{"id":"https://openalex.org/W2743050849","doi":"https://doi.org/10.1093/bioinformatics/btx492","title":"Holmes: a graphical tool for development, simulation and analysis of Petri net based models of complex biological systems","display_name":"Holmes: a graphical tool for development, simulation and analysis of Petri net based models of complex biological systems","publication_year":2017,"publication_date":"2017-08-04","ids":{"openalex":"https://openalex.org/W2743050849","doi":"https://doi.org/10.1093/bioinformatics/btx492","mag":"2743050849","pmid":"https://pubmed.ncbi.nlm.nih.gov/28961696"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btx492","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx492","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/23/3822/25168041/btx492.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/33/23/3822/25168041/btx492.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5081839975","display_name":"Marcin Radom","orcid":"https://orcid.org/0000-0002-4174-7069"},"institutions":[{"id":"https://openalex.org/I4210152414","display_name":"Institute of Bioorganic Chemistry, Polish Academy of Sciences","ror":"https://ror.org/04ejdtr48","country_code":"PL","type":"facility","lineage":["https://openalex.org/I4210152414","https://openalex.org/I99542240"]},{"id":"https://openalex.org/I46597724","display_name":"Pozna\u0144 University of Technology","ror":"https://ror.org/00p7p3302","country_code":"PL","type":"education","lineage":["https://openalex.org/I46597724"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Marcin Radom","raw_affiliation_strings":["Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland","Institute of Computing Science, Poznan University of Technology, Poznan, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland","institution_ids":["https://openalex.org/I4210152414"]},{"raw_affiliation_string":"Institute of Computing Science, Poznan University of Technology, Poznan, Poland","institution_ids":["https://openalex.org/I46597724"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027621077","display_name":"Agnieszka Rybarczyk","orcid":"https://orcid.org/0000-0003-4115-0737"},"institutions":[{"id":"https://openalex.org/I4210152414","display_name":"Institute of Bioorganic Chemistry, Polish Academy of Sciences","ror":"https://ror.org/04ejdtr48","country_code":"PL","type":"facility","lineage":["https://openalex.org/I4210152414","https://openalex.org/I99542240"]},{"id":"https://openalex.org/I46597724","display_name":"Pozna\u0144 University of Technology","ror":"https://ror.org/00p7p3302","country_code":"PL","type":"education","lineage":["https://openalex.org/I46597724"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Agnieszka Rybarczyk","raw_affiliation_strings":["Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland","Institute of Computing Science, Poznan University of Technology, Poznan, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland","institution_ids":["https://openalex.org/I4210152414"]},{"raw_affiliation_string":"Institute of Computing Science, Poznan University of Technology, Poznan, Poland","institution_ids":["https://openalex.org/I46597724"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067065872","display_name":"Bart\u0142omiej Szawulak","orcid":"https://orcid.org/0000-0002-7584-7383"},"institutions":[{"id":"https://openalex.org/I46597724","display_name":"Pozna\u0144 University of Technology","ror":"https://ror.org/00p7p3302","country_code":"PL","type":"education","lineage":["https://openalex.org/I46597724"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Bart\u0142omiej Szawulak","raw_affiliation_strings":["Institute of Computing Science, Poznan University of Technology, Poznan, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Computing Science, Poznan University of Technology, Poznan, Poland","institution_ids":["https://openalex.org/I46597724"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091825148","display_name":"Hubert Andrzejewski","orcid":null},"institutions":[{"id":"https://openalex.org/I46597724","display_name":"Pozna\u0144 University of Technology","ror":"https://ror.org/00p7p3302","country_code":"PL","type":"education","lineage":["https://openalex.org/I46597724"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Hubert Andrzejewski","raw_affiliation_strings":["Institute of Computing Science, Poznan University of Technology, Poznan, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Computing Science, Poznan University of Technology, Poznan, Poland","institution_ids":["https://openalex.org/I46597724"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035154602","display_name":"Piotr Chabelski","orcid":null},"institutions":[{"id":"https://openalex.org/I46597724","display_name":"Pozna\u0144 University of Technology","ror":"https://ror.org/00p7p3302","country_code":"PL","type":"education","lineage":["https://openalex.org/I46597724"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Piotr Chabelski","raw_affiliation_strings":["Institute of Computing Science, Poznan University of Technology, Poznan, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Computing Science, Poznan University of Technology, Poznan, Poland","institution_ids":["https://openalex.org/I46597724"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001643415","display_name":"Adam Kozak","orcid":"https://orcid.org/0000-0002-4914-4705"},"institutions":[{"id":"https://openalex.org/I46597724","display_name":"Pozna\u0144 University of Technology","ror":"https://ror.org/00p7p3302","country_code":"PL","type":"education","lineage":["https://openalex.org/I46597724"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Adam Kozak","raw_affiliation_strings":["Institute of Computing Science, Poznan University of Technology, Poznan, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Computing Science, Poznan University of Technology, Poznan, Poland","institution_ids":["https://openalex.org/I46597724"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5054092040","display_name":"Piotr Formanowicz","orcid":"https://orcid.org/0000-0003-2719-3677"},"institutions":[{"id":"https://openalex.org/I4210152414","display_name":"Institute of Bioorganic Chemistry, Polish Academy of Sciences","ror":"https://ror.org/04ejdtr48","country_code":"PL","type":"facility","lineage":["https://openalex.org/I4210152414","https://openalex.org/I99542240"]},{"id":"https://openalex.org/I46597724","display_name":"Pozna\u0144 University of Technology","ror":"https://ror.org/00p7p3302","country_code":"PL","type":"education","lineage":["https://openalex.org/I46597724"]}],"countries":["PL"],"is_corresponding":true,"raw_author_name":"Piotr Formanowicz","raw_affiliation_strings":["Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland","Institute of Computing Science, Poznan University of Technology, Poznan, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland","institution_ids":["https://openalex.org/I4210152414"]},{"raw_affiliation_string":"Institute of Computing Science, Poznan University of Technology, Poznan, Poland","institution_ids":["https://openalex.org/I46597724"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5054092040"],"corresponding_institution_ids":["https://openalex.org/I4210152414","https://openalex.org/I46597724"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.1135,"has_fulltext":true,"cited_by_count":24,"citation_normalized_percentile":{"value":0.76761169,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"33","issue":"23","first_page":"3822","last_page":"3823"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.48750001192092896,"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":0.48750001192092896,"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/T14135","display_name":"Cancer and biochemical research","score":0.16930000483989716,"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/T11125","display_name":"Petri Nets in System Modeling","score":0.052000001072883606,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/petri-net","display_name":"Petri net","score":0.8263078331947327},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7053840160369873},{"id":"https://openalex.org/keywords/net","display_name":"Net (polyhedron)","score":0.4833204746246338},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.4258444607257843},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.4186723232269287},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.10654386878013611}],"concepts":[{"id":"https://openalex.org/C38677869","wikidata":"https://www.wikidata.org/wiki/Q724168","display_name":"Petri net","level":2,"score":0.8263078331947327},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7053840160369873},{"id":"https://openalex.org/C14166107","wikidata":"https://www.wikidata.org/wiki/Q253829","display_name":"Net (polyhedron)","level":2,"score":0.4833204746246338},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.4258444607257843},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.4186723232269287},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.10654386878013611},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0}],"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":"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":"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":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btx492","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx492","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/23/3822/25168041/btx492.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:28961696","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28961696","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}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btx492","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx492","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/23/3822/25168041/btx492.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":[],"awards":[{"id":"https://openalex.org/G765666886","display_name":null,"funder_award_id":"2012/07/B/ST6/01537","funder_id":"https://openalex.org/F4320322511","funder_display_name":"Narodowe Centrum Nauki"}],"funders":[{"id":"https://openalex.org/F4320322511","display_name":"Narodowe Centrum Nauki","ror":"https://ror.org/03ha2q922"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2743050849.pdf","grobid_xml":"https://content.openalex.org/works/W2743050849.grobid-xml"},"referenced_works_count":6,"referenced_works":["https://openalex.org/W95898642","https://openalex.org/W1568573127","https://openalex.org/W1996109622","https://openalex.org/W2097446858","https://openalex.org/W2134784304","https://openalex.org/W4249484115"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W1551257573","https://openalex.org/W4230983483","https://openalex.org/W1980200158","https://openalex.org/W2132799268","https://openalex.org/W2154794415","https://openalex.org/W1538101305","https://openalex.org/W791317142","https://openalex.org/W2285033125","https://openalex.org/W2119655921"],"abstract_inverted_index":{"SUMMARY:":[0],"Model":[1],"development":[2,28,103],"and":[3,61,104,130,178],"its":[4],"analysis":[5,68,105,114,137],"is":[6,143],"a":[7,19,23,32,47,55,82,86,97,165],"fundamental":[8],"step":[9],"in":[10,81,89],"systems":[11],"biology.":[12],"The":[13,155],"theory":[14],"of":[15,29,34,49,64,92,119,150,157],"Petri":[16,37,101,120],"nets":[17,38,74,102],"offers":[18],"tool":[20,99],"for":[21,36,72,100,112],"such":[22,158],"task.":[24],"Since":[25],"the":[26,67,75,79,90,144,148,175],"rapid":[27],"computer":[30],"science,":[31],"variety":[33],"tools":[35],"emerged,":[39],"offering":[40],"various":[41],"analytical":[42,153],"algorithms.":[43],"From":[44],"this":[45],"follows":[46],"problem":[48],"using":[50],"different":[51,62,117],"programs":[52],"to":[53,77,146,167,174],"analyse":[54],"single":[56],"model.":[57],"Many":[58],"file":[59],"formats":[60],"representations":[63],"results":[65,80,149],"make":[66],"much":[69],"harder.":[70],"Especially":[71],"larger":[73],"ability":[76,145],"visualize":[78,147],"proper":[83],"form":[84],"provides":[85],"huge":[87],"help":[88],"understanding":[91],"their":[93],"significance.":[94],"We":[95],"present":[96],"new":[98],"called":[106],"Holmes.":[107],"Our":[108],"program":[109],"contains":[110],"algorithms":[111,134],"model":[113,176],"based":[115],"on":[116],"types":[118],"nets,":[121],"e.g.":[122],"invariant":[123],"generator,":[124],"Maximum":[125],"Common":[126],"Transitions":[127],"(MCT)":[128],"sets":[129],"cluster":[131],"modules,":[132],"simulation":[133],"or":[135,171],"knockout":[136],"tools.":[138],"A":[139],"very":[140],"important":[141],"feature":[142],"almost":[151],"all":[152],"modules.":[154],"integration":[156],"modules":[159],"into":[160],"one":[161],"graphical":[162],"environment":[163],"allows":[164],"researcher":[166],"fully":[168],"devote":[169],"his":[170],"her":[172],"time":[173],"building":[177],"analysis.":[179],"AVAILABILITY":[180],"AND":[181],"IMPLEMENTATION:":[182],"Available":[183],"at":[184],"http://www.cs.put.poznan.pl/mradom/Holmes/holmes.html.":[185],"CONTACT:":[186],"piotr@cs.put.poznan.pl.":[187]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":1}],"updated_date":"2026-08-18T07:49:30.821534","created_date":"2025-10-10T00:00:00"}
