has_fulltext":false,"cited_by_count":45,"citation_normalized_percentile":{"value":0.81833854,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"22","issue":"5","first_page":"628","last_page":"629"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9998000264167786,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9998000264167786,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9994000196456909,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9973000288009644,"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":0.9961059093475342},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7747017741203308},{"id":"https://openalex.org/keywords/license","display_name":"License","score":0.6285810470581055},{"id":"https://openalex.org/keywords/markup-language","display_name":"Markup language","score":0.5439687967300415},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.49340763688087463},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.48147788643836975},{"id":"https://openalex.org/keywords/mit-license","display_name":"MIT License","score":0.4633311331272125},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.3294604420661926},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.2179778516292572},{"id":"https://openalex.org/keywords/xml","display_name":"XML","score":0.09671327471733093}],"concepts":[{"id":"https://openalex.org/C87186988","wikidata":"https://www.wikidata.org/wiki/Q452197","display_name":"SBML","level":4,"score":0.9961059093475342},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7747017741203308},{"id":"https://openalex.org/C2780560020","wikidata":"https://www.wikidata.org/wiki/Q79719","display_name":"License","level":2,"score":0.6285810470581055},{"id":"https://openalex.org/C45874996","wikidata":"https://www.wikidata.org/wiki/Q37045","display_name":"Markup language","level":3,"score":0.5439687967300415},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.49340763688087463},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.48147788643836975},{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.4633311331272125},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.3294604420661926},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.2179778516292572},{"id":"https://openalex.org/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"score":0.09671327471733093}],"mesh":[{"descriptor_ui":"D001671","descriptor_name":"Biochemistry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D001671","descriptor_name":"Biochemistry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D001671","descriptor_name":"Biochemistry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D001671","descriptor_name":"Biochemistry","qualifier_ui":"Q000379","qualifier_name":"methods","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":"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":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","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":"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":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btk042","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btk042","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/22/5/628/48840093/bioinformatics_22_5_628.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:16410323","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16410323","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}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btk042","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btk042","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/22/5/628/48840093/bioinformatics_22_5_628.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320334629","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2117792713.pdf","grobid_xml":"https://content.openalex.org/works/W2117792713.grobid-xml"},"referenced_works_count":6,"referenced_works":["https://openalex.org/W1495660511","https://openalex.org/W2014118496","https://openalex.org/W2036862428","https://openalex.org/W2150908245","https://openalex.org/W2155418451","https://openalex.org/W2170032647"],"related_works":["https://openalex.org/W2082621456","https://openalex.org/W2150908245","https://openalex.org/W2981332207","https://openalex.org/W2159912904","https://openalex.org/W2211443823","https://openalex.org/W2100525485","https://openalex.org/W2040642413","https://openalex.org/W3048335229","https://openalex.org/W2146744007","https://openalex.org/W2890725831"],"abstract_inverted_index":{"All":[0],"tools":[1],"described":[2],"are":[3,8],"available":[4],"from":[5],"http://www.basis.ncl.ac.uk/software":[6],"and":[7],"licensed":[9],"under":[10],"GNU":[11],"General":[12],"Public":[13],"License.":[14]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":8},{"year":2012,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
