{"id":"https://openalex.org/W44416928","doi":null,"title":"Agile modelling of cellular signalling a simple illustration of the rule-based approach","display_name":"Agile modelling of cellular signalling a simple illustration of the rule-based approach","publication_year":2008,"publication_date":"2008-01-01","ids":{"openalex":"https://openalex.org/W44416928","mag":"44416928"},"language":"en","primary_location":{"id":"mag:44416928","doi":null,"is_oa":false,"landing_page_url":"http://www.inf.ed.ac.uk/teaching/courses/sbm/pdfs/sbm6.pdf","pdf_url":null,"source":null,"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},"volume":null,"type":"article","is_traditional":true,"indexed_in":[],"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/A5111482850","display_name":"Vincent Danos","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Vincent Danos","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":["https://openalex.org/A5111482850"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.00408061,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9980000257492065,"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":0.9980000257492065,"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/T10778","display_name":"Philosophy of Biology and Scientific Explanation","score":0.00019999999494757503,"subfield":{"id":"https://openalex.org/subfields/1207","display_name":"History and Philosophy of Science"},"field":{"id":"https://openalex.org/fields/12","display_name":"Arts and Humanities"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},{"id":"https://openalex.org/T11829","display_name":"Mathematical Biology Tumor Growth","score":9.999999747378752e-05,"subfield":{"id":"https://openalex.org/subfields/2611","display_name":"Modeling and Simulation"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/signal-transduction","display_name":"signal transduction","score":0.8180000185966492},{"id":"https://openalex.org/keywords/rule-based-modeling","display_name":"rule-based models","score":0.9779999852180481},{"id":"https://openalex.org/keywords/bionetgen","display_name":"BioNetGen","score":0.7950000166893005},{"id":"https://openalex.org/keywords/combinatorial-explosion","display_name":"combinatorial explosion","score":0.9810000061988831},{"id":"https://openalex.org/keywords/process-calculus","display_name":"process algebra","score":0.46799999475479126}],"concepts":[{"id":"https://openalex.org/C171268870","wikidata":"https://www.wikidata.org/wiki/Q1486676","display_name":"GRASP","level":2,"score":0.7119206786155701},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7061707973480225},{"id":"https://openalex.org/C2780586882","wikidata":"https://www.wikidata.org/wiki/Q7520643","display_name":"Simple (philosophy)","level":2,"score":0.576602041721344},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.5249488353729248},{"id":"https://openalex.org/C66746571","wikidata":"https://www.wikidata.org/wiki/Q1134833","display_name":"ENCODE","level":3,"score":0.49507656693458557},{"id":"https://openalex.org/C34146451","wikidata":"https://www.wikidata.org/wiki/Q5048094","display_name":"Cascade","level":2,"score":0.43875208497047424},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.43552473187446594},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.42643028497695923},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.42295634746551514},{"id":"https://openalex.org/C115908005","wikidata":"https://www.wikidata.org/wiki/Q2668364","display_name":"Combinatorial explosion","level":2,"score":0.41779449582099915},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.18058443069458008},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.15503227710723877},{"id":"https://openalex.org/C43617362","wikidata":"https://www.wikidata.org/wiki/Q170050","display_name":"Chromatography","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"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/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"mag:44416928","doi":null,"is_oa":false,"landing_page_url":"http://www.inf.ed.ac.uk/teaching/courses/sbm/pdfs/sbm6.pdf","pdf_url":null,"source":null,"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":13,"referenced_works":["https://openalex.org/W1586735752","https://openalex.org/W1595516773","https://openalex.org/W1986649132","https://openalex.org/W1986968087","https://openalex.org/W2007006124","https://openalex.org/W2041603328","https://openalex.org/W2069941324","https://openalex.org/W2070658593","https://openalex.org/W2105946516","https://openalex.org/W2144063122","https://openalex.org/W2155418451","https://openalex.org/W2663300410","https://openalex.org/W2913004508"],"related_works":["https://openalex.org/W1500381309","https://openalex.org/W2144063122","https://openalex.org/W1965694523","https://openalex.org/W7099347823","https://openalex.org/W2295181068","https://openalex.org/W1563071114","https://openalex.org/W2342245708","https://openalex.org/W2120866542","https://openalex.org/W7099025292","https://openalex.org/W168236614"],"abstract_inverted_index":{"The":[0],"purpose":[1],"of":[2,10,30,54,63,67,119,123,134,161,192,197,206],"this":[3,89,143],"note":[4,168],"is":[5,23,32,83,128],"to":[6,16,78,84,104,114,129,209],"demonstrate":[7],"the":[8,21,27,41,64,120,124,131,158,166,185,190,213,219,234],"flexibility":[9],"a":[11,51,60,68,163,198,203,242,254],"structured":[12],"and":[13,73,100,110,245,248],"rulebased":[14],"approach":[15,22,125],"modelling":[17],"cellular":[18],"signalling.":[19],"Although":[20],"especially":[24],"useful":[25],"when":[26],"biological":[28,239],"system":[29],"interest":[31],"highly":[33],"combinatorial,":[34],"we":[35,47,126,230],"will":[36,169],"use":[37,231],"an":[38],"example":[39,140],"that":[40,187],"intuition":[42],"can":[43,148],"grasp":[44],"comfortably.":[45],"Specifically":[46],"shall:":[48],"start":[49],"with":[50],"basic":[52],"motive":[53],"reversible":[55],"covalent":[56],"modification":[57],"[1];":[58],"obtain":[59],"rule-based":[61],"version":[62],"Huang-Ferell":[65],"model":[66,205],"protein":[69],"activation":[70],"cascade":[71,77,90],"[2];":[72],"finally,":[74],"rewire":[75],"our":[76],"illustrate":[79],"how":[80],"easy":[81],"it":[82,92],"do":[85,179],"so.":[86],"Simple":[87],"as":[88,226,249],"is,":[91],"already":[93],"generates":[94],"about":[95],"six":[96],"hundred":[97],"different":[98],"species,":[99],"would":[101],"be":[102,149],"tedious":[103],"specify":[105],"by":[106],"traditional":[107,135],"reaction-based":[108],"methods,":[109],"even":[111],"more":[112,138,211,221,243],"so":[113],"modify.":[115],"In":[116],"fact":[117,186],"one":[118,155],"major":[121],"advantages":[122],"advocate":[127],"avoid":[130],"combinatorial":[132],"explosion":[133],"approaches.":[136],"A":[137],"complex":[139],"which":[141,165,217],"illustrates":[142],"point":[144],"in":[145,151,181,212,241],"spectacular":[146],"fashion":[147],"found":[150],"Ref.":[152],"[3].":[153],"There":[154],"also":[156,252],"considers":[157],"causal":[159],"analysis":[160],"models,":[162],"topic":[164],"present":[167],"not":[170],"discuss.":[171],"Other":[172],"approaches":[173],"using":[174],"process-algebraic":[175],"languages":[176,224],"[4\u20138]":[177],"could":[178],"well":[180],"principle":[182],"but":[183],"for":[184],"they":[188],"require":[189],"enumeration":[191],"all":[193],"possible":[194],"internal":[195,215],"states":[196],"process.":[199],"Those":[200],"based":[201],"on":[202],"binary":[204],"communication":[207],"need":[208],"encode":[210],"processes":[214],"states,":[216],"makes":[218],"problem":[220],"acute.":[222],"Rule-based":[223],"such":[225,250],"Kappa":[227],"[9]":[228],"-which":[229],"here,":[232],"or":[233],"BioNetGen":[235],"language":[236],"[10]":[237],"describe":[238],"interactions":[240],"natural":[244],"intuitive":[246],"way":[247],"are":[251],"at":[253],"clear":[255],"practical":[256],"advantage.":[257]},"counts_by_year":[],"updated_date":"2026-11-06T12:05:46.655746","created_date":"2016-06-24T00:00:00"}
