{"id":"https://openalex.org/W95584486","doi":null,"title":"A multidisciplinary survey of modeling techniques forbiochemical networks","display_name":"A multidisciplinary survey of modeling techniques forbiochemical networks","publication_year":2006,"publication_date":"2006-01-01","ids":{"openalex":"https://openalex.org/W95584486","mag":"95584486"},"language":"en","primary_location":{"id":"mag:95584486","doi":null,"is_oa":false,"landing_page_url":"http://doras.dcu.ie/4602/1/abstract.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/A5090163774","display_name":"James Decraene","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I42934936","display_name":"Dublin City University","ror":"https://ror.org/04a1a1e81","country_code":"IE","type":"education","lineage":["https://openalex.org/I42934936"]}],"countries":["IE"],"is_corresponding":false,"raw_author_name":"James Decraene","raw_affiliation_strings":["Dublin City University#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dublin City University#TAB#","institution_ids":["https://openalex.org/I42934936"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018987403","display_name":"Peter Dittrich","orcid":"https://orcid.org/0000-0002-2541-6745","observed_orcids":["https://orcid.org/0000-0002-2541-6745"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Peter Dittrich","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0002-2541-6745","affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007754301","display_name":"Thomas Hinze","orcid":"https://orcid.org/0000-0001-8661-5425","observed_orcids":["https://orcid.org/0000-0001-8661-5425"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Thomas Hinze","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0001-8661-5425","affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046892467","display_name":"Thorsten Lenser","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Thorsten Lenser","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052239696","display_name":"Barry McMullin","orcid":"https://orcid.org/0000-0002-5789-2068","observed_orcids":["https://orcid.org/0000-0002-5789-2068"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Barry McMullin","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0002-5789-2068","affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5039836915","display_name":"George G. Mitchell","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"George G. Mitchell","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.2246,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.4480613,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.0006000000284984708,"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":0.0003000000142492354,"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/ordinary-differential-equations","display_name":"ordinary differential equations","score":0.9190000295639038},{"id":"https://openalex.org/keywords/partial-differential-equations","display_name":"partial differential equations","score":0.953000009059906},{"id":"https://openalex.org/keywords/stochastic-simulation-algorithm","display_name":"stochastic simulation algorithm","score":0.9419999718666077},{"id":"https://openalex.org/keywords/bayesian-networks","display_name":"Bayesian networks","score":0.9890000224113464},{"id":"https://openalex.org/keywords/markov-chains","display_name":"Markov chains","score":0.9959999918937683},{"id":"https://openalex.org/keywords/process-calculus","display_name":"process algebra","score":0.9860000014305115},{"id":"https://openalex.org/keywords/term-rewriting-systems","display_name":"term rewriting systems","score":0.9950000047683716},{"id":"https://openalex.org/keywords/state-based-systems","display_name":"state-based systems","score":0.9340000152587891},{"id":"https://openalex.org/keywords/hybrid-modeling","display_name":"hybrid modeling","score":0.531000018119812},{"id":"https://openalex.org/keywords/artificial-chemistry","display_name":"artificial chemistry","score":0.8989999890327454},{"id":"https://openalex.org/keywords/evolutionary-computation","display_name":"evolutionary computation","score":0.9679999947547913},{"id":"https://openalex.org/keywords/in-silico-analysis","display_name":"in silico analysis","score":0.8029999732971191},{"id":"https://openalex.org/keywords/network-dynamics","display_name":"network dynamics","score":0.5960000157356262}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7313792705535889},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.5585012435913086},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.4965899586677551},{"id":"https://openalex.org/C9652623","wikidata":"https://www.wikidata.org/wiki/Q190109","display_name":"Field (mathematics)","level":2,"score":0.47885724902153015},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.4728950560092926},{"id":"https://openalex.org/C174348530","wikidata":"https://www.wikidata.org/wiki/Q188635","display_name":"Bridging (networking)","level":2,"score":0.46801695227622986},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.4661102890968323},{"id":"https://openalex.org/C98763669","wikidata":"https://www.wikidata.org/wiki/Q176645","display_name":"Markov chain","level":2,"score":0.43899351358413696},{"id":"https://openalex.org/C177774035","wikidata":"https://www.wikidata.org/wiki/Q1246948","display_name":"Granularity","level":2,"score":0.43296903371810913},{"id":"https://openalex.org/C33724603","wikidata":"https://www.wikidata.org/wiki/Q812540","display_name":"Bayesian network","level":2,"score":0.4311069846153259},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3834688067436218},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.37148594856262207},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3662492334842682},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.13724258542060852},{"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/C202444582","wikidata":"https://www.wikidata.org/wiki/Q837863","display_name":"Pure mathematics","level":1,"score":0.0},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C31258907","wikidata":"https://www.wikidata.org/wiki/Q1301371","display_name":"Computer network","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}],"mesh":[],"locations_count":1,"locations":[{"id":"mag:95584486","doi":null,"is_oa":false,"landing_page_url":"http://doras.dcu.ie/4602/1/abstract.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":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2112414589","https://openalex.org/W7096329443","https://openalex.org/W2243874335","https://openalex.org/W2395301294","https://openalex.org/W1643465022","https://openalex.org/W2905450522","https://openalex.org/W2046154060","https://openalex.org/W19354151","https://openalex.org/W7100406107","https://openalex.org/W1524850258"],"abstract_inverted_index":{"All":[0],"processes":[1],"of":[2,8,14,24,30,46,52,86,122,169,192,198,210,217,223],"life":[3],"are":[4,106],"dominated":[5],"by":[6,236,246],"networks":[7,17,95,162,235],"interacting":[9],"biochemical":[10,94,128,234],"components.":[11],"The":[12],"purpose":[13],"modeling":[15,93,104,233],"these":[16],"is":[18,96],"manifold.":[19],"From":[20,48],"a":[21,49,87,119,142,229],"theoretical":[22],"point":[23,51],"view":[25],"it":[26],"allows":[27],"the":[28,42,70,84,100,114,123,146,167,190,221,259],"exploration":[29],"network":[31],"structures":[32],"and":[33,44,99,152,163,166,177,186,213,240],"dynamics,":[34],"to":[35,40,67,77,126],"find":[36],"emergent":[37],"properties":[38],"or":[39,65,80,82,196],"explain":[41],"organization":[43],"evolution":[45],"networks.":[47,129],"practical":[50],"view,":[53],"in":[54,69,145,252,258],"silico":[55],"experiments":[56,79],"can":[57,207],"be":[58,62],"performed":[59],"that":[60],"would":[61],"very":[63],"expensive":[64],"impossible":[66],"achieve":[68],"laboratory,":[71],"such":[72,188],"as":[73,189],"hypothesis-testing":[74],"with":[75,150,157,172],"regard":[76],"knockout":[78],"overexpression,":[81],"checking":[83],"validity":[85],"proposed":[88],"molecular":[89],"mechanism.\r\n\r\nThe":[90],"literature":[91],"on":[92,134],"growing":[97],"rapidly":[98],"motivations":[101],"behind":[102],"different":[103,124],"techniques":[105,212,219],"sometimes":[107],"quite":[108],"distant":[109],"from":[110],"each":[111,181],"other.":[112],"To\r\nclarify":[113],"current":[115],"context,":[116],"we":[117,183,203,227],"present":[118],"systematic":[120],"overview":[121],"philosophies":[125],"model":[127],"We":[130],"put":[131],"particular":[132],"emphasis":[133],"three":[135],"main":[136],"domains":[137],"which":[138],"have":[139],"been":[140],"playing":[141],"major":[143],"role":[144],"past,":[147],"namely:":[148],"mathematics":[149],"ordinary":[151],"partial":[153],"differential":[154],"equations,":[155],"statistics":[156],"stochastic":[158],"simulation":[159],"algorithms,":[160],"Bayesian":[161],"Markov":[164],"chains,":[165],"field":[168],"computer":[170],"science":[171],"process":[173],"calculi,":[174],"term":[175],"rewriting\r\nsystems":[176],"state":[178],"based":[179],"systems.\r\n\r\nFor":[180],"school,":[182],"evaluate":[184],"advantages":[185,216],"disadvantages":[187],"granularity":[191],"representation,":[193],"scalability,":[194],"accessibility":[195],"availability":[197],"analysis":[199],"tools.":[200,225],"Following":[201],"this,":[202],"describe":[204],"how":[205],"one":[206],"combine":[208],"some":[209],"those":[211],"thus":[214],"take":[215],"several":[218],"through":[220],"use":[222],"bridging":[224],"Finally,":[226],"propose":[228],"next":[230],"step":[231],"for":[232],"using":[237],"artificial":[238],"chemistries":[239],"evolutionary":[241],"computation.\r\n\r\nThis":[242],"work":[243],"was":[244],"funded":[245],"ESIGNET":[247],"(Evolving":[248],"Cell":[249],"Signaling":[250],"Networks":[251],"Silico),":[253],"an":[254],"European":[255],"Integrated":[256],"Project":[257],"EU":[260],"FP6":[261],"NEST":[262],"Initiative":[263],"(contract":[264],"no.":[265],"12789).":[266]},"counts_by_year":[],"updated_date":"2025-11-06T04:12:42.849631","created_date":"2016-06-24T00:00:00"}
