{"id":"https://openalex.org/W1976425198","doi":"https://doi.org/10.1109/bibm.2011.124","title":"Formal Modeling and Analysis of Biological Regulatory Networks Using SPIN","display_name":"Formal Modeling and Analysis of Biological Regulatory Networks Using SPIN","publication_year":2011,"publication_date":"2011-11-01","ids":{"openalex":"https://openalex.org/W1976425198","doi":"https://doi.org/10.1109/bibm.2011.124","mag":"1976425198"},"language":"en","primary_location":{"id":"doi:10.1109/bibm.2011.124","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2011.124","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2011 IEEE International Conference on Bioinformatics and Biomedicine","raw_type":"proceedings-article"},"type":"conference-paper","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/A5008763262","display_name":"Usman Rauf","orcid":"https://orcid.org/0000-0003-3667-4974"},"institutions":[{"id":"https://openalex.org/I312958679","display_name":"National University of Science and Technology","ror":"https://ror.org/02kesvt12","country_code":"ZW","type":"education","lineage":["https://openalex.org/I312958679"]}],"countries":["ZW"],"is_corresponding":false,"raw_author_name":"Usman Rauf","raw_affiliation_strings":["Research Center of Modeling and Simulation (RCMS), National University of Science and Technology, Islamabad, Pakistan","Res. Center for Modeling & Simulation (RCMS), Nat. Univ. of Sci. & Technol. (NUST) Islamabad, Islamabad, Pakistan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Research Center of Modeling and Simulation (RCMS), National University of Science and Technology, Islamabad, Pakistan","institution_ids":[]},{"raw_affiliation_string":"Res. Center for Modeling & Simulation (RCMS), Nat. Univ. of Sci. & Technol. (NUST) Islamabad, Islamabad, Pakistan","institution_ids":["https://openalex.org/I312958679"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036366006","display_name":"Umair Siddique","orcid":"https://orcid.org/0000-0001-6871-5289"},"institutions":[{"id":"https://openalex.org/I312958679","display_name":"National University of Science and Technology","ror":"https://ror.org/02kesvt12","country_code":"ZW","type":"education","lineage":["https://openalex.org/I312958679"]}],"countries":["ZW"],"is_corresponding":false,"raw_author_name":"Umair Siddique","raw_affiliation_strings":["Research Center of Modeling and Simulation (RCMS), National University of Science and Technology, Islamabad, Pakistan","Res. Center for Modeling & Simulation (RCMS), Nat. Univ. of Sci. & Technol. (NUST) Islamabad, Islamabad, Pakistan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Research Center of Modeling and Simulation (RCMS), National University of Science and Technology, Islamabad, Pakistan","institution_ids":[]},{"raw_affiliation_string":"Res. Center for Modeling & Simulation (RCMS), Nat. Univ. of Sci. & Technol. (NUST) Islamabad, Islamabad, Pakistan","institution_ids":["https://openalex.org/I312958679"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101815655","display_name":"Jamil Ahmad","orcid":"https://orcid.org/0000-0002-2137-7611"},"institutions":[{"id":"https://openalex.org/I312958679","display_name":"National University of Science and Technology","ror":"https://ror.org/02kesvt12","country_code":"ZW","type":"education","lineage":["https://openalex.org/I312958679"]}],"countries":["ZW"],"is_corresponding":false,"raw_author_name":"Jamil Ahmad","raw_affiliation_strings":["Research Center of Modeling and Simulation (RCMS), National University of Science and Technology, Islamabad, Pakistan","Res. Center for Modeling & Simulation (RCMS), Nat. Univ. of Sci. & Technol. (NUST) Islamabad, Islamabad, Pakistan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Research Center of Modeling and Simulation (RCMS), National University of Science and Technology, Islamabad, Pakistan","institution_ids":[]},{"raw_affiliation_string":"Res. Center for Modeling & Simulation (RCMS), Nat. Univ. of Sci. & Technol. (NUST) Islamabad, Islamabad, Pakistan","institution_ids":["https://openalex.org/I312958679"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5082507956","display_name":"Umar Niazi","orcid":"https://orcid.org/0000-0001-7176-8883"},"institutions":[{"id":"https://openalex.org/I312958679","display_name":"National University of Science and Technology","ror":"https://ror.org/02kesvt12","country_code":"ZW","type":"education","lineage":["https://openalex.org/I312958679"]}],"countries":["ZW"],"is_corresponding":false,"raw_author_name":"Umar Niazi","raw_affiliation_strings":["Research Center of Modeling and Simulation (RCMS), National University of Science and Technology, Islamabad, Pakistan","Res. Center for Modeling & Simulation (RCMS), Nat. Univ. of Sci. & Technol. (NUST) Islamabad, Islamabad, Pakistan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Research Center of Modeling and Simulation (RCMS), National University of Science and Technology, Islamabad, Pakistan","institution_ids":[]},{"raw_affiliation_string":"Res. Center for Modeling & Simulation (RCMS), Nat. Univ. of Sci. & Technol. (NUST) Islamabad, Islamabad, Pakistan","institution_ids":["https://openalex.org/I312958679"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I312958679"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":6,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":"60","issue":null,"first_page":"304","last_page":"308"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9991000294685364,"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":0.9991000294685364,"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":0.9896000027656555,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9847000241279602,"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/model-checking","display_name":"Model checking","score":0.8715025186538696},{"id":"https://openalex.org/keywords/soundness","display_name":"Soundness","score":0.81374192237854},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.690272867679596},{"id":"https://openalex.org/keywords/temporal-logic","display_name":"Temporal logic","score":0.6463780403137207},{"id":"https://openalex.org/keywords/formal-verification","display_name":"Formal verification","score":0.6233739852905273},{"id":"https://openalex.org/keywords/linear-temporal-logic","display_name":"Linear temporal logic","score":0.5575027465820312},{"id":"https://openalex.org/keywords/reliability","display_name":"Reliability (semiconductor)","score":0.4991750717163086},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.46700605750083923},{"id":"https://openalex.org/keywords/formal-methods","display_name":"Formal methods","score":0.4653409719467163},{"id":"https://openalex.org/keywords/systems-modeling","display_name":"Systems modeling","score":0.45237621665000916},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.25848519802093506},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.23875153064727783}],"concepts":[{"id":"https://openalex.org/C110251889","wikidata":"https://www.wikidata.org/wiki/Q1569697","display_name":"Model checking","level":2,"score":0.8715025186538696},{"id":"https://openalex.org/C39920170","wikidata":"https://www.wikidata.org/wiki/Q693083","display_name":"Soundness","level":2,"score":0.81374192237854},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.690272867679596},{"id":"https://openalex.org/C25016198","wikidata":"https://www.wikidata.org/wiki/Q781833","display_name":"Temporal logic","level":2,"score":0.6463780403137207},{"id":"https://openalex.org/C111498074","wikidata":"https://www.wikidata.org/wiki/Q173326","display_name":"Formal verification","level":2,"score":0.6233739852905273},{"id":"https://openalex.org/C4777664","wikidata":"https://www.wikidata.org/wiki/Q1536492","display_name":"Linear temporal logic","level":2,"score":0.5575027465820312},{"id":"https://openalex.org/C43214815","wikidata":"https://www.wikidata.org/wiki/Q7310987","display_name":"Reliability (semiconductor)","level":3,"score":0.4991750717163086},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.46700605750083923},{"id":"https://openalex.org/C75606506","wikidata":"https://www.wikidata.org/wiki/Q1049183","display_name":"Formal methods","level":2,"score":0.4653409719467163},{"id":"https://openalex.org/C110963975","wikidata":"https://www.wikidata.org/wiki/Q12070446","display_name":"Systems modeling","level":2,"score":0.45237621665000916},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.25848519802093506},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.23875153064727783},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C163258240","wikidata":"https://www.wikidata.org/wiki/Q25342","display_name":"Power (physics)","level":2,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm.2011.124","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2011.124","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2011 IEEE International Conference on Bioinformatics and Biomedicine","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":17,"referenced_works":["https://openalex.org/W198918365","https://openalex.org/W202898619","https://openalex.org/W1489480103","https://openalex.org/W1496007014","https://openalex.org/W1498432697","https://openalex.org/W1507959092","https://openalex.org/W1517173520","https://openalex.org/W1905380539","https://openalex.org/W1962072139","https://openalex.org/W2058221907","https://openalex.org/W2060095702","https://openalex.org/W2073144071","https://openalex.org/W2115309705","https://openalex.org/W2121149194","https://openalex.org/W2167978186","https://openalex.org/W2472540485","https://openalex.org/W4393906106"],"related_works":["https://openalex.org/W2124110813","https://openalex.org/W2763487042","https://openalex.org/W2521108391","https://openalex.org/W1532447905","https://openalex.org/W2031188261","https://openalex.org/W3021103820","https://openalex.org/W4285022830","https://openalex.org/W4232446061","https://openalex.org/W2077520193","https://openalex.org/W1513400763"],"abstract_inverted_index":{"In":[0,45],"the":[1,14,66,69,86,108,117],"last":[2],"two":[3],"decades,":[4],"formal":[5,15,58],"verification":[6],"has":[7],"emerged":[8],"as":[9],"an":[10],"important":[11],"technique":[12],"for":[13,57,65,89,116],"modeling":[16,59,90],"and":[17,23,40,60,101,126],"analysis":[18,35,118],"of":[19,29,42,68,73,81,98,110,119],"real":[20],"time":[21],"reactive":[22],"unpredictable":[24],"systems.":[25],"The":[26,78],"main":[27,79],"advantage":[28],"model":[30,54,104],"checking":[31],"over":[32],"simulation":[33],"based":[34,92],"is":[36],"its":[37],"inherent":[38],"soundness":[39],"reliability":[41],"computed":[43],"results.":[44],"this":[46,82],"paper,":[47],"we":[48,113],"propose":[49],"to":[50],"use":[51],"explicit":[52],"state":[53],"checker":[55],"(SPIN)":[56],"Linear":[61],"Temporal":[62],"Logic":[63,97],"(LTL)":[64],"exploration":[67],"complex":[70],"dynamics":[71],"(cycles)":[72],"biological":[74],"regulatory":[75],"networks":[76],"(BRNs).":[77],"contribution":[80],"paper":[83],"also":[84],"includes":[85],"generalized":[87],"framework":[88],"BRNs":[91],"on":[93],"well":[94],"known":[95],"Kinetic":[96],"Rene":[99],"Thomas":[100],"state-of-the-art":[102],"SPIN":[103],"checker.":[105],"To":[106],"demonstrate":[107],"usefulness":[109],"current":[111],"work,":[112],"utilized":[114],"it":[115],"mucus":[120],"production":[121],"system":[122],"in":[123],"Pseudomonas":[124],"aeruginosa":[125],"BRN":[127],"involving":[128],"Indoleamine":[129],"2,":[130],"3-dioxygenase":[131],"(IDO).":[132]},"counts_by_year":[{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2015,"cited_by_count":2},{"year":2013,"cited_by_count":1}],"updated_date":"2026-07-14T23:27:15.235271","created_date":"2025-10-10T00:00:00"}
