{"id":"https://openalex.org/W2990683873","doi":"https://doi.org/10.3233/fi-2020-1888","title":"Integrating Petri Nets and Flux Balance Methods in Computational Biology Models: a Methodological and Computational Practice","display_name":"Integrating Petri Nets and Flux Balance Methods in Computational Biology Models: a Methodological and Computational Practice","publication_year":2019,"publication_date":"2019-10-23","ids":{"openalex":"https://openalex.org/W2990683873","doi":"https://doi.org/10.3233/fi-2020-1888","mag":"2990683873"},"language":"en","primary_location":{"id":"doi:10.3233/fi-2020-1888","is_oa":false,"landing_page_url":"https://doi.org/10.3233/fi-2020-1888","pdf_url":null,"source":{"id":"https://openalex.org/S39012697","display_name":"Fundamenta Informaticae","issn_l":"0169-2968","issn":["0169-2968","1875-8681"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310318577","host_organization_name":"IOS Press","host_organization_lineage":["https://openalex.org/P4310318577"],"host_organization_lineage_names":["IOS Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Fundamenta Informaticae","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"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/A5082219669","display_name":"Simone Pernice","orcid":"https://orcid.org/0000-0001-7124-4676"},"institutions":[{"id":"https://openalex.org/I55143463","display_name":"University of Turin","ror":"https://ror.org/048tbm396","country_code":"IT","type":"education","lineage":["https://openalex.org/I55143463"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Pernice Simone","raw_affiliation_strings":["Department of Computer Science, University of Torino, Italy"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Torino, Italy","institution_ids":["https://openalex.org/I55143463"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023290184","display_name":"Laura Follia","orcid":"https://orcid.org/0000-0003-1580-0505"},"institutions":[{"id":"https://openalex.org/I55143463","display_name":"University of Turin","ror":"https://ror.org/048tbm396","country_code":"IT","type":"education","lineage":["https://openalex.org/I55143463"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Follia Laura","raw_affiliation_strings":["Department of Computer Science, University of Torino, Italy"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Torino, Italy","institution_ids":["https://openalex.org/I55143463"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056160729","display_name":"Gianfranco Balbo","orcid":"https://orcid.org/0000-0001-8719-9267"},"institutions":[{"id":"https://openalex.org/I55143463","display_name":"University of Turin","ror":"https://ror.org/048tbm396","country_code":"IT","type":"education","lineage":["https://openalex.org/I55143463"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Balbo Gianfranco","raw_affiliation_strings":["Department of Computer Science, University of Torino, Italy"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Torino, Italy","institution_ids":["https://openalex.org/I55143463"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088629765","display_name":"Luciano Milanesi","orcid":"https://orcid.org/0000-0002-1201-3939"},"institutions":[{"id":"https://openalex.org/I4210154278","display_name":"Institute of Biomedical Technologies","ror":"https://ror.org/04ehykb85","country_code":"IT","type":"facility","lineage":["https://openalex.org/I4210154278","https://openalex.org/I4210155236"]},{"id":"https://openalex.org/I4210155236","display_name":"National Research Council","ror":"https://ror.org/04zaypm56","country_code":"IT","type":"funder","lineage":["https://openalex.org/I4210155236"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Milanesi Luciano","raw_affiliation_strings":["Institute for Biomendical Technologies, National Research Council, Segrate (Milan), Italy"],"affiliations":[{"raw_affiliation_string":"Institute for Biomendical Technologies, National Research Council, Segrate (Milan), Italy","institution_ids":["https://openalex.org/I4210154278","https://openalex.org/I4210155236"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002323291","display_name":"Sartini Giulia","orcid":null},"institutions":[{"id":"https://openalex.org/I55143463","display_name":"University of Turin","ror":"https://ror.org/048tbm396","country_code":"IT","type":"education","lineage":["https://openalex.org/I55143463"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Sartini Giulia","raw_affiliation_strings":["Department of Life Sciences and Systems Biology, University of Torino, Italy"],"affiliations":[{"raw_affiliation_string":"Department of Life Sciences and Systems Biology, University of Torino, Italy","institution_ids":["https://openalex.org/I55143463"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021852862","display_name":"Niccol\u00f2 Totis","orcid":"https://orcid.org/0000-0002-4138-582X"},"institutions":[{"id":"https://openalex.org/I55143463","display_name":"University of Turin","ror":"https://ror.org/048tbm396","country_code":"IT","type":"education","lineage":["https://openalex.org/I55143463"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Totis Niccol\u00f3","raw_affiliation_strings":["Department of Life Sciences and Systems Biology, University of Torino, Italy"],"affiliations":[{"raw_affiliation_string":"Department of Life Sciences and Systems Biology, University of Torino, Italy","institution_ids":["https://openalex.org/I55143463"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056748708","display_name":"P\u00edetro Li\u00f3","orcid":"https://orcid.org/0000-0002-0540-5053"},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Li\u00f3 Pietro","raw_affiliation_strings":["Computer Laboratory, University of Cambridge, GB. pl219@cam.ac.uk"],"affiliations":[{"raw_affiliation_string":"Computer Laboratory, University of Cambridge, GB. pl219@cam.ac.uk","institution_ids":["https://openalex.org/I241749"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066010774","display_name":"Merelli Ivan","orcid":null},"institutions":[{"id":"https://openalex.org/I4210155236","display_name":"National Research Council","ror":"https://ror.org/04zaypm56","country_code":"IT","type":"funder","lineage":["https://openalex.org/I4210155236"]},{"id":"https://openalex.org/I4210154278","display_name":"Institute of Biomedical Technologies","ror":"https://ror.org/04ehykb85","country_code":"IT","type":"facility","lineage":["https://openalex.org/I4210154278","https://openalex.org/I4210155236"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Merelli Ivan","raw_affiliation_strings":["Institute for Biomendical Technologies, National Research Council, Segrate (Milan), Italy"],"affiliations":[{"raw_affiliation_string":"Institute for Biomendical Technologies, National Research Council, Segrate (Milan), Italy","institution_ids":["https://openalex.org/I4210154278","https://openalex.org/I4210155236"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064773200","display_name":"Francesca Cordero","orcid":"https://orcid.org/0000-0002-3143-3330"},"institutions":[{"id":"https://openalex.org/I55143463","display_name":"University of Turin","ror":"https://ror.org/048tbm396","country_code":"IT","type":"education","lineage":["https://openalex.org/I55143463"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Cordero Francesca","raw_affiliation_strings":["Department of Computer Science, University of Torino, Italy"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Torino, Italy","institution_ids":["https://openalex.org/I55143463"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5002392135","display_name":"Marco Beccuti","orcid":"https://orcid.org/0000-0001-6125-9460"},"institutions":[{"id":"https://openalex.org/I55143463","display_name":"University of Turin","ror":"https://ror.org/048tbm396","country_code":"IT","type":"education","lineage":["https://openalex.org/I55143463"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Beccuti Marco","raw_affiliation_strings":["Department of Computer Science, University of Torino, Italy"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Torino, Italy","institution_ids":["https://openalex.org/I55143463"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":10,"corresponding_author_ids":["https://openalex.org/A5023290184","https://openalex.org/A5082219669"],"corresponding_institution_ids":["https://openalex.org/I55143463"],"apc_list":null,"apc_paid":null,"fwci":0.7671,"has_fulltext":false,"cited_by_count":11,"citation_normalized_percentile":{"value":0.71385497,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"171","issue":"1-4","first_page":"367","last_page":"392"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9987000226974487,"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":0.9987000226974487,"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":0.9857000112533569,"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":0.9822999835014343,"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/interpretability","display_name":"Interpretability","score":0.6875453591346741},{"id":"https://openalex.org/keywords/petri-net","display_name":"Petri net","score":0.6817567348480225},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6398853063583374},{"id":"https://openalex.org/keywords/flux-balance-analysis","display_name":"Flux balance analysis","score":0.6167958378791809},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.5414526462554932},{"id":"https://openalex.org/keywords/modelling-biological-systems","display_name":"Modelling biological systems","score":0.5187492370605469},{"id":"https://openalex.org/keywords/ordinary-differential-equation","display_name":"Ordinary differential equation","score":0.4641951322555542},{"id":"https://openalex.org/keywords/computational-model","display_name":"Computational model","score":0.46176213026046753},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.4420681297779083},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3990923762321472},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.26830267906188965},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.2623048722743988},{"id":"https://openalex.org/keywords/distributed-computing","display_name":"Distributed computing","score":0.19348734617233276},{"id":"https://openalex.org/keywords/differential-equation","display_name":"Differential equation","score":0.1816818118095398},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.161089688539505}],"concepts":[{"id":"https://openalex.org/C2781067378","wikidata":"https://www.wikidata.org/wiki/Q17027399","display_name":"Interpretability","level":2,"score":0.6875453591346741},{"id":"https://openalex.org/C38677869","wikidata":"https://www.wikidata.org/wiki/Q724168","display_name":"Petri net","level":2,"score":0.6817567348480225},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6398853063583374},{"id":"https://openalex.org/C167091322","wikidata":"https://www.wikidata.org/wiki/Q5463029","display_name":"Flux balance analysis","level":2,"score":0.6167958378791809},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.5414526462554932},{"id":"https://openalex.org/C137866125","wikidata":"https://www.wikidata.org/wiki/Q4299308","display_name":"Modelling biological systems","level":3,"score":0.5187492370605469},{"id":"https://openalex.org/C51544822","wikidata":"https://www.wikidata.org/wiki/Q465274","display_name":"Ordinary differential equation","level":3,"score":0.4641951322555542},{"id":"https://openalex.org/C66024118","wikidata":"https://www.wikidata.org/wiki/Q1122506","display_name":"Computational model","level":2,"score":0.46176213026046753},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.4420681297779083},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3990923762321472},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.26830267906188965},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.2623048722743988},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.19348734617233276},{"id":"https://openalex.org/C78045399","wikidata":"https://www.wikidata.org/wiki/Q11214","display_name":"Differential equation","level":2,"score":0.1816818118095398},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.161089688539505},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.3233/fi-2020-1888","is_oa":false,"landing_page_url":"https://doi.org/10.3233/fi-2020-1888","pdf_url":null,"source":{"id":"https://openalex.org/S39012697","display_name":"Fundamenta Informaticae","issn_l":"0169-2968","issn":["0169-2968","1875-8681"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310318577","host_organization_name":"IOS Press","host_organization_lineage":["https://openalex.org/P4310318577"],"host_organization_lineage_names":["IOS Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Fundamenta Informaticae","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W4386563820","https://openalex.org/W631732704","https://openalex.org/W1968058641","https://openalex.org/W1971436540","https://openalex.org/W2020641517","https://openalex.org/W2155261113","https://openalex.org/W1748979965","https://openalex.org/W2057769265","https://openalex.org/W3199870583","https://openalex.org/W207829213"],"abstract_inverted_index":{"Computational":[0],"Biology":[1],"is":[2,7,126,143,162],"a":[3,20,47,90,149,189,200],"fast-growing":[4],"field":[5],"that":[6],"enriched":[8],"by":[9,15,145],"different":[10,40],"data-driven":[11],"methodological":[12],"approaches":[13,29],"and":[14,17,33,57,61,94,96,104,172,175,202,214,217,222,231,237,255],"findings":[16],"applications":[18],"in":[19,92,159],"broad":[21],"range":[22],"of":[23,64,74,79,118,152,165,168,188,211,229],"biological":[24,65],"areas.":[25],"Fundamental":[26],"to":[27,37,107,128,241,247],"these":[28],"are":[30,87,105],"the":[31,39,72,119,124,141,146,163,186,209,227,243],"mathematical":[32,109],"computational":[34,244],"models":[35,233],"used":[36],"describe":[38],"state":[41],"s":[42],"at":[43,54],"microscopic":[44],"(for":[45],"example":[46,112],"biochemical":[48],"reaction),":[49],"mesoscopic":[50],"(the":[51],"signalling":[52,139],"effects":[53],"tissue":[55],"level),":[56],"macroscopic":[58],"levels":[59],"(physiological":[60],"pathological":[62],"effects)":[63],"processes.":[66],"In":[67],"this":[68,160,249,258],"paper":[69,161],"we":[70],"address":[71],"problem":[73],"combining":[75],"two":[76],"powerful":[77],"classes":[78],"methodologies:":[80],"Flux":[81],"Balance":[82],"Analysis":[83],"(FBA)":[84],"methods":[85,174],"which":[86,100],"now":[88],"producing":[89],"revolution":[91],"biotechnology":[93],"medicine,":[95],"Petri":[97],"Nets":[98],"(PNs)":[99],"allow":[101],"system":[102],"generalisation":[103],"central":[106],"various":[108],"treatments,":[110],"for":[111,136,148,208],"Ordinary":[113],"Differential":[114],"Equation":[115],"(ODE)":[116],"specification":[117],"biosystem":[120],"under":[121],"study.":[122],"While":[123],"former":[125],"limited":[127],"modelling":[129],"metabolic":[130,153,215],"networks,":[131],"i.e.":[132],"does":[133],"not":[134],"account":[135],"intermittent":[137],"dynamical":[138],"events,":[140],"latter":[142],"hampered":[144],"need":[147],"large":[150],"amount":[151],"data.":[154,180],"A":[155],"first":[156],"result":[157],"presented":[158],"identification":[164],"three":[166],"types":[167],"cross-talks":[169],"between":[170],"PNs":[171],"FBA":[173,232],"their":[176],"dependencies":[177],"on":[178,257],"available":[179],"We":[181,193,224,251],"exemplify":[182],"our":[183,196],"insights":[184],"with":[185,253],"analysis":[187],"pancreatic":[190],"cancer":[191],"model.":[192],"discuss":[194,225],"how":[195,226],"reasoning":[197],"framework":[198],"provides":[199],"biologically":[201],"mathematically":[203],"grounded":[204],"decision":[205],"making":[206],"setting":[207],"integration":[210],"regulatory,":[212],"signalling,":[213],"networks":[216],"greatly":[218],"increases":[219],"model":[220],"interpretability":[221],"reusability.":[223],"parameters":[228],"PN":[230],"can":[234],"be":[235],"tuned":[236],"combined":[238],"together":[239],"so":[240],"highlight":[242],"effort":[245],"needed":[246],"perform":[248],"task.":[250],"conclude":[252],"speculations":[254],"suggestions":[256],"new":[259],"promising":[260],"research":[261],"direction.":[262]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":5},{"year":2019,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
