{"id":"https://openalex.org/W2553512552","doi":"https://doi.org/10.1109/hldvt.2016.7748270","title":"SyQUAL: a platform for qualitative modelling and simulation of biological systems","display_name":"SyQUAL: a platform for qualitative modelling and simulation of biological systems","publication_year":2016,"publication_date":"2016-10-01","ids":{"openalex":"https://openalex.org/W2553512552","doi":"https://doi.org/10.1109/hldvt.2016.7748270","mag":"2553512552"},"language":"en","primary_location":{"id":"doi:10.1109/hldvt.2016.7748270","is_oa":false,"landing_page_url":"https://doi.org/10.1109/hldvt.2016.7748270","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2016 IEEE International High Level Design Validation and Test Workshop (HLDVT)","raw_type":"proceedings-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/A5031773625","display_name":"Rosario Distefano","orcid":"https://orcid.org/0000-0001-7241-7751"},"institutions":[{"id":"https://openalex.org/I119439378","display_name":"University of Verona","ror":"https://ror.org/039bp8j42","country_code":"IT","type":"education","lineage":["https://openalex.org/I119439378"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Rosario Distefano","raw_affiliation_strings":["Department of Computer Science, University of Verona, Italy"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Verona, Italy","institution_ids":["https://openalex.org/I119439378"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068716500","display_name":"Nickolas Goncharenko","orcid":null},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Nickolas Goncharenko","raw_affiliation_strings":["The Donnelly Centre, University of Toronto, Toronto, ON, Canada"],"affiliations":[{"raw_affiliation_string":"The Donnelly Centre, University of Toronto, Toronto, ON, Canada","institution_ids":["https://openalex.org/I185261750"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040302302","display_name":"Franco Fummi","orcid":"https://orcid.org/0000-0002-4404-5791"},"institutions":[{"id":"https://openalex.org/I119439378","display_name":"University of Verona","ror":"https://ror.org/039bp8j42","country_code":"IT","type":"education","lineage":["https://openalex.org/I119439378"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Franco Fummi","raw_affiliation_strings":["Department of Computer Science, University of Verona, Italy"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Verona, Italy","institution_ids":["https://openalex.org/I119439378"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002057785","display_name":"Rosalba Giugno","orcid":"https://orcid.org/0000-0001-9843-7638"},"institutions":[{"id":"https://openalex.org/I119439378","display_name":"University of Verona","ror":"https://ror.org/039bp8j42","country_code":"IT","type":"education","lineage":["https://openalex.org/I119439378"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Rosalba Giugno","raw_affiliation_strings":["Department of Computer Science, University of Verona, Italy"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Verona, Italy","institution_ids":["https://openalex.org/I119439378"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000247660","display_name":"Gary D. Badery","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Gary D. Badery","raw_affiliation_strings":["University of Toronto, Toronto, ON, CA"],"affiliations":[{"raw_affiliation_string":"University of Toronto, Toronto, ON, CA","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5088231786","display_name":"Nicola Bombieri","orcid":"https://orcid.org/0000-0003-3256-5885"},"institutions":[{"id":"https://openalex.org/I119439378","display_name":"University of Verona","ror":"https://ror.org/039bp8j42","country_code":"IT","type":"education","lineage":["https://openalex.org/I119439378"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Nicola Bombieri","raw_affiliation_strings":["Department of Computer Science, University of Verona, Italy"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Verona, Italy","institution_ids":["https://openalex.org/I119439378"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5031773625"],"corresponding_institution_ids":["https://openalex.org/I119439378"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.09448932,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"155","last_page":"161"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9988999962806702,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9988999962806702,"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/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":0.9930999875068665,"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/sbml","display_name":"SBML","score":0.9108532667160034},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7947371006011963},{"id":"https://openalex.org/keywords/robustness","display_name":"Robustness (evolution)","score":0.6805225014686584},{"id":"https://openalex.org/keywords/systemc","display_name":"SystemC","score":0.6149690747261047},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.5283710956573486},{"id":"https://openalex.org/keywords/distributed-computing","display_name":"Distributed computing","score":0.5231966972351074},{"id":"https://openalex.org/keywords/biological-network","display_name":"Biological network","score":0.4617275297641754},{"id":"https://openalex.org/keywords/reuse","display_name":"Reuse","score":0.4531330466270447},{"id":"https://openalex.org/keywords/markup-language","display_name":"Markup language","score":0.4504559338092804},{"id":"https://openalex.org/keywords/modelling-biological-systems","display_name":"Modelling biological systems","score":0.44227537512779236},{"id":"https://openalex.org/keywords/discrete-event-simulation","display_name":"Discrete event simulation","score":0.42200303077697754},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.33911722898483276},{"id":"https://openalex.org/keywords/simulation","display_name":"Simulation","score":0.20220845937728882},{"id":"https://openalex.org/keywords/computer-architecture","display_name":"Computer architecture","score":0.19256320595741272},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.1272742748260498},{"id":"https://openalex.org/keywords/xml","display_name":"XML","score":0.09805715084075928}],"concepts":[{"id":"https://openalex.org/C87186988","wikidata":"https://www.wikidata.org/wiki/Q452197","display_name":"SBML","level":4,"score":0.9108532667160034},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7947371006011963},{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.6805225014686584},{"id":"https://openalex.org/C2776928060","wikidata":"https://www.wikidata.org/wiki/Q1753563","display_name":"SystemC","level":2,"score":0.6149690747261047},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.5283710956573486},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.5231966972351074},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.4617275297641754},{"id":"https://openalex.org/C206588197","wikidata":"https://www.wikidata.org/wiki/Q846574","display_name":"Reuse","level":2,"score":0.4531330466270447},{"id":"https://openalex.org/C45874996","wikidata":"https://www.wikidata.org/wiki/Q37045","display_name":"Markup language","level":3,"score":0.4504559338092804},{"id":"https://openalex.org/C137866125","wikidata":"https://www.wikidata.org/wiki/Q4299308","display_name":"Modelling biological systems","level":3,"score":0.44227537512779236},{"id":"https://openalex.org/C147203929","wikidata":"https://www.wikidata.org/wiki/Q574814","display_name":"Discrete event simulation","level":2,"score":0.42200303077697754},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.33911722898483276},{"id":"https://openalex.org/C44154836","wikidata":"https://www.wikidata.org/wiki/Q45045","display_name":"Simulation","level":1,"score":0.20220845937728882},{"id":"https://openalex.org/C118524514","wikidata":"https://www.wikidata.org/wiki/Q173212","display_name":"Computer architecture","level":1,"score":0.19256320595741272},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.1272742748260498},{"id":"https://openalex.org/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"score":0.09805715084075928},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"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}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/hldvt.2016.7748270","is_oa":false,"landing_page_url":"https://doi.org/10.1109/hldvt.2016.7748270","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2016 IEEE International High Level Design Validation and Test Workshop (HLDVT)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.4699999988079071,"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":29,"referenced_works":["https://openalex.org/W22950313","https://openalex.org/W1830972360","https://openalex.org/W1969547738","https://openalex.org/W1981480991","https://openalex.org/W1981898075","https://openalex.org/W1989284002","https://openalex.org/W2000233729","https://openalex.org/W2000982470","https://openalex.org/W2003003919","https://openalex.org/W2008633581","https://openalex.org/W2046538693","https://openalex.org/W2054039423","https://openalex.org/W2057331291","https://openalex.org/W2069157810","https://openalex.org/W2069233518","https://openalex.org/W2075941967","https://openalex.org/W2090020814","https://openalex.org/W2103454055","https://openalex.org/W2103723044","https://openalex.org/W2123125245","https://openalex.org/W2127020923","https://openalex.org/W2132935366","https://openalex.org/W2146009166","https://openalex.org/W2147714160","https://openalex.org/W2157573465","https://openalex.org/W2160145365","https://openalex.org/W2161636210","https://openalex.org/W2236808273","https://openalex.org/W3105538867"],"related_works":["https://openalex.org/W2082621456","https://openalex.org/W2150908245","https://openalex.org/W2128782793","https://openalex.org/W2981332207","https://openalex.org/W2211443823","https://openalex.org/W2146744007","https://openalex.org/W2040642413","https://openalex.org/W3091139413","https://openalex.org/W2152827261","https://openalex.org/W2367709763"],"abstract_inverted_index":{"Qualitative":[0],"modelling":[1,32,61],"in":[2,84],"systems":[3,16,23,117],"biology":[4],"is":[5],"increasingly":[6],"adopted":[7],"as":[8],"it":[9],"allows":[10,77,114],"predicting":[11],"important":[12],"properties":[13,95],"of":[14,21,39,64,69,123,128,150],"biological":[15,51,65],"even":[17],"when":[18],"quantitative":[19],"information":[20],"such":[22],"are":[24],"unknown.":[25],"Even":[26],"though":[27],"different":[28,126],"tools":[29],"for":[30,59],"qualitative":[31,60],"have":[33],"been":[34,136],"recently":[35],"proposed,":[36],"their":[37,42,47],"lack":[38],"automatism":[40],"and":[41,62,98,142],"unstructured":[43],"simulation":[44,63],"core":[45,111],"limit":[46],"applicability":[48],"to":[49,79,96,138,143],"non-complex":[50],"networks.":[52],"This":[53],"paper":[54,131],"presents":[55],"SyQUAL,":[56],"a":[57,73,109,119],"platform":[58],"systems.":[66],"It":[67],"consists":[68],"two":[70],"main":[71],"layers:":[72],"Web-based":[74],"framework":[75],"that":[76,107,113],"users":[78],"(i)":[80],"import":[81],"models":[82],"described":[83],"the":[85,104,116,140,145,151],"standard":[86],"Systems":[87],"Biology":[88],"Markup":[89],"Language":[90],"(SBML),":[91],"(ii)":[92],"easily":[93],"define":[94],"observe,":[97],"(iii)":[99],"run":[100],"simulations":[101],"by":[102],"hiding":[103],"underlying":[105],"layer,":[106],"is,":[108],"SystemC-based":[110],"simulator":[112],"simulating":[115],"through":[118],"discrete":[120],"event-based":[121],"model":[122],"computation":[124],"at":[125],"levels":[127],"details.":[129],"The":[130],"shows":[132],"how":[133],"SyQUAL":[134],"has":[135],"applied":[137],"identify":[139],"attractors":[141],"analyse":[144],"system":[146],"robustness/sensitivity":[147],"under":[148],"perturbations":[149],"Colitis-associated":[152],"Colon":[153],"Cancer":[154],"(CAC)":[155],"network.":[156]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
