{"id":"https://openalex.org/W2134897855","doi":"https://doi.org/10.4204/eptcs.6.3","title":"BioDiVinE: A Framework for Parallel Analysis of Biological Models","display_name":"BioDiVinE: A Framework for Parallel Analysis of Biological Models","publication_year":2009,"publication_date":"2009-10-08","ids":{"openalex":"https://openalex.org/W2134897855","doi":"https://doi.org/10.4204/eptcs.6.3","mag":"2134897855"},"language":"en","primary_location":{"id":"doi:10.4204/eptcs.6.3","is_oa":true,"landing_page_url":"https://doi.org/10.4204/eptcs.6.3","pdf_url":null,"source":{"id":"https://openalex.org/S4210216316","display_name":"Electronic Proceedings in Theoretical Computer Science","issn_l":"2075-2180","issn":["2075-2180"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310318029","host_organization_name":"Open Publishing Association","host_organization_lineage":["https://openalex.org/P4310318029"],"host_organization_lineage_names":["Open Publishing Association"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Electronic Proceedings in Theoretical Computer Science","raw_type":"journal-article"},"type":"article","indexed_in":["arxiv","crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://doi.org/10.4204/eptcs.6.3","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5085421461","display_name":"J\u01d0\u0155\u0131 Barnat","orcid":"https://orcid.org/0000-0003-2044-2861"},"institutions":[{"id":"https://openalex.org/I21449261","display_name":"Masaryk University","ror":"https://ror.org/02j46qs45","country_code":"CZ","type":"education","lineage":["https://openalex.org/I21449261"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"Ji\u0159\u00ed Barnat","raw_affiliation_strings":["Masaryk University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Masaryk University","institution_ids":["https://openalex.org/I21449261"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001461435","display_name":"Lubo\u0161 Brim","orcid":"https://orcid.org/0000-0001-9393-7545"},"institutions":[{"id":"https://openalex.org/I21449261","display_name":"Masaryk University","ror":"https://ror.org/02j46qs45","country_code":"CZ","type":"education","lineage":["https://openalex.org/I21449261"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"Lubo\u0161 Brim","raw_affiliation_strings":["Masaryk University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Masaryk University","institution_ids":["https://openalex.org/I21449261"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014178090","display_name":"Ivana \u010cern\u00e1","orcid":"https://orcid.org/0000-0002-0711-9552"},"institutions":[{"id":"https://openalex.org/I21449261","display_name":"Masaryk University","ror":"https://ror.org/02j46qs45","country_code":"CZ","type":"education","lineage":["https://openalex.org/I21449261"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"Ivana \u010cern\u00e1","raw_affiliation_strings":["Masaryk University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Masaryk University","institution_ids":["https://openalex.org/I21449261"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009361156","display_name":"Sven Dra\u017ean","orcid":null},"institutions":[{"id":"https://openalex.org/I21449261","display_name":"Masaryk University","ror":"https://ror.org/02j46qs45","country_code":"CZ","type":"education","lineage":["https://openalex.org/I21449261"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"Sven Dra\u017ean","raw_affiliation_strings":["Masaryk University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Masaryk University","institution_ids":["https://openalex.org/I21449261"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011888070","display_name":"J. Fabrikov\u00e1","orcid":null},"institutions":[{"id":"https://openalex.org/I21449261","display_name":"Masaryk University","ror":"https://ror.org/02j46qs45","country_code":"CZ","type":"education","lineage":["https://openalex.org/I21449261"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"Jana Fabrikov\u00e1","raw_affiliation_strings":["Masaryk University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Masaryk University","institution_ids":["https://openalex.org/I21449261"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043222283","display_name":"Jan L\u00e1n\u00edk","orcid":null},"institutions":[{"id":"https://openalex.org/I21449261","display_name":"Masaryk University","ror":"https://ror.org/02j46qs45","country_code":"CZ","type":"education","lineage":["https://openalex.org/I21449261"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"Jan L\u00e1n\u00edk","raw_affiliation_strings":["Masaryk University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Masaryk University","institution_ids":["https://openalex.org/I21449261"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061586199","display_name":"David \u0160afr\u00e1nek","orcid":"https://orcid.org/0000-0002-0713-2431"},"institutions":[{"id":"https://openalex.org/I21449261","display_name":"Masaryk University","ror":"https://ror.org/02j46qs45","country_code":"CZ","type":"education","lineage":["https://openalex.org/I21449261"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"David \u0160afr\u00e1nek","raw_affiliation_strings":["Masaryk University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Masaryk University","institution_ids":["https://openalex.org/I21449261"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100856709","display_name":"Hongwu Ma","orcid":null},"institutions":[{"id":"https://openalex.org/I98677209","display_name":"University of Edinburgh","ror":"https://ror.org/01nrxwf90","country_code":"GB","type":"education","lineage":["https://openalex.org/I98677209"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Hongwu Ma","raw_affiliation_strings":["University of Edinburgh"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Edinburgh","institution_ids":["https://openalex.org/I98677209"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.6751,"has_fulltext":false,"cited_by_count":16,"citation_normalized_percentile":{"value":0.70094719,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"6","issue":null,"first_page":"31","last_page":"45"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9997000098228455,"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":0.9997000098228455,"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":0.992900013923645,"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/T13286","display_name":"Modeling and Simulation Systems","score":0.98089998960495,"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/abstraction","display_name":"Abstraction","score":0.7239834666252136},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6896347403526306},{"id":"https://openalex.org/keywords/affine-transformation","display_name":"Affine transformation","score":0.5796200037002563},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5662839412689209},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.5066431164741516},{"id":"https://openalex.org/keywords/key","display_name":"Key (lock)","score":0.488343209028244},{"id":"https://openalex.org/keywords/state-space","display_name":"State space","score":0.4773942828178406},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.46792104840278625},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.25107306241989136},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.20482349395751953}],"concepts":[{"id":"https://openalex.org/C124304363","wikidata":"https://www.wikidata.org/wiki/Q673661","display_name":"Abstraction","level":2,"score":0.7239834666252136},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6896347403526306},{"id":"https://openalex.org/C92757383","wikidata":"https://www.wikidata.org/wiki/Q382497","display_name":"Affine transformation","level":2,"score":0.5796200037002563},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5662839412689209},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.5066431164741516},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.488343209028244},{"id":"https://openalex.org/C72434380","wikidata":"https://www.wikidata.org/wiki/Q230930","display_name":"State space","level":2,"score":0.4773942828178406},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.46792104840278625},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.25107306241989136},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.20482349395751953},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"score":0.0},{"id":"https://openalex.org/C202444582","wikidata":"https://www.wikidata.org/wiki/Q837863","display_name":"Pure mathematics","level":1,"score":0.0}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.4204/eptcs.6.3","is_oa":true,"landing_page_url":"https://doi.org/10.4204/eptcs.6.3","pdf_url":null,"source":{"id":"https://openalex.org/S4210216316","display_name":"Electronic Proceedings in Theoretical Computer Science","issn_l":"2075-2180","issn":["2075-2180"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310318029","host_organization_name":"Open Publishing Association","host_organization_lineage":["https://openalex.org/P4310318029"],"host_organization_lineage_names":["Open Publishing Association"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Electronic Proceedings in Theoretical Computer Science","raw_type":"journal-article"},{"id":"pmh:oai:arXiv.org:0910.0928","is_oa":true,"landing_page_url":"http://arxiv.org/abs/0910.0928","pdf_url":"https://arxiv.org/pdf/0910.0928","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"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":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.169.9800","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.169.9800","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://anna.fi.muni.cz/papers/src/public/0a1c4ee87b39137f3b00882d311bf41a.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.182.2801","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.182.2801","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.fi.muni.cz/%7Exsafran1/publications/compmod09.pdf","raw_type":"text"},{"id":"pmh:oai:doaj.org/article:b0bd8ba67c8c46f7994e69d016802d99","is_oa":true,"landing_page_url":"https://doaj.org/article/b0bd8ba67c8c46f7994e69d016802d99","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":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Electronic Proceedings in Theoretical Computer Science, Vol 6, Iss Proc. COMPMOD 2009, Pp 31-45 (2009)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.4204/eptcs.6.3","is_oa":true,"landing_page_url":"https://doi.org/10.4204/eptcs.6.3","pdf_url":null,"source":{"id":"https://openalex.org/S4210216316","display_name":"Electronic Proceedings in Theoretical Computer Science","issn_l":"2075-2180","issn":["2075-2180"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310318029","host_organization_name":"Open Publishing Association","host_organization_lineage":["https://openalex.org/P4310318029"],"host_organization_lineage_names":["Open Publishing Association"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Electronic Proceedings in Theoretical Computer Science","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":20,"referenced_works":["https://openalex.org/W1485333286","https://openalex.org/W1503466301","https://openalex.org/W1540191989","https://openalex.org/W1568609840","https://openalex.org/W1569248486","https://openalex.org/W1976369232","https://openalex.org/W1979627774","https://openalex.org/W1988383139","https://openalex.org/W1995087505","https://openalex.org/W2065630126","https://openalex.org/W2094781369","https://openalex.org/W2102653059","https://openalex.org/W2114578185","https://openalex.org/W2119510512","https://openalex.org/W2129388048","https://openalex.org/W2158036406","https://openalex.org/W2167094312","https://openalex.org/W2340735175","https://openalex.org/W2913350541","https://openalex.org/W6683200452"],"related_works":["https://openalex.org/W2045155990","https://openalex.org/W4313163053","https://openalex.org/W4300973204","https://openalex.org/W3045811229","https://openalex.org/W273478400","https://openalex.org/W4388675521","https://openalex.org/W2108135022","https://openalex.org/W3148810651","https://openalex.org/W2789077243","https://openalex.org/W2898772359"],"abstract_inverted_index":{"In":[0,65],"this":[1],"paper":[2],"a":[3,25,35,82],"novel":[4],"tool":[5,15,70],"BioDiVinEfor":[6],"parallel":[7,56],"analysis":[8,17,57],"of":[9,18,24,27,37,48,81],"biological":[10,19],"models":[11,20],"is":[12,77],"presented.":[13],"The":[14],"allows":[16],"specified":[21],"in":[22],"terms":[23],"set":[26],"chemical":[28],"reactions.":[29],"Chemical":[30],"reactions":[31],"are":[32,63,72],"transformed":[33],"into":[34],"system":[36],"multi-affine":[38],"differential":[39],"equations.":[40],"BioDiVinE":[41],"employs":[42],"techniques":[43],"for":[44],"finite":[45],"discrete":[46],"abstraction":[47],"the":[49,66,68],"continuous":[50],"state":[51],"space.":[52],"At":[53],"that":[54],"level,":[55],"algorithms":[58],"based":[59],"on":[60],"model":[61],"checking":[62],"provided.":[64],"paper,":[67],"key":[69],"features":[71],"described":[73],"and":[74],"their":[75],"application":[76],"demonstrated":[78],"by":[79],"means":[80],"case":[83],"study.":[84]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
