{"id":"https://openalex.org/W2504449983","doi":"https://doi.org/10.1007/978-3-319-39086-4_8","title":"AB-QSSPN: Integration of Agent-Based Simulation of Cellular Populations with Quasi-Steady State Simulation of Genome Scale Intracellular Networks","display_name":"AB-QSSPN: Integration of Agent-Based Simulation of Cellular Populations with Quasi-Steady State Simulation of Genome Scale Intracellular Networks","publication_year":2016,"publication_date":"2016-01-01","ids":{"openalex":"https://openalex.org/W2504449983","doi":"https://doi.org/10.1007/978-3-319-39086-4_8","mag":"2504449983"},"language":"en","primary_location":{"id":"doi:10.1007/978-3-319-39086-4_8","is_oa":true,"landing_page_url":"https://doi.org/10.1007/978-3-319-39086-4_8","pdf_url":null,"source":{"id":"https://openalex.org/S106296714","display_name":"Lecture notes in computer science","issn_l":"0302-9743","issn":["0302-9743","1611-3349"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"book series"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Lecture Notes in Computer Science","raw_type":"book-chapter"},"type":"conference-paper","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://doi.org/10.1007/978-3-319-39086-4_8","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5016812917","display_name":"Wojciech Ptak","orcid":null},"institutions":[{"id":"https://openalex.org/I4654613","display_name":"University of Warsaw","ror":"https://ror.org/039bjqg32","country_code":"PL","type":"education","lineage":["https://openalex.org/I4654613"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Wojciech Ptak","raw_affiliation_strings":["Institute of Informatics, University of Warsaw, Warsaw, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Informatics, University of Warsaw, Warsaw, Poland","institution_ids":["https://openalex.org/I4654613"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015589509","display_name":"Andrzej Kierzek","orcid":"https://orcid.org/0000-0002-2605-9057"},"institutions":[{"id":"https://openalex.org/I28290843","display_name":"University of Surrey","ror":"https://ror.org/00ks66431","country_code":"GB","type":"education","lineage":["https://openalex.org/I28290843"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Andrzej M. Kierzek","raw_affiliation_strings":["Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK","institution_ids":["https://openalex.org/I28290843"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5091346096","display_name":"Jacek Sroka","orcid":"https://orcid.org/0000-0002-1714-9667"},"institutions":[{"id":"https://openalex.org/I4654613","display_name":"University of Warsaw","ror":"https://ror.org/039bjqg32","country_code":"PL","type":"education","lineage":["https://openalex.org/I4654613"]}],"countries":["PL"],"is_corresponding":true,"raw_author_name":"Jacek Sroka","raw_affiliation_strings":["Institute of Informatics, University of Warsaw, Warsaw, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Informatics, University of Warsaw, Warsaw, Poland","institution_ids":["https://openalex.org/I4654613"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5091346096"],"corresponding_institution_ids":["https://openalex.org/I4654613"],"apc_list":{"value":5000,"currency":"EUR","value_usd":5392},"apc_paid":{"value":5000,"currency":"EUR","value_usd":5392},"fwci":0.8196,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.78648829,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":null,"issue":null,"first_page":"113","last_page":"122"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9995999932289124,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9995999932289124,"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":0.9987999796867371,"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":0.9710999727249146,"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/computer-science","display_name":"Computer science","score":0.7674882411956787},{"id":"https://openalex.org/keywords/scale","display_name":"Scale (ratio)","score":0.6109228134155273},{"id":"https://openalex.org/keywords/steady-state","display_name":"Steady state (chemistry)","score":0.5702679753303528},{"id":"https://openalex.org/keywords/state","display_name":"State (computer science)","score":0.48268556594848633},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.344706654548645},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.14537382125854492},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.12294504046440125},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.12291547656059265},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.11311888694763184},{"id":"https://openalex.org/keywords/physical-chemistry","display_name":"Physical chemistry","score":0.07970714569091797}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7674882411956787},{"id":"https://openalex.org/C2778755073","wikidata":"https://www.wikidata.org/wiki/Q10858537","display_name":"Scale (ratio)","level":2,"score":0.6109228134155273},{"id":"https://openalex.org/C8171440","wikidata":"https://www.wikidata.org/wiki/Q903414","display_name":"Steady state (chemistry)","level":2,"score":0.5702679753303528},{"id":"https://openalex.org/C48103436","wikidata":"https://www.wikidata.org/wiki/Q599031","display_name":"State (computer science)","level":2,"score":0.48268556594848633},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.344706654548645},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.14537382125854492},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.12294504046440125},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.12291547656059265},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.11311888694763184},{"id":"https://openalex.org/C147789679","wikidata":"https://www.wikidata.org/wiki/Q11372","display_name":"Physical chemistry","level":1,"score":0.07970714569091797},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1007/978-3-319-39086-4_8","is_oa":true,"landing_page_url":"https://doi.org/10.1007/978-3-319-39086-4_8","pdf_url":null,"source":{"id":"https://openalex.org/S106296714","display_name":"Lecture notes in computer science","issn_l":"0302-9743","issn":["0302-9743","1611-3349"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"book series"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Lecture Notes in Computer Science","raw_type":"book-chapter"}],"best_oa_location":{"id":"doi:10.1007/978-3-319-39086-4_8","is_oa":true,"landing_page_url":"https://doi.org/10.1007/978-3-319-39086-4_8","pdf_url":null,"source":{"id":"https://openalex.org/S106296714","display_name":"Lecture notes in computer science","issn_l":"0302-9743","issn":["0302-9743","1611-3349"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"book series"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Lecture Notes in Computer Science","raw_type":"book-chapter"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":11,"referenced_works":["https://openalex.org/W1448681276","https://openalex.org/W1969067437","https://openalex.org/W2044935306","https://openalex.org/W2066196011","https://openalex.org/W2078355959","https://openalex.org/W2082382448","https://openalex.org/W2131975293","https://openalex.org/W2133552211","https://openalex.org/W2158497698","https://openalex.org/W2173213060","https://openalex.org/W2296335794"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052","https://openalex.org/W2382290278","https://openalex.org/W4395014643"],"abstract_inverted_index":{"We":[0],"present":[1,68],"a":[2,31,113,126,149],"tool":[3,143],"for":[4,63],"simulation":[5],"of":[6,8,74,76,93,129,137,156],"populations":[7,73],"living":[9],"cells":[10,78],"interacting":[11,77],"in":[12,53,80,107,117],"spatial":[13,81],"structures.":[14],"Each":[15],"cell":[16],"is":[17,44,172],"modelled":[18],"with":[19,30],"the":[20,48,54,100,105,122,138,168,175,181],"Quasi-Steady":[21],"Petri":[22,32],"Net":[23,33],"that":[24,97],"integrates":[25],"dynamic":[26],"regulatory":[27],"network":[28],"expressed":[29],"(PN)":[34],"and":[35,103,154,165,174],"Genome":[36],"Scale":[37],"Metabolic":[38],"Networks":[39],"(GSMN)":[40],"where":[41],"linear":[42],"programming":[43],"used":[45,86,146],"to":[46,71,87,133,147],"explore":[47],"steady-state":[49,139],"metabolic":[50,140],"flux":[51],"distributions":[52],"whole-cell":[55],"model.":[56],"Similar":[57],"simulations":[58],"have":[59],"already":[60],"been":[61],"conducted":[62],"single":[64],"cells,":[65],"but":[66],"we":[67,98,124],"an":[69,108],"architecture":[70],"simulate":[72],"millions":[75],"organized":[79],"structures":[82],"which":[83],"can":[84,144],"be":[85,145,178],"model":[88],"tumour":[89],"growth":[90],"or":[91],"formation":[92],"tuberculosis":[94],"lesions.":[95],"For":[96],"use":[99],"Spark":[101],"framework":[102],"organize":[104],"computation":[106,136],"agent":[109],"based":[110],"\u201cthink":[111],"like":[112,119],"vertex\u201d":[114],"fashion":[115],"as":[116,180],"Pregel":[118],"systems.":[120],"In":[121],"cluster":[123],"introduce":[125],"special":[127],"kind":[128],"per":[130],"node":[131],"caching":[132],"speed":[134],"up":[135],"flux.":[141],"Our":[142],"provide":[148],"mechanistic":[150],"link":[151],"between":[152],"genotype":[153],"behaviour":[155],"multicellular":[157],"system.":[158],"These":[159],"keywords":[160,176],"were":[161],"added":[162],"by":[163,167],"machine":[164],"not":[166],"authors.":[169],"This":[170],"process":[171],"experimental":[173],"may":[177],"updated":[179],"learning":[182],"algorithm":[183],"improves.":[184]},"counts_by_year":[{"year":2021,"cited_by_count":1},{"year":2017,"cited_by_count":1}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-10-10T00:00:00"}