{"id":"https://openalex.org/W4255959959","doi":"https://doi.org/10.1109/wsc.2014.7019887","title":"Multi-level modeling and simulation of cell biological systems with ML-Rules - A tutorial","display_name":"Multi-level modeling and simulation of cell biological systems with ML-Rules - A tutorial","publication_year":2014,"publication_date":"2014-12-01","ids":{"openalex":"https://openalex.org/W4255959959","doi":"https://doi.org/10.1109/wsc.2014.7019887"},"language":"en","primary_location":{"id":"doi:10.1109/wsc.2014.7019887","is_oa":false,"landing_page_url":"https://doi.org/10.1109/wsc.2014.7019887","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the Winter Simulation Conference 2014","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/A5109384221","display_name":"Tobias Helms","orcid":null},"institutions":[{"id":"https://openalex.org/I4210155092","display_name":"Czech Academy of Sciences, Institute of Computer Science","ror":"https://ror.org/0496n6574","country_code":"CZ","type":"facility","lineage":["https://openalex.org/I202391551","https://openalex.org/I4210155092"]},{"id":"https://openalex.org/I4665924","display_name":"University of Rostock","ror":"https://ror.org/03zdwsf69","country_code":"DE","type":"education","lineage":["https://openalex.org/I4665924"]}],"countries":["CZ","DE"],"is_corresponding":false,"raw_author_name":"Tobias Helms","raw_affiliation_strings":["Institute of Computer Science, University of Rostock, Rostock, GERMANY"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Computer Science, University of Rostock, Rostock, GERMANY","institution_ids":["https://openalex.org/I4210155092","https://openalex.org/I4665924"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077806089","display_name":"Carsten Maus","orcid":null},"institutions":[{"id":"https://openalex.org/I17937529","display_name":"German Cancer Research Center","ror":"https://ror.org/04cdgtt98","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I17937529"]},{"id":"https://openalex.org/I223822909","display_name":"Heidelberg University","ror":"https://ror.org/038t36y30","country_code":"DE","type":"education","lineage":["https://openalex.org/I223822909"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Carsten Maus","raw_affiliation_strings":["Division of Theoretical Systems Biology German Cancer Research Center, Heidelberg, GERMANY"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Theoretical Systems Biology German Cancer Research Center, Heidelberg, GERMANY","institution_ids":["https://openalex.org/I17937529","https://openalex.org/I223822909"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090554724","display_name":"Fiete Haack","orcid":"https://orcid.org/0000-0003-3713-8313"},"institutions":[{"id":"https://openalex.org/I4210155092","display_name":"Czech Academy of Sciences, Institute of Computer Science","ror":"https://ror.org/0496n6574","country_code":"CZ","type":"facility","lineage":["https://openalex.org/I202391551","https://openalex.org/I4210155092"]},{"id":"https://openalex.org/I4665924","display_name":"University of Rostock","ror":"https://ror.org/03zdwsf69","country_code":"DE","type":"education","lineage":["https://openalex.org/I4665924"]}],"countries":["CZ","DE"],"is_corresponding":false,"raw_author_name":"Fiete Haack","raw_affiliation_strings":["Institute of Computer Science, University of Rostock, Rostock, GERMANY"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Computer Science, University of Rostock, Rostock, GERMANY","institution_ids":["https://openalex.org/I4210155092","https://openalex.org/I4665924"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5063515034","display_name":"Adelinde M. Uhrmacher","orcid":"https://orcid.org/0000-0001-5256-4682"},"institutions":[{"id":"https://openalex.org/I4210155092","display_name":"Czech Academy of Sciences, Institute of Computer Science","ror":"https://ror.org/0496n6574","country_code":"CZ","type":"facility","lineage":["https://openalex.org/I202391551","https://openalex.org/I4210155092"]},{"id":"https://openalex.org/I4665924","display_name":"University of Rostock","ror":"https://ror.org/03zdwsf69","country_code":"DE","type":"education","lineage":["https://openalex.org/I4665924"]}],"countries":["CZ","DE"],"is_corresponding":false,"raw_author_name":"Adelinde M. Uhrmacher","raw_affiliation_strings":["Institute of Computer Science, University of Rostock, Rostock, GERMANY"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Computer Science, University of Rostock, Rostock, GERMANY","institution_ids":["https://openalex.org/I4210155092","https://openalex.org/I4665924"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.42684703,"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":"177","last_page":"191"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11195","display_name":"Simulation Techniques and Applications","score":0.9916999936103821,"subfield":{"id":"https://openalex.org/subfields/1803","display_name":"Management Science and Operations Research"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},"topics":[{"id":"https://openalex.org/T11195","display_name":"Simulation Techniques and Applications","score":0.9916999936103821,"subfield":{"id":"https://openalex.org/subfields/1803","display_name":"Management Science and Operations Research"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9872999787330627,"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/T11450","display_name":"Model-Driven Software Engineering Techniques","score":0.98580002784729,"subfield":{"id":"https://openalex.org/subfields/1712","display_name":"Software"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.791991114616394},{"id":"https://openalex.org/keywords/nesting","display_name":"Nesting (process)","score":0.629338264465332},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.5612655282020569},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.5478401780128479},{"id":"https://openalex.org/keywords/modelling-biological-systems","display_name":"Modelling biological systems","score":0.45489731431007385},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.4532507359981537},{"id":"https://openalex.org/keywords/modeling-language","display_name":"Modeling language","score":0.4289487898349762},{"id":"https://openalex.org/keywords/complex-system","display_name":"Complex system","score":0.42839640378952026},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.3613748848438263},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.35592901706695557},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2601025104522705},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.09814521670341492},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.09278792142868042}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.791991114616394},{"id":"https://openalex.org/C2776937656","wikidata":"https://www.wikidata.org/wiki/Q2229669","display_name":"Nesting (process)","level":2,"score":0.629338264465332},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.5612655282020569},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5478401780128479},{"id":"https://openalex.org/C137866125","wikidata":"https://www.wikidata.org/wiki/Q4299308","display_name":"Modelling biological systems","level":3,"score":0.45489731431007385},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.4532507359981537},{"id":"https://openalex.org/C179603123","wikidata":"https://www.wikidata.org/wiki/Q1941921","display_name":"Modeling language","level":3,"score":0.4289487898349762},{"id":"https://openalex.org/C47822265","wikidata":"https://www.wikidata.org/wiki/Q854457","display_name":"Complex system","level":2,"score":0.42839640378952026},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.3613748848438263},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.35592901706695557},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2601025104522705},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.09814521670341492},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.09278792142868042},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","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/C191897082","wikidata":"https://www.wikidata.org/wiki/Q11467","display_name":"Metallurgy","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/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/wsc.2014.7019887","is_oa":false,"landing_page_url":"https://doi.org/10.1109/wsc.2014.7019887","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the Winter Simulation Conference 2014","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/4","display_name":"Quality Education","score":0.699999988079071}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":59,"referenced_works":["https://openalex.org/W14739406","https://openalex.org/W53536421","https://openalex.org/W1489074606","https://openalex.org/W1515942843","https://openalex.org/W1958967754","https://openalex.org/W1969001723","https://openalex.org/W1973016141","https://openalex.org/W1974143589","https://openalex.org/W1995876304","https://openalex.org/W2001598892","https://openalex.org/W2014386075","https://openalex.org/W2018670096","https://openalex.org/W2023332291","https://openalex.org/W2023568310","https://openalex.org/W2045490693","https://openalex.org/W2052896413","https://openalex.org/W2055913285","https://openalex.org/W2057485245","https://openalex.org/W2059719532","https://openalex.org/W2084924279","https://openalex.org/W2087760732","https://openalex.org/W2098769288","https://openalex.org/W2099529102","https://openalex.org/W2102653059","https://openalex.org/W2104473872","https://openalex.org/W2108706121","https://openalex.org/W2114124738","https://openalex.org/W2120043685","https://openalex.org/W2121490181","https://openalex.org/W2124204260","https://openalex.org/W2124924107","https://openalex.org/W2132302738","https://openalex.org/W2133552211","https://openalex.org/W2135430752","https://openalex.org/W2135648313","https://openalex.org/W2146919891","https://openalex.org/W2148895036","https://openalex.org/W2149173084","https://openalex.org/W2149502453","https://openalex.org/W2155028447","https://openalex.org/W2155418451","https://openalex.org/W2163480486","https://openalex.org/W2163493106","https://openalex.org/W2170697535","https://openalex.org/W2175715045","https://openalex.org/W2181917526","https://openalex.org/W3139746985","https://openalex.org/W3140181677","https://openalex.org/W3140663969","https://openalex.org/W3142083247","https://openalex.org/W3147047397","https://openalex.org/W4205814206","https://openalex.org/W4214717370","https://openalex.org/W4246131743","https://openalex.org/W4250357165","https://openalex.org/W4250377352","https://openalex.org/W4386106448","https://openalex.org/W6630538123","https://openalex.org/W6675898697"],"related_works":["https://openalex.org/W4386563820","https://openalex.org/W631732704","https://openalex.org/W2155261113","https://openalex.org/W2064988479","https://openalex.org/W1748979965","https://openalex.org/W3199870583","https://openalex.org/W1991327188","https://openalex.org/W1497779830","https://openalex.org/W4254550161","https://openalex.org/W2090602812"],"abstract_inverted_index":{"Multi-level":[0],"modeling":[1,26,106,118],"is":[2,18,87],"concerned":[3],"with":[4,84,121],"describing":[5],"a":[6,19,54],"system":[7],"at":[8,50],"different":[9],"levels":[10],"of":[11,27,40,44,57,67,104],"organization":[12],"and":[13,46,53,80,95,107,119],"relating":[14],"their":[15],"dynamics.":[16],"ML-Rules":[17,62,85],"rule-based":[20],"language":[21],"developed":[22,100],"for":[23,72,93],"supporting":[24],"the":[25,36,42,64,102,105],"cell":[28],"biological":[29],"systems.":[30],"It":[31],"supports":[32],"nested":[33],"rule":[34],"schemata,":[35],"hierarchical":[37],"dynamic":[38],"nesting":[39],"species,":[41],"assignment":[43],"attributes":[45],"solutions":[47],"to":[48],"species":[49],"each":[51],"level,":[52],"flexible":[55],"definition":[56],"reaction":[58],"rate":[59],"kinetics.":[60],"As":[61],"allows":[63],"compact":[65],"description":[66],"rather":[68],"complex":[69],"models,":[70],"means":[71],"an":[73],"efficient":[74],"execution":[75],"were":[76],"developed,":[77],"e.g.,":[78],"approximate":[79],"adaptive":[81],"algorithms.":[82],"Experimentation":[83],"models":[86],"further":[88],"supported":[89],"by":[90],"domain-specific":[91],"languages":[92],"instrumentation":[94],"experimentation":[96],"which":[97],"have":[98],"been":[99],"in":[101],"context":[103],"simulation":[108,120],"framework":[109],"JAMES":[110],"II.":[111],"A":[112],"signaling":[113],"pathway":[114],"example":[115],"will":[116],"illustrate":[117],"ML-Rules.":[122]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1}],"updated_date":"2026-07-29T14:22:42.915294","created_date":"2025-10-10T00:00:00"}