{"id":"https://openalex.org/W4394789019","doi":"https://doi.org/10.1515/jib-2024-0008","title":"The simulation experiment description markup language (SED-ML): language specification for level 1 version 5","display_name":"The simulation experiment description markup language (SED-ML): language specification for level 1 version 5","publication_year":2024,"publication_date":"2024-03-01","ids":{"openalex":"https://openalex.org/W4394789019","doi":"https://doi.org/10.1515/jib-2024-0008","pmid":"https://pubmed.ncbi.nlm.nih.gov/38613325"},"language":"en","primary_location":{"id":"doi:10.1515/jib-2024-0008","is_oa":true,"landing_page_url":"https://doi.org/10.1515/jib-2024-0008","pdf_url":"https://www.degruyter.com/document/doi/10.1515/jib-2024-0008/pdf","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":"diamond","oa_url":"https://www.degruyter.com/document/doi/10.1515/jib-2024-0008/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"]},{"id":"https://openalex.org/I58610484","display_name":"Seattle University","ror":"https://ror.org/02jqc0m91","country_code":"US","type":"education","lineage":["https://openalex.org/I58610484"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Lucian P. Smith","raw_affiliation_strings":["7284 University of Washington , Seattle , USA"],"affiliations":[{"raw_affiliation_string":"7284 University of Washington , Seattle , USA","institution_ids":["https://openalex.org/I201448701","https://openalex.org/I58610484"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076617999","display_name":"Frank Bergmann","orcid":"https://orcid.org/0000-0001-5553-4702"},"institutions":[{"id":"https://openalex.org/I223822909","display_name":"Heidelberg University","ror":"https://ror.org/038t36y30","country_code":"DE","type":"education","lineage":["https://openalex.org/I223822909"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Frank T. Bergmann","raw_affiliation_strings":["BioQUANT/COS , 132140 Heidelberg University , Heidelberg , Germany"],"affiliations":[{"raw_affiliation_string":"BioQUANT/COS , 132140 Heidelberg University , Heidelberg , Germany","institution_ids":["https://openalex.org/I223822909"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073607042","display_name":"Alan Garny","orcid":"https://orcid.org/0000-0001-7606-5888"},"institutions":[{"id":"https://openalex.org/I154130895","display_name":"University of Auckland","ror":"https://ror.org/03b94tp07","country_code":"NZ","type":"education","lineage":["https://openalex.org/I154130895"]}],"countries":["NZ"],"is_corresponding":false,"raw_author_name":"Alan Garny","raw_affiliation_strings":["Auckland Bioengineering Institute , 428614 The University of Auckland , Auckland , New Zealand"],"affiliations":[{"raw_affiliation_string":"Auckland Bioengineering Institute , 428614 The University of Auckland , Auckland , New Zealand","institution_ids":["https://openalex.org/I154130895"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073371703","display_name":"Tom\u00e1\u0161 Helikar","orcid":"https://orcid.org/0000-0003-3653-1906"},"institutions":[{"id":"https://openalex.org/I114395901","display_name":"University of Nebraska\u2013Lincoln","ror":"https://ror.org/043mer456","country_code":"US","type":"education","lineage":["https://openalex.org/I114395901"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tom\u00e1\u0161 Helikar","raw_affiliation_strings":["University of Nebraska , Lincoln , USA"],"affiliations":[{"raw_affiliation_string":"University of Nebraska , Lincoln , USA","institution_ids":["https://openalex.org/I114395901"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016750554","display_name":"Jonathan R. Karr","orcid":"https://orcid.org/0000-0002-2605-5080"},"institutions":[{"id":"https://openalex.org/I98704320","display_name":"Icahn School of Medicine at Mount Sinai","ror":"https://ror.org/04a9tmd77","country_code":"US","type":"education","lineage":["https://openalex.org/I1320796813","https://openalex.org/I98704320"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jonathan Karr","raw_affiliation_strings":["5925 Icahn School of Medicine at Mount Sinai , New York , USA"],"affiliations":[{"raw_affiliation_string":"5925 Icahn School of Medicine at Mount Sinai , New York , USA","institution_ids":["https://openalex.org/I98704320"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086460310","display_name":"David Nickerson","orcid":"https://orcid.org/0000-0003-4667-9779"},"institutions":[{"id":"https://openalex.org/I154130895","display_name":"University of Auckland","ror":"https://ror.org/03b94tp07","country_code":"NZ","type":"education","lineage":["https://openalex.org/I154130895"]}],"countries":["NZ"],"is_corresponding":false,"raw_author_name":"David Nickerson","raw_affiliation_strings":["Auckland Bioengineering Institute , 428614 The University of Auckland , Auckland , New Zealand"],"affiliations":[{"raw_affiliation_string":"Auckland Bioengineering Institute , 428614 The University of Auckland , Auckland , New Zealand","institution_ids":["https://openalex.org/I154130895"]}]},{"author_position":"middle","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"]},{"id":"https://openalex.org/I58610484","display_name":"Seattle University","ror":"https://ror.org/02jqc0m91","country_code":"US","type":"education","lineage":["https://openalex.org/I58610484"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Herbert Sauro","raw_affiliation_strings":["7284 University of Washington , Seattle , USA"],"affiliations":[{"raw_affiliation_string":"7284 University of Washington , Seattle , USA","institution_ids":["https://openalex.org/I201448701","https://openalex.org/I58610484"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103188993","display_name":"Dagmar Waltemath","orcid":"https://orcid.org/0000-0002-5886-5563"},"institutions":[{"id":"https://openalex.org/I36522303","display_name":"Universit\u00e4t Greifswald","ror":"https://ror.org/00r1edq15","country_code":"DE","type":"education","lineage":["https://openalex.org/I36522303"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Dagmar Waltemath","raw_affiliation_strings":["University of Greifswald , Greifswald , Germany"],"affiliations":[{"raw_affiliation_string":"University of Greifswald , Greifswald , Germany","institution_ids":["https://openalex.org/I36522303"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5012727458","display_name":"Matthias K\u00f6nig","orcid":"https://orcid.org/0000-0003-1725-179X"},"institutions":[{"id":"https://openalex.org/I39343248","display_name":"Humboldt-Universit\u00e4t zu Berlin","ror":"https://ror.org/01hcx6992","country_code":"DE","type":"education","lineage":["https://openalex.org/I39343248"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Matthias K\u00f6nig","raw_affiliation_strings":["9373 Humboldt University , Berlin , Germany"],"affiliations":[{"raw_affiliation_string":"9373 Humboldt University , Berlin , Germany","institution_ids":["https://openalex.org/I39343248"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5067339679"],"corresponding_institution_ids":["https://openalex.org/I201448701","https://openalex.org/I58610484"],"apc_list":null,"apc_paid":null,"fwci":1.963,"has_fulltext":true,"cited_by_count":4,"citation_normalized_percentile":{"value":0.86029913,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":96},"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/T11195","display_name":"Simulation Techniques and Applications","score":0.9883000254631042,"subfield":{"id":"https://openalex.org/subfields/1803","display_name":"Management Science and Operations Research"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},"topics":[{"id":"https://openalex.org/T11195","display_name":"Simulation Techniques and Applications","score":0.9883000254631042,"subfield":{"id":"https://openalex.org/subfields/1803","display_name":"Management Science and Operations Research"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.9876000285148621,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9779000282287598,"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/markup-language","display_name":"Markup language","score":0.8291587829589844},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7698661684989929},{"id":"https://openalex.org/keywords/sbml","display_name":"SBML","score":0.632537305355072},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5321109890937805},{"id":"https://openalex.org/keywords/sed","display_name":"sed","score":0.4984707832336426},{"id":"https://openalex.org/keywords/xml","display_name":"XML","score":0.2946050763130188},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.28032925724983215},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.15276160836219788}],"concepts":[{"id":"https://openalex.org/C45874996","wikidata":"https://www.wikidata.org/wiki/Q37045","display_name":"Markup language","level":3,"score":0.8291587829589844},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7698661684989929},{"id":"https://openalex.org/C87186988","wikidata":"https://www.wikidata.org/wiki/Q452197","display_name":"SBML","level":4,"score":0.632537305355072},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5321109890937805},{"id":"https://openalex.org/C126707884","wikidata":"https://www.wikidata.org/wiki/Q305876","display_name":"sed","level":2,"score":0.4984707832336426},{"id":"https://openalex.org/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"score":0.2946050763130188},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.28032925724983215},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.15276160836219788}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":"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":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","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":"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1515/jib-2024-0008","is_oa":true,"landing_page_url":"https://doi.org/10.1515/jib-2024-0008","pdf_url":"https://www.degruyter.com/document/doi/10.1515/jib-2024-0008/pdf","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:38613325","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38613325","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":null},{"id":"pmh:oai:pubmedcentral.nih.gov:11294059","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11294059","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11294059/pdf/jib-21-1-jib-2024-0008.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"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:ecf0894e52704818b8ab11825f64a6c9","is_oa":true,"landing_page_url":"https://doaj.org/article/ecf0894e52704818b8ab11825f64a6c9","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Integrative Bioinformatics, Vol 21, Iss 1 (2024)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1515/jib-2024-0008","is_oa":true,"landing_page_url":"https://doi.org/10.1515/jib-2024-0008","pdf_url":"https://www.degruyter.com/document/doi/10.1515/jib-2024-0008/pdf","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/G1675061984","display_name":null,"funder_award_id":"P41GM109824","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G2500937128","display_name":null,"funder_award_id":"2020-2022","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G4919189094","display_name":null,"funder_award_id":"GM123032","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G5088104505","display_name":null,"funder_award_id":"de.NBI","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G5573860753","display_name":null,"funder_award_id":"R01GM123032","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G5592793877","display_name":null,"funder_award_id":"23032","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G5704377073","display_name":null,"funder_award_id":"GM109824","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G5704623888","display_name":null,"funder_award_id":"P41GM109824","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G5921281487","display_name":null,"funder_award_id":"number","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6321517409","display_name":null,"funder_award_id":"1933453","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6755165505","display_name":null,"funder_award_id":"award","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6784366563","display_name":null,"funder_award_id":"16-2018","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6811219481","display_name":null,"funder_award_id":"R35GM119771","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G6955755495","display_name":null,"funder_award_id":"Germany","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G848032724","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320321114","display_name":"Bundesministerium f\u00fcr Bildung und Forschung","ror":"https://ror.org/04pz7b180"},{"id":"https://openalex.org/F4320330124","display_name":"German Network for Bioinformatics Infrastructure","ror":null},{"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":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4394789019.pdf"},"referenced_works_count":17,"referenced_works":["https://openalex.org/W109947125","https://openalex.org/W1645305843","https://openalex.org/W1991339919","https://openalex.org/W2096951208","https://openalex.org/W2113777491","https://openalex.org/W2123783513","https://openalex.org/W2126662515","https://openalex.org/W2145435867","https://openalex.org/W2150908245","https://openalex.org/W2170122529","https://openalex.org/W2316765580","https://openalex.org/W2405441773","https://openalex.org/W2531582823","https://openalex.org/W3201819843","https://openalex.org/W4249676104","https://openalex.org/W4254697110","https://openalex.org/W4256307980"],"related_works":["https://openalex.org/W2082621456","https://openalex.org/W2150908245","https://openalex.org/W2128782793","https://openalex.org/W2981332207","https://openalex.org/W2211443823","https://openalex.org/W2146744007","https://openalex.org/W2040642413","https://openalex.org/W3048335229","https://openalex.org/W2100525485","https://openalex.org/W3041939341"],"abstract_inverted_index":{"Modern":[0],"biological":[1],"research":[2],"is":[3,54,133,171],"increasingly":[4,27],"informed":[5],"by":[6,62,71,135],"computational":[7],"simulation":[8,51,110,159],"experiments,":[9],"which":[10],"necessitate":[11],"the":[12,22,46,59,84,94,128],"development":[13],"of":[14,81,86,139],"methods":[15],"for":[16,58,149],"annotating,":[17],"archiving,":[18],"sharing,":[19],"and":[20,34,69,74,125,143,154,157,165],"reproducing":[21],"conducted":[23],"experiments.":[24,52],"These":[25],"simulations":[26,90],"require":[28],"extensive":[29],"collaboration":[30],"among":[31],"modelers,":[32],"experimentalists,":[33],"engineers.":[35],"The":[36],"Minimum":[37],"Information":[38],"About":[39],"a":[40,55,66,109,136],"Simulation":[41,96],"Experiment":[42],"(MIASE)":[43],"guidelines":[44],"outline":[45],"information":[47,60,168],"needed":[48],"to":[49,88,107,119],"share":[50],"SED-ML":[53,82,92,132,170],"computer-readable":[56],"format":[57],"outlined":[61],"MIASE,":[63],"created":[64],"as":[65,130],"community":[67],"project":[68],"supported":[70,134],"many":[72,158],"investigators":[73],"software":[75,144],"tools.":[76],"Level":[77],"1":[78],"Version":[79,105,114],"5":[80,115],"expands":[83],"ability":[85],"modelers":[87],"define":[89,108,120],"in":[91,104],"using":[93,112,127],"Kinetic":[95],"Algorithm":[97],"Onotoloy":[98],"(KiSAO).":[99],"While":[100],"it":[101],"was":[102],"possible":[103],"4":[106],"entirely":[111],"KiSAO,":[113],"now":[116],"allows":[117],"users":[118],"tasks,":[121],"model":[122,141,163],"changes,":[123],"ranges,":[124],"outputs":[126],"ontology":[129],"well.":[131],"growing":[137],"ecosystem":[138],"investigators,":[140],"languages,":[142],"tools,":[145,160],"including":[146],"various":[147],"languages":[148],"constraint-based,":[150],"kinetic,":[151],"qualitative,":[152],"rule-based,":[153],"spatial":[155],"models,":[156],"visual":[161],"editors,":[162],"repositories,":[164],"validators.":[166],"Additional":[167],"about":[169],"available":[172],"at":[173],"https://sed-ml.org/.":[174]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":2}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}
