{"id":"https://openalex.org/W4386909827","doi":"https://doi.org/10.1515/jib-2024-0002","title":"MakeSBML: a tool for converting between Antimony and SBML","display_name":"MakeSBML: a tool for converting between Antimony and SBML","publication_year":2024,"publication_date":"2024-03-01","ids":{"openalex":"https://openalex.org/W4386909827","doi":"https://doi.org/10.1515/jib-2024-0002","pmid":"https://pubmed.ncbi.nlm.nih.gov/37731653"},"language":"en","primary_location":{"id":"doi:10.1515/jib-2024-0002","is_oa":true,"landing_page_url":"https://doi.org/10.1515/jib-2024-0002","pdf_url":null,"source":{"id":"https://openalex.org/S4393917359","display_name":"Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics","issn_l":"1432-4385","issn":["1432-4385","1613-4516"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Integrative Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1515/jib-2024-0002","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5075392246","display_name":"Bartholomew Jardine","orcid":"https://orcid.org/0009-0004-7187-6306"},"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":"Bartholomew E. Jardine","raw_affiliation_strings":["Department of Bioengineering , University of Washington , Box 355061 , Seattle , 98195 , WA , USA"],"raw_orcid":"https://orcid.org/0009-0004-7187-6306","affiliations":[{"raw_affiliation_string":"Department of Bioengineering , University of Washington , Box 355061 , Seattle , 98195 , WA , USA","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","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":false,"raw_author_name":"Lucian P. Smith","raw_affiliation_strings":["Department of Bioengineering , University of Washington , Box 355061 , Seattle , 98195 , WA , USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioengineering , University of Washington , Box 355061 , Seattle , 98195 , WA , USA","institution_ids":["https://openalex.org/I201448701"]}]},{"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":true,"raw_author_name":"Herbert M. Sauro","raw_affiliation_strings":["Department of Bioengineering , University of Washington , Box 355061 , Seattle , 98195 , WA , USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioengineering , University of Washington , Box 355061 , Seattle , 98195 , WA , USA","institution_ids":["https://openalex.org/I201448701"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5044484291","https://openalex.org/A5075392246"],"corresponding_institution_ids":["https://openalex.org/I201448701"],"apc_list":{"value":1000,"currency":"EUR","value_usd":1082},"apc_paid":{"value":1000,"currency":"EUR","value_usd":1082},"fwci":0.4665,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.58016986,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":97},"biblio":{"volume":"21","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9771000146865845,"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":0.9771000146865845,"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/T11975","display_name":"Evolutionary Algorithms and Applications","score":0.907800018787384,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/sbml","display_name":"SBML","score":0.8591812252998352},{"id":"https://openalex.org/keywords/antimony","display_name":"Antimony","score":0.7129189372062683},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.514462947845459},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5117835402488708},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.32426613569259644},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.2148911952972412},{"id":"https://openalex.org/keywords/materials-science","display_name":"Materials science","score":0.1767391562461853},{"id":"https://openalex.org/keywords/markup-language","display_name":"Markup language","score":0.1512291431427002},{"id":"https://openalex.org/keywords/metallurgy","display_name":"Metallurgy","score":0.07715073227882385}],"concepts":[{"id":"https://openalex.org/C87186988","wikidata":"https://www.wikidata.org/wiki/Q452197","display_name":"SBML","level":4,"score":0.8591812252998352},{"id":"https://openalex.org/C541565711","wikidata":"https://www.wikidata.org/wiki/Q1099","display_name":"Antimony","level":2,"score":0.7129189372062683},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.514462947845459},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5117835402488708},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.32426613569259644},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.2148911952972412},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.1767391562461853},{"id":"https://openalex.org/C45874996","wikidata":"https://www.wikidata.org/wiki/Q37045","display_name":"Markup language","level":3,"score":0.1512291431427002},{"id":"https://openalex.org/C191897082","wikidata":"https://www.wikidata.org/wiki/Q11467","display_name":"Metallurgy","level":1,"score":0.07715073227882385},{"id":"https://openalex.org/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"score":0.0}],"mesh":[],"locations_count":6,"locations":[{"id":"doi:10.1515/jib-2024-0002","is_oa":true,"landing_page_url":"https://doi.org/10.1515/jib-2024-0002","pdf_url":null,"source":{"id":"https://openalex.org/S4393917359","display_name":"Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics","issn_l":"1432-4385","issn":["1432-4385","1613-4516"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Integrative Bioinformatics","raw_type":"journal-article"},{"id":"pmid:37731653","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37731653","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":"ArXiv","raw_type":"Preprint"},{"id":"pmid:38860571","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38860571","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":"Journal of integrative bioinformatics","raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:10508829","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10508829","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10508829/pdf/nihpp-2309.03344v1.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ArXiv","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:11294058","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11294058","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11294058/pdf/jib-21-1-jib-2024-0002.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Integr Bioinform","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:d3755ccf88c14fee85023b9c54c5c842","is_oa":true,"landing_page_url":"https://doaj.org/article/d3755ccf88c14fee85023b9c54c5c842","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Integrative Bioinformatics, Vol 21, Iss 1, Pp 524-31 (2024)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1515/jib-2024-0002","is_oa":true,"landing_page_url":"https://doi.org/10.1515/jib-2024-0002","pdf_url":null,"source":{"id":"https://openalex.org/S4393917359","display_name":"Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics","issn_l":"1432-4385","issn":["1432-4385","1613-4516"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Integrative Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G114059409","display_name":null,"funder_award_id":"P41EB023912","funder_id":"https://openalex.org/F4320337363","funder_display_name":"National Institute of Biomedical Imaging and Bioengineering"},{"id":"https://openalex.org/G1363728023","display_name":null,"funder_award_id":"P41EB02391","funder_id":"https://openalex.org/F4320337363","funder_display_name":"National Institute of Biomedical Imaging and Bioengineering"},{"id":"https://openalex.org/G3332417720","display_name":null,"funder_award_id":"P41EB023912","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G3745874374","display_name":"High Performance Simulation Libraries for Systems Biology","funder_award_id":"5r01gm123032-04","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4536393517","display_name":"Center for Reproducible Systems for Biomedical Modeling","funder_award_id":"2p41eb023912-06","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G719674503","display_name":null,"funder_award_id":"R01 GM123032","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320310094","display_name":"University of Washington","ror":"https://ror.org/00cvxb145"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320337363","display_name":"National Institute of Biomedical Imaging and Bioengineering","ror":"https://ror.org/00372qc85"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":11,"referenced_works":["https://openalex.org/W2038264484","https://openalex.org/W2097319997","https://openalex.org/W2102653059","https://openalex.org/W2125615370","https://openalex.org/W2134221731","https://openalex.org/W2150908245","https://openalex.org/W2156487548","https://openalex.org/W2884300959","https://openalex.org/W2988361147","https://openalex.org/W3019461979","https://openalex.org/W4226518778"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2748952813","https://openalex.org/W1568154633","https://openalex.org/W1833372769","https://openalex.org/W1994518768","https://openalex.org/W2082621456","https://openalex.org/W104010570","https://openalex.org/W2150908245","https://openalex.org/W2069162648","https://openalex.org/W1987628135"],"abstract_inverted_index":{"We":[0,126],"describe":[1,107],"a":[2,25,48,64],"web-based":[3,49],"tool,":[4],"MakeSBML":[5,23,46,60],"(https://sys-bio.github.io/makesbml/),":[6],"that":[7,29],"provides":[8],"an":[9,89],"installation-free":[10],"application":[11,28,50],"for":[12,20,81],"creating,":[13],"editing,":[14],"and":[15,43,111,139],"searching":[16],"the":[17,37,56,68,129],"Biomodels":[18],"repository":[19],"SBML-based":[21],"models.":[22,142],"is":[24,47,61,92,99,119],"client-based":[26,69],"web":[27],"translates":[30],"models":[31,114],"expressed":[32],"in":[33,102],"human-readable":[34,130],"Antimony":[35,131],"to":[36,74,76,106,121,133,137],"System":[38],"Biology":[39],"Markup":[40],"Language":[41],"(SBML)":[42],"vice-versa.":[44],"Since":[45],"it":[51,72,135],"requires":[52],"no":[53],"installation":[54],"on":[55,63],"user's":[57],"part.":[58],"Currently,":[59],"hosted":[62],"GitHub":[65],"page":[66],"where":[67],"design":[70],"makes":[71,112],"trivial":[73],"move":[75],"other":[77],"hosts.":[78],"This":[79],"model":[80],"software":[82],"deployment":[83],"also":[84],"reduces":[85],"maintenance":[86],"costs":[87],"since":[88],"active":[90],"server":[91],"not":[93,124],"required.":[94],"The":[95],"SBML":[96,118,141],"modeling":[97],"language":[98,132],"often":[100],"used":[101],"systems":[103],"biology":[104],"research":[105],"complex":[108],"biochemical":[109],"networks":[110],"reproducing":[113],"much":[115],"easier.":[116],"However,":[117],"designed":[120],"be":[122],"computer-readable,":[123],"human-readable.":[125],"therefore":[127],"employ":[128],"make":[134],"easy":[136],"create":[138],"edit":[140]},"counts_by_year":[{"year":2024,"cited_by_count":3}],"updated_date":"2026-08-28T12:50:07.497085","created_date":"2023-09-22T00:00:00"}
