{"id":"https://openalex.org/W2196501986","doi":"https://doi.org/10.1186/s12918-015-0237-0","title":"JigCell Run Manager (JC-RM): a tool for managing large sets of biochemical model parametrizations","display_name":"JigCell Run Manager (JC-RM): a tool for managing large sets of biochemical model parametrizations","publication_year":2015,"publication_date":"2015-12-01","ids":{"openalex":"https://openalex.org/W2196501986","doi":"https://doi.org/10.1186/s12918-015-0237-0","mag":"2196501986","pmid":"https://pubmed.ncbi.nlm.nih.gov/26704692"},"language":"en","primary_location":{"id":"doi:10.1186/s12918-015-0237-0","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12918-015-0237-0","pdf_url":"https://bmcsystbiol.biomedcentral.com/track/pdf/10.1186/s12918-015-0237-0","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Systems Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://bmcsystbiol.biomedcentral.com/track/pdf/10.1186/s12918-015-0237-0","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5089800114","display_name":"Alida Palmisano","orcid":"https://orcid.org/0000-0002-1859-3719"},"institutions":[{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Alida Palmisano","raw_affiliation_strings":["Department of Biological Sciences, Virginia Tech, 1405 Perry Street, Blacksburg, 24061, VA, USA. alida.palmisano@gmail.com","Department of Computer Science, Virginia Tech, 2202 Kraft Drive, Blacksburg, 24060, VA, USA. alida.palmisano@gmail.com","Department of Computer Science, Virginia Tech, 2202 Kraft Drive, Blacksburg, 24060, VA, USA"],"raw_orcid":"https://orcid.org/0000-0002-1859-3719","affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, Virginia Tech, 1405 Perry Street, Blacksburg, 24061, VA, USA. alida.palmisano@gmail.com","institution_ids":["https://openalex.org/I859038795"]},{"raw_affiliation_string":"Department of Computer Science, Virginia Tech, 2202 Kraft Drive, Blacksburg, 24060, VA, USA. alida.palmisano@gmail.com","institution_ids":["https://openalex.org/I859038795"]},{"raw_affiliation_string":"Department of Computer Science, Virginia Tech, 2202 Kraft Drive, Blacksburg, 24060, VA, USA","institution_ids":["https://openalex.org/I859038795"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108092912","display_name":"Stefan Hoops","orcid":null},"institutions":[{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Stefan Hoops","raw_affiliation_strings":["Virginia Bioinformatics Institute, 1015 Life Science Circle, Blacksburg, 24061, VA, USA. shoops@vbi.vt.edu","Virginia Bioinformatics Institute, 1015 Life Science Circle, Blacksburg, 24061, VA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Virginia Bioinformatics Institute, 1015 Life Science Circle, Blacksburg, 24061, VA, USA. shoops@vbi.vt.edu","institution_ids":["https://openalex.org/I859038795"]},{"raw_affiliation_string":"Virginia Bioinformatics Institute, 1015 Life Science Circle, Blacksburg, 24061, VA, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108116806","display_name":"Layne T. Watson","orcid":null},"institutions":[{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Layne T. Watson","raw_affiliation_strings":["Department of Computer Science, Virginia Tech, 2202 Kraft Drive, Blacksburg, 24060, VA, USA. ltw@vt.edu","Department of Mathematics, Virginia Tech, 225 Stanger Street, Blacksburg, 24061, VA, USA. ltw@vt.edu","Department of Computer Science, Virginia Tech, 2202 Kraft Drive, Blacksburg, 24060, VA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Virginia Tech, 2202 Kraft Drive, Blacksburg, 24060, VA, USA. ltw@vt.edu","institution_ids":["https://openalex.org/I859038795"]},{"raw_affiliation_string":"Department of Mathematics, Virginia Tech, 225 Stanger Street, Blacksburg, 24061, VA, USA. ltw@vt.edu","institution_ids":["https://openalex.org/I859038795"]},{"raw_affiliation_string":"Department of Computer Science, Virginia Tech, 2202 Kraft Drive, Blacksburg, 24060, VA, USA","institution_ids":["https://openalex.org/I859038795"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007228634","display_name":"Thomas C. Jones","orcid":"https://orcid.org/0000-0001-9264-1507"},"institutions":[{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Thomas C. Jones","raw_affiliation_strings":["Department of Computer Science, Virginia Tech, 2202 Kraft Drive, Blacksburg, 24060, VA, USA. tjones21@vt.edu","Department of Computer Science, Virginia Tech, 2202 Kraft Drive, Blacksburg, 24060, VA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Virginia Tech, 2202 Kraft Drive, Blacksburg, 24060, VA, USA. tjones21@vt.edu","institution_ids":["https://openalex.org/I859038795"]},{"raw_affiliation_string":"Department of Computer Science, Virginia Tech, 2202 Kraft Drive, Blacksburg, 24060, VA, USA","institution_ids":["https://openalex.org/I859038795"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028908910","display_name":"John J. Tyson","orcid":"https://orcid.org/0000-0001-7560-6013"},"institutions":[{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"John J. Tyson","raw_affiliation_strings":["Department of Biological Sciences, Virginia Tech, 1405 Perry Street, Blacksburg, 24061, VA, USA. tyson@vt.edu","Department of Biological Sciences, Virginia Tech, 1405 Perry Street, Blacksburg, 24061, VA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, Virginia Tech, 1405 Perry Street, Blacksburg, 24061, VA, USA. tyson@vt.edu","institution_ids":["https://openalex.org/I859038795"]},{"raw_affiliation_string":"Department of Biological Sciences, Virginia Tech, 1405 Perry Street, Blacksburg, 24061, VA, USA","institution_ids":["https://openalex.org/I859038795"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5012542741","display_name":"Clifford A. Shaffer","orcid":"https://orcid.org/0000-0003-0001-0295"},"institutions":[{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Clifford A. Shaffer","raw_affiliation_strings":["Department of Computer Science, Virginia Tech, 2202 Kraft Drive, Blacksburg, 24060, VA, USA. shaffer@cs.vt.edu","Department of Computer Science, Virginia Tech, 2202 Kraft Drive, Blacksburg, 24060, VA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Virginia Tech, 2202 Kraft Drive, Blacksburg, 24060, VA, USA. shaffer@cs.vt.edu","institution_ids":["https://openalex.org/I859038795"]},{"raw_affiliation_string":"Department of Computer Science, Virginia Tech, 2202 Kraft Drive, Blacksburg, 24060, VA, USA","institution_ids":["https://openalex.org/I859038795"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5089800114"],"corresponding_institution_ids":["https://openalex.org/I859038795"],"apc_list":null,"apc_paid":null,"fwci":0.3012,"has_fulltext":true,"cited_by_count":4,"citation_normalized_percentile":{"value":0.62838322,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"9","issue":"1","first_page":"95","last_page":"95"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.6865000128746033,"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":0.6865000128746033,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.15649999678134918,"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":0.030899999663233757,"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/hierarchy","display_name":"Hierarchy","score":0.6563806533813477},{"id":"https://openalex.org/keywords/sbml","display_name":"SBML","score":0.6560212969779968},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6354740858078003},{"id":"https://openalex.org/keywords/parameterized-complexity","display_name":"Parameterized complexity","score":0.50297611951828},{"id":"https://openalex.org/keywords/plot","display_name":"Plot (graphics)","score":0.48396992683410645},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.4239426255226135},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.42190513014793396},{"id":"https://openalex.org/keywords/java","display_name":"Java","score":0.412628173828125},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.3178911805152893},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3004017472267151},{"id":"https://openalex.org/keywords/markup-language","display_name":"Markup language","score":0.2533923387527466},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.24837446212768555},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.19127070903778076},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.1777067482471466},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.1053125262260437}],"concepts":[{"id":"https://openalex.org/C31170391","wikidata":"https://www.wikidata.org/wiki/Q188619","display_name":"Hierarchy","level":2,"score":0.6563806533813477},{"id":"https://openalex.org/C87186988","wikidata":"https://www.wikidata.org/wiki/Q452197","display_name":"SBML","level":4,"score":0.6560212969779968},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6354740858078003},{"id":"https://openalex.org/C165464430","wikidata":"https://www.wikidata.org/wiki/Q1570441","display_name":"Parameterized complexity","level":2,"score":0.50297611951828},{"id":"https://openalex.org/C167651023","wikidata":"https://www.wikidata.org/wiki/Q1474611","display_name":"Plot (graphics)","level":2,"score":0.48396992683410645},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.4239426255226135},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.42190513014793396},{"id":"https://openalex.org/C548217200","wikidata":"https://www.wikidata.org/wiki/Q251","display_name":"Java","level":2,"score":0.412628173828125},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.3178911805152893},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3004017472267151},{"id":"https://openalex.org/C45874996","wikidata":"https://www.wikidata.org/wiki/Q37045","display_name":"Markup language","level":3,"score":0.2533923387527466},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.24837446212768555},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.19127070903778076},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1777067482471466},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.1053125262260437},{"id":"https://openalex.org/C34447519","wikidata":"https://www.wikidata.org/wiki/Q179522","display_name":"Market economy","level":1,"score":0.0},{"id":"https://openalex.org/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","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":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":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","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":4,"locations":[{"id":"doi:10.1186/s12918-015-0237-0","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12918-015-0237-0","pdf_url":"https://bmcsystbiol.biomedcentral.com/track/pdf/10.1186/s12918-015-0237-0","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Systems Biology","raw_type":"journal-article"},{"id":"pmid:26704692","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26704692","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":"BMC systems biology","raw_type":null},{"id":"pmh:oai:vtechworks.lib.vt.edu:10919/73647","is_oa":true,"landing_page_url":"http://hdl.handle.net/10919/73647","pdf_url":null,"source":{"id":"https://openalex.org/S4306400248","display_name":"VTechWorks (Virginia Tech)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I859038795","host_organization_name":"Virginia Tech","host_organization_lineage":["https://openalex.org/I859038795"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:4690432","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4690432","pdf_url":null,"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":"BMC Syst Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12918-015-0237-0","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12918-015-0237-0","pdf_url":"https://bmcsystbiol.biomedcentral.com/track/pdf/10.1186/s12918-015-0237-0","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Systems Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2495017755","display_name":null,"funder_award_id":"R01-GM078989","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4902092621","display_name":null,"funder_award_id":"R01\u2013GM080219","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8430918491","display_name":null,"funder_award_id":"R01GM078989","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"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"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2196501986.pdf","grobid_xml":"https://content.openalex.org/works/W2196501986.grobid-xml"},"referenced_works_count":11,"referenced_works":["https://openalex.org/W1987081240","https://openalex.org/W2038264484","https://openalex.org/W2097319997","https://openalex.org/W2100058250","https://openalex.org/W2102653059","https://openalex.org/W2114124738","https://openalex.org/W2117822125","https://openalex.org/W2123783513","https://openalex.org/W2133552211","https://openalex.org/W2146685645","https://openalex.org/W2150750144"],"related_works":["https://openalex.org/W2150908245","https://openalex.org/W2211443823","https://openalex.org/W2097410126","https://openalex.org/W2136043941","https://openalex.org/W2043776573","https://openalex.org/W2735157934","https://openalex.org/W3080133182","https://openalex.org/W1869813392","https://openalex.org/W2026725606","https://openalex.org/W2020641517"],"abstract_inverted_index":{"BACKGROUND:":[0],"Most":[1],"biomolecular":[2],"reaction":[3],"modeling":[4,89,156],"tools":[5],"allow":[6],"users":[7],"to":[8,28,38,70,87,101,113,131,168,217,229],"build":[9],"models":[10],"with":[11,117,143,200,257],"a":[12,19,43,53,103,141,157,196,219,231],"single":[13],"list":[14,146],"of":[15,25,33,45,52,78,105,124,147,172,178,195,221],"parameter":[16,106,148,222],"values.":[17],"However,":[18],"common":[20],"scenario":[21,58],"involves":[22],"different":[23,166],"parameterizations":[24],"the":[26,31,40,68,79,92,99,118,152,173,183,192,215,237,247,272],"model":[27,65,142],"account":[29,169],"for":[30,36,42,136,170,176],"results":[32],"related":[34,179],"experiments,":[35],"example,":[37],"define":[39,102,218],"phenotypes":[41],"variety":[44],"mutations":[46,171],"(gene":[47],"knockout,":[48],"over":[49],"expression,":[50],"etc.)":[51],"specific":[54],"biochemical":[55],"network.":[56],"This":[57],"is":[59,150,241],"not":[60],"well":[61,128],"supported":[62],"by":[63],"existing":[64],"editors,":[66],"forcing":[67],"user":[69,264],"manually":[71],"generate,":[72],"store,":[73],"and":[74,109,112,133,203,210,225,228,236,245,266],"maintain":[75,230],"many":[76,165],"variations":[77],"same":[80],"model.":[81,120,239],"RESULTS:":[82],"We":[83],"developed":[84],"an":[85],"extension":[86],"our":[88],"editor":[90],"called":[91],"JigCell":[93],"Run":[94],"Manager":[95],"(JC-RM).":[96],"JC-RM":[97,121,185,213,240,250],"allows":[98,214],"modeler":[100,216],"hierarchy":[104,220,235],"values,":[107,223],"simulations,":[108],"plot":[110,226],"settings,":[111,227],"save":[114],"them":[115],"together":[116],"initial":[119,145,238],"supports":[122,191],"generation":[123],"simulation":[125],"plots,":[126],"as":[127,129],"export":[130],"COPASI":[132,248,273],"SBML":[134],"(L3V1)":[135],"further":[137],"analysis.":[138],"CONCLUSIONS:":[139],"Developing":[140],"its":[144,201],"values":[149],"just":[151],"first":[153],"step":[154],"in":[155,164,243],"biological":[158],"system.":[159],"Models":[160],"are":[161],"often":[162],"parameterized":[163],"ways":[167],"organism":[174],"and/or":[175],"sets":[177],"experiments":[180],"performed":[181],"on":[182,252],"organism.":[184],"offers":[186],"two":[187],"critical":[188],"features:":[189],"it":[190,204],"everyday":[193],"management":[194],"large":[197],"model,":[198],"complete":[199],"parameterizations,":[202],"facilitates":[205],"sharing":[206],"this":[207,234],"information":[208],"before":[209],"after":[211],"publication.":[212],"simulation,":[224],"relationship":[232],"between":[233],"implemented":[242],"Java":[244],"uses":[246],"API.":[249],"runs":[251],"all":[253],"major":[254],"operating":[255],"systems,":[256],"minimal":[258],"system":[259],"requirements.":[260],"Installers,":[261],"source":[262],"code,":[263],"manual,":[265],"examples":[267],"can":[268],"be":[269],"found":[270],"at":[271],"website":[274],"(":[275],"http://www.copasi.org/Projects":[276],").":[277]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":2}],"updated_date":"2026-04-29T09:16:38.111599","created_date":"2025-10-10T00:00:00"}
