{"id":"https://openalex.org/W1996984709","doi":"https://doi.org/10.1186/1471-2105-11-404","title":"RuleMonkey: software for stochastic simulation of rule-based models","display_name":"RuleMonkey: software for stochastic simulation of rule-based models","publication_year":2010,"publication_date":"2010-07-30","ids":{"openalex":"https://openalex.org/W1996984709","doi":"https://doi.org/10.1186/1471-2105-11-404","mag":"1996984709","pmid":"https://pubmed.ncbi.nlm.nih.gov/20673321"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-11-404","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-11-404","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-11-404","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","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 Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-11-404","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5061748422","display_name":"Joshua Colvin","orcid":"https://orcid.org/0000-0001-5938-3059"},"institutions":[{"id":"https://openalex.org/I1284308235","display_name":"Translational Genomics Research Institute","ror":"https://ror.org/02hfpnk21","country_code":"US","type":"facility","lineage":["https://openalex.org/I1284308235"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Joshua Colvin","raw_affiliation_strings":["Clinical Translational Research Division, Translational Genomics Research Institute, Phoenix, AZ 85004, USA","Translational Genomics Research Institute"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Clinical Translational Research Division, Translational Genomics Research Institute, Phoenix, AZ 85004, USA","institution_ids":["https://openalex.org/I1284308235"]},{"raw_affiliation_string":"Translational Genomics Research Institute","institution_ids":["https://openalex.org/I1284308235"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036070075","display_name":"Michael Monine","orcid":"https://orcid.org/0000-0001-8381-1594"},"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":false,"raw_author_name":"Michael I Monine","raw_affiliation_strings":["Theoretical Biology and Biophysics Group, Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA","Theoretical Biology and Biophysics Group, Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Theoretical Biology and Biophysics Group, Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA","institution_ids":["https://openalex.org/I1343871089"]},{"raw_affiliation_string":"Theoretical Biology and Biophysics Group, Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, USA","institution_ids":["https://openalex.org/I1343871089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056381387","display_name":"Ryan N. Gutenkunst","orcid":"https://orcid.org/0000-0002-8659-0579"},"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":false,"raw_author_name":"Ryan N Gutenkunst","raw_affiliation_strings":["Theoretical Biology and Biophysics Group, Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA","Theoretical Biology and Biophysics Group, Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Theoretical Biology and Biophysics Group, Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA","institution_ids":["https://openalex.org/I1343871089"]},{"raw_affiliation_string":"Theoretical Biology and Biophysics Group, Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, USA","institution_ids":["https://openalex.org/I1343871089"]}]},{"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"]},{"id":"https://openalex.org/I169521973","display_name":"University of New Mexico","ror":"https://ror.org/05fs6jp91","country_code":"US","type":"education","lineage":["https://openalex.org/I169521973"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"William S Hlavacek","raw_affiliation_strings":["Department of Biology, University of New Mexico, Albuquerque, NM, 87131, USA","Theoretical Biology and Biophysics Group, Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA","Los Alamos National Laboratory","University of New Mexico"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology, University of New Mexico, Albuquerque, NM, 87131, USA","institution_ids":["https://openalex.org/I169521973"]},{"raw_affiliation_string":"Theoretical Biology and Biophysics Group, Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA","institution_ids":["https://openalex.org/I1343871089"]},{"raw_affiliation_string":"Los Alamos National Laboratory","institution_ids":["https://openalex.org/I1343871089"]},{"raw_affiliation_string":"University of New Mexico","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080900202","display_name":"Daniel D. Von Hoff","orcid":"https://orcid.org/0000-0003-4723-7681"},"institutions":[{"id":"https://openalex.org/I1284308235","display_name":"Translational Genomics Research Institute","ror":"https://ror.org/02hfpnk21","country_code":"US","type":"facility","lineage":["https://openalex.org/I1284308235"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Daniel D Von Hoff","raw_affiliation_strings":["Clinical Translational Research Division, Translational Genomics Research Institute, Phoenix, AZ, 85004, USA","Translational Genomics Research Institute"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Clinical Translational Research Division, Translational Genomics Research Institute, Phoenix, AZ, 85004, USA","institution_ids":["https://openalex.org/I1284308235"]},{"raw_affiliation_string":"Translational Genomics Research Institute","institution_ids":["https://openalex.org/I1284308235"]}]},{"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/I1284308235","display_name":"Translational Genomics Research Institute","ror":"https://ror.org/02hfpnk21","country_code":"US","type":"facility","lineage":["https://openalex.org/I1284308235"]},{"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":["Clinical Translational Research Division, Translational Genomics Research Institute, Phoenix, AZ, 85004, USA","Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA","Translational Genomics Research Institute","Northern Arizona University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Clinical Translational Research Division, Translational Genomics Research Institute, Phoenix, AZ, 85004, USA","institution_ids":["https://openalex.org/I1284308235"]},{"raw_affiliation_string":"Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA","institution_ids":["https://openalex.org/I203172682"]},{"raw_affiliation_string":"Translational Genomics Research Institute","institution_ids":["https://openalex.org/I1284308235"]},{"raw_affiliation_string":"Northern Arizona University","institution_ids":["https://openalex.org/I203172682"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5064022214"],"corresponding_institution_ids":["https://openalex.org/I1284308235","https://openalex.org/I203172682"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":3.404,"has_fulltext":true,"cited_by_count":56,"citation_normalized_percentile":{"value":0.92698113,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"11","issue":"1","first_page":"404","last_page":"404"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9413999915122986,"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":0.9413999915122986,"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":0.01679999940097332,"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":0.006800000090152025,"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/computer-science","display_name":"Computer science","score":0.6594398021697998},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5372066497802734},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.4119178056716919},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.38319826126098633},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.3758431673049927},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.33020031452178955},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.3171560764312744},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.19437599182128906},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.12800922989845276}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6594398021697998},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5372066497802734},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.4119178056716919},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.38319826126098633},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.3758431673049927},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.33020031452178955},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.3171560764312744},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.19437599182128906},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.12800922989845276},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"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":"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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"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":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","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":5,"locations":[{"id":"doi:10.1186/1471-2105-11-404","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-11-404","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-11-404","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","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 Bioinformatics","raw_type":"journal-article"},{"id":"pmid:20673321","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20673321","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 bioinformatics","raw_type":null},{"id":"pmh:oai:osti.gov:1626271","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1626271","pdf_url":"https://www.osti.gov/servlets/purl/1626271","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:doaj.org/article:a5dd51bb29aa4b7dba8bc5367220db45","is_oa":false,"landing_page_url":"https://doaj.org/article/a5dd51bb29aa4b7dba8bc5367220db45","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 11, Iss 1, p 404 (2010)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2921409","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2921409","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 Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-11-404","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-11-404","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-11-404","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","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 Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3521391358","display_name":null,"funder_award_id":"CA109552","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"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/G3678775592","display_name":null,"funder_award_id":"AI35997","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G4883031359","display_name":null,"funder_award_id":"GM076570","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/G61956310","display_name":null,"funder_award_id":"NS042262","funder_id":"https://openalex.org/F4320337359","funder_display_name":"National Institute of Neurological Disorders and Stroke"},{"id":"https://openalex.org/G928841278","display_name":null,"funder_award_id":"contract DE-AC52-06NA25396","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"}],"funders":[{"id":"https://openalex.org/F4320306084","display_name":"U.S. Department of Energy","ror":"https://ror.org/01bj3aw27"},{"id":"https://openalex.org/F4320332140","display_name":"Arizona Biomedical Research Commission","ror":"https://ror.org/01smpj292"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"},{"id":"https://openalex.org/F4320337359","display_name":"National Institute of Neurological Disorders and Stroke","ror":"https://ror.org/01s5ya894"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1996984709.pdf","grobid_xml":"https://content.openalex.org/works/W1996984709.grobid-xml"},"referenced_works_count":57,"referenced_works":["https://openalex.org/W323766208","https://openalex.org/W1495323209","https://openalex.org/W1607824205","https://openalex.org/W1619146604","https://openalex.org/W1659468365","https://openalex.org/W1963674484","https://openalex.org/W1969369091","https://openalex.org/W1971713290","https://openalex.org/W1973641880","https://openalex.org/W1974974415","https://openalex.org/W1977290213","https://openalex.org/W1985911638","https://openalex.org/W1987129107","https://openalex.org/W2010152893","https://openalex.org/W2013245328","https://openalex.org/W2016493782","https://openalex.org/W2025672284","https://openalex.org/W2034269086","https://openalex.org/W2034492556","https://openalex.org/W2040860090","https://openalex.org/W2042629507","https://openalex.org/W2054047789","https://openalex.org/W2054279875","https://openalex.org/W2069941324","https://openalex.org/W2078734278","https://openalex.org/W2079704365","https://openalex.org/W2081098704","https://openalex.org/W2082874501","https://openalex.org/W2097319997","https://openalex.org/W2099693848","https://openalex.org/W2104655345","https://openalex.org/W2105038431","https://openalex.org/W2121811364","https://openalex.org/W2134923619","https://openalex.org/W2135354983","https://openalex.org/W2137561154","https://openalex.org/W2139941949","https://openalex.org/W2144063122","https://openalex.org/W2145006655","https://openalex.org/W2147985467","https://openalex.org/W2148315081","https://openalex.org/W2149999958","https://openalex.org/W2151251638","https://openalex.org/W2157989234","https://openalex.org/W2159629828","https://openalex.org/W2163493106","https://openalex.org/W2165700291","https://openalex.org/W2165714871","https://openalex.org/W2166522131","https://openalex.org/W2167101540","https://openalex.org/W2167154952","https://openalex.org/W2169193349","https://openalex.org/W2170780924","https://openalex.org/W2174466165","https://openalex.org/W2175715045","https://openalex.org/W2611943439","https://openalex.org/W4251538155"],"related_works":["https://openalex.org/W2415545834","https://openalex.org/W2069695727","https://openalex.org/W2118505788","https://openalex.org/W4254166511","https://openalex.org/W2150084125","https://openalex.org/W1542823905","https://openalex.org/W1490878237","https://openalex.org/W2990314835","https://openalex.org/W2131319730","https://openalex.org/W2059850119"],"abstract_inverted_index":{"BACKGROUND:":[0],"The":[1,41,117,177],"system-level":[2],"dynamics":[3,81],"of":[4,33,48,59,73,85,94,114,119,126,129,146,149,168,233,260,279],"many":[5,74],"molecular":[6],"interactions,":[7,10],"particularly":[8],"protein-protein":[9],"can":[11,19,185],"be":[12,20,67,186],"conveniently":[13],"represented":[14],"using":[15,22],"reaction":[16,39,42,235,286],"rules,":[17],"which":[18,161,283],"specified":[21],"model-specification":[23],"languages,":[24],"such":[25,136,199],"as":[26,55,200,307,316],"the":[27,60,71,95,111,127,142,208,224,231,234,277,284],"BioNetGen":[28],"language":[29],"(BNGL).":[30],"A":[31],"set":[32,47],"rules":[34,49,64,193,201],"implicitly":[35],"defines":[36],"a":[37,46,56,83,156,163,308,317,322],"(bio)chemical":[38],"network.":[40],"network":[43,61,80,86,115],"implied":[44,62,131],"by":[45,63,132],"is":[50,82,124,138,172,179,210,291,304,313],"often":[51],"very":[52],"large,":[53],"and":[54,144,247,328],"result,":[57],"generation":[58],"tends":[65],"to":[66,174],"computationally":[68],"expensive.":[69],"Moreover,":[70],"cost":[72,118],"commonly":[75],"used":[76],"methods":[77,101,123,137,216],"for":[78,102,141,166,181,202,257,282,296,325],"simulating":[79,103],"function":[84],"size.":[87],"Together":[88],"these":[89,120],"factors":[90],"have":[91,106,195,301],"limited":[92],"application":[93,197,310],"rule-based":[96,104,147,169,182,261,280,330],"modeling":[97],"approach.":[98],"Recently,":[99],"several":[100],"models":[105,148,170,183,191,281],"been":[107],"developed":[108],"that":[109,171,184,194,217,227,241,299],"avoid":[110],"expensive":[112],"step":[113],"generation.":[116],"\"network-free\"":[121],"simulation":[122,143,167,225,245,259,272,278,318],"independent":[125],"number":[128],"reactions":[130],"rules.":[133],"Software":[134],"implementing":[135,270],"now":[139],"needed":[140],"analysis":[145],"biochemical":[150],"systems.":[151],"RESULTS:":[152],"Here,":[153],"we":[154,248,300],"present":[155],"software":[157],"tool":[158,256],"called":[159],"RuleMonkey,":[160],"implements":[162],"network-free":[164,215,258,271],"method":[165,178,209],"similar":[173],"Gillespie's":[175],"method.":[176],"suitable":[180],"encoded":[187],"in":[188,223],"BNGL,":[189],"including":[190],"with":[192],"global":[196],"conditions,":[198],"intramolecular":[203],"association":[204],"reactions.":[205],"In":[206],"addition,":[207],"rejection":[211],"free,":[212],"unlike":[213],"other":[214],"introduce":[218],"null":[219],"events,":[220],"i.e.,":[221],"steps":[222],"procedure":[226],"do":[228],"not":[229],"change":[230],"state":[232],"system":[236],"being":[237],"simulated.":[238],"We":[239,263],"verify":[240],"RuleMonkey":[242,266,275,303],"produces":[243],"correct":[244],"results,":[246],"compare":[249,265],"its":[250],"performance":[251],"against":[252,267],"DYNSTOC,":[253],"another":[254],"BNGL-compliant":[255],"models.":[262,331],"also":[264,314],"problem-specific":[268],"codes":[269],"methods.":[273],"CONCLUSIONS:":[274],"enables":[276],"underlying":[285],"networks":[287],"are":[288],"large.":[289],"It":[290,312],"typically":[292],"faster":[293],"than":[294],"DYNSTOC":[295],"benchmark":[297],"problems":[298],"examined.":[302],"freely":[305],"available":[306,315],"stand-alone":[309],"http://public.tgen.org/rulemonkey.":[311],"engine":[319],"within":[320],"GetBonNie,":[321],"web-based":[323],"environment":[324],"building,":[326],"analyzing":[327],"sharing":[329]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":6},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":7},{"year":2013,"cited_by_count":8},{"year":2012,"cited_by_count":6}],"updated_date":"2026-06-24T13:16:06.693445","created_date":"2025-10-10T00:00:00"}
