{"id":"https://openalex.org/W2064974862","doi":"https://doi.org/10.1093/bib/bbn023","title":"The Beta Workbench: a computational tool to study the dynamics of biological systems","display_name":"The Beta Workbench: a computational tool to study the dynamics of biological systems","publication_year":2008,"publication_date":"2008-04-24","ids":{"openalex":"https://openalex.org/W2064974862","doi":"https://doi.org/10.1093/bib/bbn023","mag":"2064974862","pmid":"https://pubmed.ncbi.nlm.nih.gov/18463130"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbn023","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbn023","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5083552914","display_name":"Lorenzo Dematt\u00e9","orcid":null},"institutions":[{"id":"https://openalex.org/I193223587","display_name":"University of Trento","ror":"https://ror.org/05trd4x28","country_code":"IT","type":"education","lineage":["https://openalex.org/I193223587"]},{"id":"https://openalex.org/I2802934434","display_name":"The Microsoft Research - University of Trento Centre for Computational and Systems Biology","ror":"https://ror.org/04kcgyj43","country_code":"IT","type":"nonprofit","lineage":["https://openalex.org/I1290206253","https://openalex.org/I193223587","https://openalex.org/I2802934434","https://openalex.org/I4210164937"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"L. Dematte","raw_affiliation_strings":["ICT International Doctorate School at University of Trento and Microsoft Research, University of Trento, Centre for Computational and Systems Biology, Povo, TN, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"ICT International Doctorate School at University of Trento and Microsoft Research, University of Trento, Centre for Computational and Systems Biology, Povo, TN, Italy","institution_ids":["https://openalex.org/I2802934434","https://openalex.org/I193223587"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111931191","display_name":"C. Priami","orcid":null},"institutions":[{"id":"https://openalex.org/I193223587","display_name":"University of Trento","ror":"https://ror.org/05trd4x28","country_code":"IT","type":"education","lineage":["https://openalex.org/I193223587"]},{"id":"https://openalex.org/I2802934434","display_name":"The Microsoft Research - University of Trento Centre for Computational and Systems Biology","ror":"https://ror.org/04kcgyj43","country_code":"IT","type":"nonprofit","lineage":["https://openalex.org/I1290206253","https://openalex.org/I193223587","https://openalex.org/I2802934434","https://openalex.org/I4210164937"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"C. Priami","raw_affiliation_strings":["Corrado Priami received his PhD in Computer Science from the University of Pisa, Italy. He is currently President & CEO of the Microsoft Research, University of Trento Centre for Computational and Systems Biology and full professor of Computer Science at the University of Trento"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Corrado Priami received his PhD in Computer Science from the University of Pisa, Italy. He is currently President & CEO of the Microsoft Research, University of Trento Centre for Computational and Systems Biology and full professor of Computer Science at the University of Trento","institution_ids":["https://openalex.org/I2802934434","https://openalex.org/I193223587"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5045520201","display_name":"Alessandro Romanel","orcid":"https://orcid.org/0000-0003-4855-8620"},"institutions":[{"id":"https://openalex.org/I193223587","display_name":"University of Trento","ror":"https://ror.org/05trd4x28","country_code":"IT","type":"education","lineage":["https://openalex.org/I193223587"]},{"id":"https://openalex.org/I2802934434","display_name":"The Microsoft Research - University of Trento Centre for Computational and Systems Biology","ror":"https://ror.org/04kcgyj43","country_code":"IT","type":"nonprofit","lineage":["https://openalex.org/I1290206253","https://openalex.org/I193223587","https://openalex.org/I2802934434","https://openalex.org/I4210164937"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"A. Romanel","raw_affiliation_strings":["Alessandro Romanel is a PhD student at the ICT International Doctorate School at the University of Trento and he is also currently carrying out research activities at the Microsoft Research, University of Trento Centre for Computational and Systems Biology"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Alessandro Romanel is a PhD student at the ICT International Doctorate School at the University of Trento and he is also currently carrying out research activities at the Microsoft Research, University of Trento Centre for Computational and Systems Biology","institution_ids":["https://openalex.org/I2802934434","https://openalex.org/I193223587"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5083552914"],"corresponding_institution_ids":["https://openalex.org/I193223587","https://openalex.org/I2802934434"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":6.8067,"has_fulltext":false,"cited_by_count":82,"citation_normalized_percentile":{"value":0.97598541,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"9","issue":"5","first_page":"437","last_page":"449"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9998000264167786,"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":0.9998000264167786,"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":0.9962999820709229,"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":0.9883999824523926,"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/workbench","display_name":"Workbench","score":0.9511221647262573},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7891916036605835},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.738221287727356},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.5717089176177979},{"id":"https://openalex.org/keywords/beta","display_name":"BETA (programming language)","score":0.5509483218193054},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.3505321145057678},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.32712966203689575},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2346571385860443},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.12539711594581604},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.12460201978683472}],"concepts":[{"id":"https://openalex.org/C2779145975","wikidata":"https://www.wikidata.org/wiki/Q347690","display_name":"Workbench","level":3,"score":0.9511221647262573},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7891916036605835},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.738221287727356},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.5717089176177979},{"id":"https://openalex.org/C2776174256","wikidata":"https://www.wikidata.org/wiki/Q830842","display_name":"BETA (programming language)","level":2,"score":0.5509483218193054},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.3505321145057678},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.32712966203689575},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2346571385860443},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.12539711594581604},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.12460201978683472}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","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":false},{"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":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","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":"D012985","descriptor_name":"Software Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012985","descriptor_name":"Software Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012985","descriptor_name":"Software Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":4,"locations":[{"id":"doi:10.1093/bib/bbn023","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbn023","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:18463130","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18463130","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:arpi.unipi.it:11568/881796","is_oa":false,"landing_page_url":"http://hdl.handle.net/11568/881796","pdf_url":null,"source":{"id":"https://openalex.org/S4377196265","display_name":"CINECA IRIS Institutial research information system (University of Pisa)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I108290504","host_organization_name":"University of Pisa","host_organization_lineage":["https://openalex.org/I108290504"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:iris.unitn.it:11572/69286","is_oa":false,"landing_page_url":"http://hdl.handle.net/11572/69286","pdf_url":null,"source":{"id":"https://openalex.org/S4306401913","display_name":"Institutional Research Information System (Universit\u00e0 degli Studi di Trento)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I193223587","host_organization_name":"University of Trento","host_organization_lineage":["https://openalex.org/I193223587"],"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":"info:eu-repo/semantics/article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":36,"referenced_works":["https://openalex.org/W23582153","https://openalex.org/W291482096","https://openalex.org/W1489794659","https://openalex.org/W1499223469","https://openalex.org/W1501020965","https://openalex.org/W1502932049","https://openalex.org/W1503262942","https://openalex.org/W1513962738","https://openalex.org/W1527683148","https://openalex.org/W1542756748","https://openalex.org/W1595516773","https://openalex.org/W1759632117","https://openalex.org/W1791710463","https://openalex.org/W1855744943","https://openalex.org/W1964514022","https://openalex.org/W1971224531","https://openalex.org/W1980830179","https://openalex.org/W1986397618","https://openalex.org/W1986755980","https://openalex.org/W1990736894","https://openalex.org/W2001620484","https://openalex.org/W2041226400","https://openalex.org/W2042321087","https://openalex.org/W2065219357","https://openalex.org/W2070658593","https://openalex.org/W2076573105","https://openalex.org/W2078734278","https://openalex.org/W2088842371","https://openalex.org/W2102653059","https://openalex.org/W2110796675","https://openalex.org/W2118039525","https://openalex.org/W2129641019","https://openalex.org/W2137791798","https://openalex.org/W2152604899","https://openalex.org/W2160533336","https://openalex.org/W2238201325"],"related_works":["https://openalex.org/W2388509490","https://openalex.org/W2109648960","https://openalex.org/W2166015079","https://openalex.org/W2050384624","https://openalex.org/W2776888796","https://openalex.org/W2388480422","https://openalex.org/W4241678738","https://openalex.org/W2048496244","https://openalex.org/W2513537424","https://openalex.org/W139548500"],"abstract_inverted_index":{"We":[0,25],"introduce":[1],"the":[2,13,27,30,36,44],"Beta":[3],"Workbench":[4],"(BWB),":[5],"a":[6,39,51],"scalable":[7],"tool":[8],"built":[9],"on":[10,38,43],"top":[11],"of":[12],"newly":[14],"defined":[15],"BlenX":[16],"language":[17],"to":[18],"model,":[19],"simulate":[20],"and":[21,29,56],"analyse":[22],"biological":[23],"systems.":[24],"show":[26],"features":[28],"incremental":[31],"modelling":[32],"process":[33],"supported":[34],"by":[35],"BWB":[37],"running":[40],"example":[41],"based":[42],"mitogen-activated":[45],"kinase":[46],"pathway.":[47],"Finally,":[48],"we":[49],"provide":[50],"comparison":[52],"with":[53],"related":[54],"approaches":[55],"some":[57],"hints":[58],"for":[59],"future":[60],"extensions.":[61]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":5},{"year":2013,"cited_by_count":12},{"year":2012,"cited_by_count":6}],"updated_date":"2026-06-16T07:32:37.131356","created_date":"2025-10-10T00:00:00"}
