{"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"],"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/I46597724","display_name":"Pozna\u0144 University of Technology","ror":"https://ror.org/00p7p3302","country_code":"PL","type":"education","lineage":["https://openalex.org/I46597724"]},{"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"]}],"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"],"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"],"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"],"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"],"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"],"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/I46597724","display_name":"Pozna\u0144 University of Technology","ror":"https://ror.org/00p7p3302","country_code":"PL","type":"education","lineage":["https://openalex.org/I46597724"]},{"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"]}],"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"],"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":7,"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":2.4982,"has_fulltext":false,"cited_by_count":24,"citation_normalized_percentile":{"value":0.90669346,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"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/T11125","display_name":"Petri Nets in System Modeling","score":0.9932000041007996,"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"}},"topics":[{"id":"https://openalex.org/T11125","display_name":"Petri Nets in System Modeling","score":0.9932000041007996,"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"}},{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.992900013923645,"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/T10142","display_name":"Formal Methods in Verification","score":0.9646999835968018,"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":{"pdf":true,"grobid_xml":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":{"piotr@cs.put.poznan.pl.":[0]},"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":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
