{"id":"https://openalex.org/W2085293660","doi":"https://doi.org/10.1016/j.entcs.2013.02.016","title":"Simulating Signalling Pathways With BioWayS","display_name":"Simulating Signalling Pathways With BioWayS","publication_year":2013,"publication_date":"2013-03-01","ids":{"openalex":"https://openalex.org/W2085293660","doi":"https://doi.org/10.1016/j.entcs.2013.02.016","mag":"2085293660"},"language":"en","primary_location":{"id":"doi:10.1016/j.entcs.2013.02.016","is_oa":true,"landing_page_url":"https://doi.org/10.1016/j.entcs.2013.02.016","pdf_url":null,"source":{"id":"https://openalex.org/S50368787","display_name":"Electronic Notes in Theoretical Computer Science","issn_l":"1571-0661","issn":["1571-0661"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"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 Notes in Theoretical Computer Science","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://doi.org/10.1016/j.entcs.2013.02.016","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5000327522","display_name":"Davide Chiarugi","orcid":"https://orcid.org/0000-0003-2752-3189"},"institutions":[{"id":"https://openalex.org/I102064193","display_name":"University of Siena","ror":"https://ror.org/01tevnk56","country_code":"IT","type":"education","lineage":["https://openalex.org/I102064193"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Davide Chiarugi","raw_affiliation_strings":["Dipartimento di Ingegneria dell\u02bcInformazione e Scienze Matematiche, Universit\u00e0 degli Studi di Siena, Italy","Dipartimento di Ingegneria dellInformazione e Scienze Matematiche, Universit\u00ed degli Studi di Siena, Italy#TAB#"],"affiliations":[{"raw_affiliation_string":"Dipartimento di Ingegneria dell\u02bcInformazione e Scienze Matematiche, Universit\u00e0 degli Studi di Siena, Italy","institution_ids":["https://openalex.org/I102064193"]},{"raw_affiliation_string":"Dipartimento di Ingegneria dellInformazione e Scienze Matematiche, Universit\u00ed degli Studi di Siena, Italy#TAB#","institution_ids":["https://openalex.org/I102064193"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053216941","display_name":"Moreno Falaschi","orcid":"https://orcid.org/0000-0002-6659-3828"},"institutions":[{"id":"https://openalex.org/I102064193","display_name":"University of Siena","ror":"https://ror.org/01tevnk56","country_code":"IT","type":"education","lineage":["https://openalex.org/I102064193"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Moreno Falaschi","raw_affiliation_strings":["Dipartimento di Ingegneria dell\u02bcInformazione e Scienze Matematiche, Universit\u00e0 degli Studi di Siena, Italy","Dipartimento di Ingegneria dellInformazione e Scienze Matematiche, Universit\u00ed degli Studi di Siena, Italy#TAB#"],"affiliations":[{"raw_affiliation_string":"Dipartimento di Ingegneria dell\u02bcInformazione e Scienze Matematiche, Universit\u00e0 degli Studi di Siena, Italy","institution_ids":["https://openalex.org/I102064193"]},{"raw_affiliation_string":"Dipartimento di Ingegneria dellInformazione e Scienze Matematiche, Universit\u00ed degli Studi di Siena, Italy#TAB#","institution_ids":["https://openalex.org/I102064193"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069128356","display_name":"Diana Hermith","orcid":"https://orcid.org/0000-0003-0710-5262"},"institutions":[{"id":"https://openalex.org/I102064193","display_name":"University of Siena","ror":"https://ror.org/01tevnk56","country_code":"IT","type":"education","lineage":["https://openalex.org/I102064193"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Diana Hermith","raw_affiliation_strings":["Dipartimento di Ingegneria dell\u02bcInformazione e Scienze Matematiche, Universit\u00e0 degli Studi di Siena, Italy","Dipartimento di Ingegneria dellInformazione e Scienze Matematiche, Universit\u00ed degli Studi di Siena, Italy#TAB#"],"affiliations":[{"raw_affiliation_string":"Dipartimento di Ingegneria dell\u02bcInformazione e Scienze Matematiche, Universit\u00e0 degli Studi di Siena, Italy","institution_ids":["https://openalex.org/I102064193"]},{"raw_affiliation_string":"Dipartimento di Ingegneria dellInformazione e Scienze Matematiche, Universit\u00ed degli Studi di Siena, Italy#TAB#","institution_ids":["https://openalex.org/I102064193"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013709966","display_name":"Michell Guzm\u00e1n","orcid":"https://orcid.org/0000-0002-3006-4414"},"institutions":[{"id":"https://openalex.org/I91732220","display_name":"Universidad del Valle","ror":"https://ror.org/00jb9vg53","country_code":"CO","type":"education","lineage":["https://openalex.org/I91732220"]}],"countries":["CO"],"is_corresponding":true,"raw_author_name":"Michell Guzman","raw_affiliation_strings":["Escuela de Ingenier\u00eda de Sistemas y Computaci\u00f3n, Universidad del Valle Cali, Colombia","Escuela de Ingenier\u00eda de Sistemas y Computaci\u00f3n Universidad del Valle Cali, Colombia"],"affiliations":[{"raw_affiliation_string":"Escuela de Ingenier\u00eda de Sistemas y Computaci\u00f3n, Universidad del Valle Cali, Colombia","institution_ids":["https://openalex.org/I91732220"]},{"raw_affiliation_string":"Escuela de Ingenier\u00eda de Sistemas y Computaci\u00f3n Universidad del Valle Cali, Colombia","institution_ids":["https://openalex.org/I91732220"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5047180960","display_name":"Carlos Olarte","orcid":"https://orcid.org/0000-0002-7264-7773"},"institutions":[{"id":"https://openalex.org/I233745408","display_name":"Pontificia Universidad Javeriana","ror":"https://ror.org/03etyjw28","country_code":"CO","type":"education","lineage":["https://openalex.org/I233745408"]}],"countries":["CO"],"is_corresponding":true,"raw_author_name":"Carlos Olarte","raw_affiliation_strings":["Departamento de Electr\u00f3nica y Ciencias de la Computaci\u00f3n, Universidad Javeriana Cali, Colombia","Departamento de Electr\u00f3nica y Ciencias de la Computaci\u00f3n, Universidad Javeriana Cali, Colombia#TAB#"],"affiliations":[{"raw_affiliation_string":"Departamento de Electr\u00f3nica y Ciencias de la Computaci\u00f3n, Universidad Javeriana Cali, Colombia","institution_ids":["https://openalex.org/I233745408"]},{"raw_affiliation_string":"Departamento de Electr\u00f3nica y Ciencias de la Computaci\u00f3n, Universidad Javeriana Cali, Colombia#TAB#","institution_ids":["https://openalex.org/I233745408"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5000327522","https://openalex.org/A5013709966","https://openalex.org/A5047180960","https://openalex.org/A5053216941","https://openalex.org/A5069128356"],"corresponding_institution_ids":["https://openalex.org/I102064193","https://openalex.org/I233745408","https://openalex.org/I91732220"],"apc_list":null,"apc_paid":null,"fwci":0.4485,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.66081961,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"293","issue":null,"first_page":"17","last_page":"34"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9991999864578247,"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":0.9991999864578247,"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":0.9980999827384949,"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":0.9929999709129333,"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/concurrency","display_name":"Concurrency","score":0.863822877407074},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7237411737442017},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.5409688353538513},{"id":"https://openalex.org/keywords/model-checking","display_name":"Model checking","score":0.5219642519950867},{"id":"https://openalex.org/keywords/process-calculus","display_name":"Process calculus","score":0.515714704990387},{"id":"https://openalex.org/keywords/biological-pathway","display_name":"Biological pathway","score":0.5151780843734741},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.5026102066040039},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.47851359844207764},{"id":"https://openalex.org/keywords/biological-network","display_name":"Biological network","score":0.4228595495223999},{"id":"https://openalex.org/keywords/distributed-computing","display_name":"Distributed computing","score":0.38364332914352417},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.20279282331466675},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.14084762334823608}],"concepts":[{"id":"https://openalex.org/C193702766","wikidata":"https://www.wikidata.org/wiki/Q1414548","display_name":"Concurrency","level":2,"score":0.863822877407074},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7237411737442017},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5409688353538513},{"id":"https://openalex.org/C110251889","wikidata":"https://www.wikidata.org/wiki/Q1569697","display_name":"Model checking","level":2,"score":0.5219642519950867},{"id":"https://openalex.org/C161771561","wikidata":"https://www.wikidata.org/wiki/Q1970286","display_name":"Process calculus","level":2,"score":0.515714704990387},{"id":"https://openalex.org/C9927688","wikidata":"https://www.wikidata.org/wiki/Q4915012","display_name":"Biological pathway","level":4,"score":0.5151780843734741},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.5026102066040039},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.47851359844207764},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.4228595495223999},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.38364332914352417},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.20279282331466675},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.14084762334823608},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"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/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1016/j.entcs.2013.02.016","is_oa":true,"landing_page_url":"https://doi.org/10.1016/j.entcs.2013.02.016","pdf_url":null,"source":{"id":"https://openalex.org/S50368787","display_name":"Electronic Notes in Theoretical Computer Science","issn_l":"1571-0661","issn":["1571-0661"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"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 Notes in Theoretical Computer Science","raw_type":"journal-article"},{"id":"pmh:oai:research-repository.griffith.edu.au:10072/421196","is_oa":false,"landing_page_url":"http://hdl.handle.net/10072/421196","pdf_url":null,"source":{"id":"https://openalex.org/S4306402548","display_name":"Griffith Research Online (Griffith University, Queensland, Australia)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I11701301","host_organization_name":"Griffith University","host_organization_lineage":["https://openalex.org/I11701301"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Conference output"},{"id":"pmh:oai:usiena-air.unisi.it:11365/40029","is_oa":true,"landing_page_url":"https://www.sciencedirect.com/science/article/pii/S1571066113000182","pdf_url":null,"source":{"id":"https://openalex.org/S4377196319","display_name":"Use Siena air (University of Siena)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I102064193","host_organization_name":"University of Siena","host_organization_lineage":["https://openalex.org/I102064193"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1016/j.entcs.2013.02.016","is_oa":true,"landing_page_url":"https://doi.org/10.1016/j.entcs.2013.02.016","pdf_url":null,"source":{"id":"https://openalex.org/S50368787","display_name":"Electronic Notes in Theoretical Computer Science","issn_l":"1571-0661","issn":["1571-0661"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"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 Notes in Theoretical Computer Science","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.5199999809265137,"id":"https://metadata.un.org/sdg/12","display_name":"Responsible consumption and production"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":47,"referenced_works":["https://openalex.org/W119938304","https://openalex.org/W154376554","https://openalex.org/W1484903112","https://openalex.org/W1524769048","https://openalex.org/W1544529442","https://openalex.org/W1549275217","https://openalex.org/W1594379317","https://openalex.org/W1608843525","https://openalex.org/W1871134734","https://openalex.org/W1964716918","https://openalex.org/W1968454452","https://openalex.org/W1986397618","https://openalex.org/W2020900711","https://openalex.org/W2030531074","https://openalex.org/W2040391135","https://openalex.org/W2041197407","https://openalex.org/W2050653042","https://openalex.org/W2055481619","https://openalex.org/W2080813736","https://openalex.org/W2085171412","https://openalex.org/W2089097516","https://openalex.org/W2096065176","https://openalex.org/W2110612987","https://openalex.org/W2119170644","https://openalex.org/W2119510512","https://openalex.org/W2120532339","https://openalex.org/W2124210471","https://openalex.org/W2159278787","https://openalex.org/W2167154952","https://openalex.org/W2180803539","https://openalex.org/W2275822647","https://openalex.org/W2500402711","https://openalex.org/W2913004508","https://openalex.org/W3000431583","https://openalex.org/W3152169895","https://openalex.org/W4301885396","https://openalex.org/W6604890268","https://openalex.org/W6606355482","https://openalex.org/W6628753435","https://openalex.org/W6631328306","https://openalex.org/W6632588589","https://openalex.org/W6636582051","https://openalex.org/W6673091215","https://openalex.org/W6677941951","https://openalex.org/W6759174716","https://openalex.org/W6794214549","https://openalex.org/W6999338344"],"related_works":["https://openalex.org/W3184499045","https://openalex.org/W2462966030","https://openalex.org/W1604894272","https://openalex.org/W2155852086","https://openalex.org/W2324339387","https://openalex.org/W188099908","https://openalex.org/W123162335","https://openalex.org/W2010690522","https://openalex.org/W1554465161","https://openalex.org/W2119035971"],"abstract_inverted_index":{"We":[0,30,77],"report":[1],"on":[2,10,56],"a":[3,14,65],"technique":[4],"for":[5,68],"modelling":[6,71],"biological":[7,75,89],"systems":[8,19],"based":[9],"the":[11,33,69,79,84,91,96,100],"ntcc":[12,36],"calculus,":[13],"model":[15,49],"of":[16,24,35,74,81,86,99],"concurrency":[17],"where":[18],"are":[20],"specified":[21],"by":[22],"means":[23],"constraints":[25],"(i.e.,":[26],"formulae":[27],"in":[28,83],"logic).":[29],"show":[31,78],"that":[32],"ability":[34],"to":[37],"express":[38],"partial":[39],"information,":[40],"concurrency,":[41],"non-determinism":[42],"and":[43,50,72,95],"timed":[44],"behaviour":[45],"makes":[46],"it":[47],"well-suited":[48],"simulate":[51],"biochemical":[52],"reactions":[53],"networks.":[54],"Based":[55],"this":[57],"technique,":[58],"we":[59],"introduce":[60],"BioWayS":[61,82],"(BIOchemical":[62],"pathWAY":[63],"Simulator),":[64],"software":[66],"tool":[67],"quantitative":[70],"analysis":[73],"systems.":[76],"applicability":[80],"context":[85],"two":[87],"well-studied":[88],"systems:":[90],"glycogen":[92],"breakdown":[93],"pathway":[94],"life":[97],"cycle":[98],"human":[101],"immunodeficiency":[102],"virus.":[103]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2015,"cited_by_count":3}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2016-06-24T00:00:00"}
