{"id":"https://openalex.org/W2164554210","doi":"https://doi.org/10.1093/bioinformatics/btv655","title":"BioNetFit: a fitting tool compatible with BioNetGen, NFsim and distributed computing environments","display_name":"BioNetFit: a fitting tool compatible with BioNetGen, NFsim and distributed computing environments","publication_year":2015,"publication_date":"2015-11-09","ids":{"openalex":"https://openalex.org/W2164554210","doi":"https://doi.org/10.1093/bioinformatics/btv655","mag":"2164554210","pmid":"https://pubmed.ncbi.nlm.nih.gov/26556387"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btv655","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv655","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/5/798/25588979/btv655.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/32/5/798/25588979/btv655.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5015924036","display_name":"Brandon R. Thomas","orcid":null},"institutions":[{"id":"https://openalex.org/I203172682","display_name":"Northern Arizona University","ror":"https://ror.org/0272j5188","country_code":"US","type":"education","lineage":["https://openalex.org/I203172682"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Brandon R. Thomas","raw_affiliation_strings":["1 Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA,","institution_ids":["https://openalex.org/I203172682"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066868527","display_name":"Lily A. Chylek","orcid":"https://orcid.org/0000-0003-1216-1250"},"institutions":[{"id":"https://openalex.org/I203172682","display_name":"Northern Arizona University","ror":"https://ror.org/0272j5188","country_code":"US","type":"education","lineage":["https://openalex.org/I203172682"]},{"id":"https://openalex.org/I205783295","display_name":"Cornell University","ror":"https://ror.org/05bnh6r87","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lily A. Chylek","raw_affiliation_strings":["1 Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA,","2 Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA,","institution_ids":["https://openalex.org/I203172682"]},{"raw_affiliation_string":"2 Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA,","institution_ids":["https://openalex.org/I205783295"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061748422","display_name":"Joshua Colvin","orcid":"https://orcid.org/0000-0001-5938-3059"},"institutions":[{"id":"https://openalex.org/I203172682","display_name":"Northern Arizona University","ror":"https://ror.org/0272j5188","country_code":"US","type":"education","lineage":["https://openalex.org/I203172682"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Joshua Colvin","raw_affiliation_strings":["1 Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA,","institution_ids":["https://openalex.org/I203172682"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079251809","display_name":"Suman Sirimulla","orcid":"https://orcid.org/0000-0003-4665-6665"},"institutions":[{"id":"https://openalex.org/I182380053","display_name":"University of Health Sciences and Pharmacy","ror":"https://ror.org/01btzz102","country_code":"US","type":"education","lineage":["https://openalex.org/I182380053"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Suman Sirimulla","raw_affiliation_strings":["3 Department of Basic Sciences, Saint Louis College of Pharmacy, Saint Louis, MO, USA,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"3 Department of Basic Sciences, Saint Louis College of Pharmacy, Saint Louis, MO, USA,","institution_ids":["https://openalex.org/I182380053"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038047143","display_name":"Andrew H. A. Clayton","orcid":"https://orcid.org/0000-0002-6182-3049"},"institutions":[{"id":"https://openalex.org/I57093077","display_name":"Swinburne University of Technology","ror":"https://ror.org/031rekg67","country_code":"AU","type":"education","lineage":["https://openalex.org/I57093077"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Andrew H.A. Clayton","raw_affiliation_strings":["4 Center for Microphotonics, Faculty of Science, Engineering and Technology, Cell Biophysics Laboratory, Swinburne University of Technology, Hawthorn, VIC, Australia and"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"4 Center for Microphotonics, Faculty of Science, Engineering and Technology, Cell Biophysics Laboratory, Swinburne University of Technology, Hawthorn, VIC, Australia and","institution_ids":["https://openalex.org/I57093077"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016126519","display_name":"William S. Hlavacek","orcid":"https://orcid.org/0000-0003-4383-8711"},"institutions":[{"id":"https://openalex.org/I1343871089","display_name":"Los Alamos National Laboratory","ror":"https://ror.org/01e41cf67","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I1343871089","https://openalex.org/I198811213","https://openalex.org/I4210120050"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"William S. Hlavacek","raw_affiliation_strings":["5 Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"5 Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA","institution_ids":["https://openalex.org/I1343871089"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5064022214","display_name":"Richard G. Posner","orcid":"https://orcid.org/0000-0002-0489-9397"},"institutions":[{"id":"https://openalex.org/I203172682","display_name":"Northern Arizona University","ror":"https://ror.org/0272j5188","country_code":"US","type":"education","lineage":["https://openalex.org/I203172682"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Richard G. Posner","raw_affiliation_strings":["1 Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA,","institution_ids":["https://openalex.org/I203172682"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5016126519","https://openalex.org/A5064022214"],"corresponding_institution_ids":["https://openalex.org/I1343871089","https://openalex.org/I203172682"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":2.2169,"has_fulltext":true,"cited_by_count":35,"citation_normalized_percentile":{"value":0.88117032,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"32","issue":"5","first_page":"798","last_page":"800"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.44909998774528503,"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":0.44909998774528503,"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/T13362","display_name":"Slime Mold and Myxomycetes Research","score":0.08910000324249268,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11829","display_name":"Mathematical Biology Tumor Growth","score":0.08799999952316284,"subfield":{"id":"https://openalex.org/subfields/2611","display_name":"Modeling and Simulation"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/perl","display_name":"Perl","score":0.8549127578735352},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8251153230667114},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.6872119307518005},{"id":"https://openalex.org/keywords/consistency","display_name":"Consistency (knowledge bases)","score":0.6402856111526489},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.6063265800476074},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.5431609749794006},{"id":"https://openalex.org/keywords/open-source","display_name":"Open source","score":0.5313743948936462},{"id":"https://openalex.org/keywords/os-x","display_name":"OS X","score":0.5130330324172974},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.45266422629356384},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.3467201590538025},{"id":"https://openalex.org/keywords/distributed-computing","display_name":"Distributed computing","score":0.33717137575149536},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.31766581535339355},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.0962158739566803},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.08695760369300842}],"concepts":[{"id":"https://openalex.org/C2777002779","wikidata":"https://www.wikidata.org/wiki/Q42478","display_name":"Perl","level":2,"score":0.8549127578735352},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8251153230667114},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.6872119307518005},{"id":"https://openalex.org/C2776436953","wikidata":"https://www.wikidata.org/wiki/Q5163215","display_name":"Consistency (knowledge bases)","level":2,"score":0.6402856111526489},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.6063265800476074},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.5431609749794006},{"id":"https://openalex.org/C3018397939","wikidata":"https://www.wikidata.org/wiki/Q3644502","display_name":"Open source","level":3,"score":0.5313743948936462},{"id":"https://openalex.org/C515153823","wikidata":"https://www.wikidata.org/wiki/Q14116","display_name":"OS X","level":3,"score":0.5130330324172974},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.45266422629356384},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.3467201590538025},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.33717137575149536},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.31766581535339355},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.0962158739566803},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.08695760369300842}],"mesh":[{"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}],"locations_count":7,"locations":[{"id":"doi:10.1093/bioinformatics/btv655","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv655","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/5/798/25588979/btv655.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:26556387","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26556387","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:osti.gov:1406198","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1406198","pdf_url":"https://www.osti.gov/servlets/purl/1406198","source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:scholarworks.utep.edu:pharm_papers-1025","is_oa":false,"landing_page_url":"https://scholarworks.utep.edu/pharm_papers/26","pdf_url":null,"source":{"id":"https://openalex.org/S4377196403","display_name":"scholarworks - UTEP (The University of Texas at El Paso)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I164936912","host_organization_name":"The University of Texas at El Paso","host_organization_lineage":["https://openalex.org/I164936912"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Departmental Papers (Pharmacy)","raw_type":"text"},{"id":"pmh:oai:open-archive.highwire.org:bioinfo:32/5/798","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/32/5/798","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"},{"id":"pmh:oai:pubmedcentral.nih.gov:4907397","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4907397","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:researchbank.swinburne.edu.au:c02707cf-ee8c-4098-86f9-b5670f986700/1","is_oa":false,"landing_page_url":"http://hdl.handle.net/1959.3/415307","pdf_url":null,"source":{"id":"https://openalex.org/S4306401157","display_name":"Swinburne Research Bank (Swinburne University of Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I57093077","host_organization_name":"Swinburne University of Technology","host_organization_lineage":["https://openalex.org/I57093077"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics, Vol. 32, no. 5 (Mar 2016), pp. 798-800","raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btv655","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv655","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/5/798/25588979/btv655.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":[{"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure","score":0.5}],"awards":[{"id":"https://openalex.org/G2613504715","display_name":null,"funder_award_id":"DE-AC52-06NA25396","funder_id":"https://openalex.org/F4320332369","funder_display_name":"National Nuclear Security Administration"},{"id":"https://openalex.org/G359075050","display_name":null,"funder_award_id":"DE-AC52-06NA25396","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G3700687868","display_name":null,"funder_award_id":"AC52-06NA25396","funder_id":"https://openalex.org/F4320338304","funder_display_name":"Los Alamos National Laboratory"},{"id":"https://openalex.org/G4293014701","display_name":null,"funder_award_id":"R01GM111510","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G5578042355","display_name":null,"funder_award_id":"R01 GM111510","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G5657628048","display_name":null,"funder_award_id":"AC52-06NA25396","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G5713387433","display_name":null,"funder_award_id":"DE-AC52-06NA25396","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5853594108","display_name":null,"funder_award_id":"P50 GM085273","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G75892134","display_name":null,"funder_award_id":"DE-AC52-06NA25396","funder_id":"https://openalex.org/F4320338304","funder_display_name":"Los Alamos National Laboratory"}],"funders":[{"id":"https://openalex.org/F4320306084","display_name":"U.S. Department of Energy","ror":"https://ror.org/01bj3aw27"},{"id":"https://openalex.org/F4320310831","display_name":"Northern Arizona University","ror":"https://ror.org/0272j5188"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320332369","display_name":"National Nuclear Security Administration","ror":"https://ror.org/03sk1we31"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320338304","display_name":"Los Alamos National Laboratory","ror":"https://ror.org/01e41cf67"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2164554210.pdf","grobid_xml":"https://content.openalex.org/works/W2164554210.grobid-xml"},"referenced_works_count":16,"referenced_works":["https://openalex.org/W1512383952","https://openalex.org/W1563071114","https://openalex.org/W1738124305","https://openalex.org/W2047121664","https://openalex.org/W2061279689","https://openalex.org/W2066732411","https://openalex.org/W2121490181","https://openalex.org/W2125620011","https://openalex.org/W2150908245","https://openalex.org/W2169193349","https://openalex.org/W2170780924","https://openalex.org/W2303100661","https://openalex.org/W2327621234","https://openalex.org/W2330374543","https://openalex.org/W3004157836","https://openalex.org/W6698159345"],"related_works":["https://openalex.org/W4386745624","https://openalex.org/W2113128227","https://openalex.org/W632256878","https://openalex.org/W4211197663","https://openalex.org/W2491403535","https://openalex.org/W3123068371","https://openalex.org/W2479811461","https://openalex.org/W2104915799","https://openalex.org/W2355429491","https://openalex.org/W645887431"],"abstract_inverted_index":{"UNLABELLED:":[0],"Rule-based":[1],"models":[2],"are":[3,60,99],"analyzed":[4],"with":[5,31,56],"specialized":[6],"simulators,":[7],"such":[8],"as":[9],"those":[10],"provided":[11],"by":[12],"the":[13],"BioNetGen":[14,32],"and":[15,33,74,77],"NFsim":[16],"open-source":[17],"software":[18],"packages.":[19],"Here,":[20],"we":[21],"present":[22],"BioNetFit,":[23],"a":[24],"general-purpose":[25],"fitting":[26,48],"tool":[27],"that":[28],"is":[29,36,91],"compatible":[30],"NFsim.":[34],"BioNetFit":[35,66,87],"designed":[37],"to":[38],"take":[39],"advantage":[40],"of":[41,51],"distributed":[42],"computing":[43],"resources.":[44],"This":[45],"feature":[46],"facilitates":[47],"(i.e.":[49],"optimization":[50],"parameter":[52],"values":[53],"for":[54],"consistency":[55],"data)":[57],"when":[58],"simulations":[59],"computationally":[61],"expensive.":[62],"AVAILABILITY":[63],"AND":[64],"IMPLEMENTATION:":[65],"can":[67],"be":[68],"used":[69],"on":[70,78],"stand-alone":[71],"Mac,":[72],"Windows/Cygwin,":[73],"Linux":[75],"platforms":[76],"Linux-based":[79],"clusters":[80],"running":[81],"SLURM,":[82],"Torque/PBS,":[83],"or":[84],"SGE.":[85],"The":[86],"source":[88],"code":[89],"(Perl)":[90],"freely":[92],"available":[93,100],"(http://bionetfit.nau.edu).":[94],"SUPPLEMENTARY":[95],"INFORMATION:":[96],"Supplementary":[97],"data":[98],"at":[101],"Bioinformatics":[102],"online.":[103],"CONTACT:":[104],"bionetgen.help@gmail.com.":[105]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":9},{"year":2018,"cited_by_count":5},{"year":2017,"cited_by_count":7},{"year":2016,"cited_by_count":3}],"updated_date":"2026-07-02T09:51:11.867554","created_date":"2025-10-10T00:00:00"}
