{"id":"https://openalex.org/W2154382177","doi":"https://doi.org/10.1093/bib/bbp067","title":"Flexible experimentation in the modeling and simulation framework JAMES II--implications for computational systems biology","display_name":"Flexible experimentation in the modeling and simulation framework JAMES II--implications for computational systems biology","publication_year":2010,"publication_date":"2010-01-28","ids":{"openalex":"https://openalex.org/W2154382177","doi":"https://doi.org/10.1093/bib/bbp067","mag":"2154382177","pmid":"https://pubmed.ncbi.nlm.nih.gov/20118105"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbp067","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbp067","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"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/A5016276885","display_name":"Roland Ewald","orcid":null},"institutions":[{"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":["DE"],"is_corresponding":false,"raw_author_name":"R. Ewald","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/I4665924"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026217014","display_name":"Jan Himmelspach","orcid":null},"institutions":[{"id":"https://openalex.org/I4210151178","display_name":"System Simulation (United Kingdom)","ror":"https://ror.org/04gf6zh40","country_code":"GB","type":"company","lineage":["https://openalex.org/I4210151178"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"J. Himmelspach","raw_affiliation_strings":["Jan Himmelspach is a postdoctoral researcher in the Computer Science Department at the University of Rostock. He received his doctorate in Computer Science from the University of Rostock. His research interests lie in software engineering for modeling and simulation, credibility of modeling and simulation, and in efficient modeling and simulation solutions"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Jan Himmelspach is a postdoctoral researcher in the Computer Science Department at the University of Rostock. He received his doctorate in Computer Science from the University of Rostock. His research interests lie in software engineering for modeling and simulation, credibility of modeling and simulation, and in efficient modeling and simulation solutions","institution_ids":["https://openalex.org/I4210151178"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035808972","display_name":"Matthias Jeschke","orcid":null},"institutions":[{"id":"https://openalex.org/I4210151178","display_name":"System Simulation (United Kingdom)","ror":"https://ror.org/04gf6zh40","country_code":"GB","type":"company","lineage":["https://openalex.org/I4210151178"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"M. Jeschke","raw_affiliation_strings":["Matthias Jeschke holds a diploma in Computer Science from the Technical University of Dresden and pursues a PhD at the Modeling and Simulation Group at the University of Rostock. His main research interests lie in stochastic and spatial simulation algorithms and their applications in systems biology"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Matthias Jeschke holds a diploma in Computer Science from the Technical University of Dresden and pursues a PhD at the Modeling and Simulation Group at the University of Rostock. His main research interests lie in stochastic and spatial simulation algorithms and their applications in systems biology","institution_ids":["https://openalex.org/I4210151178"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5109849000","display_name":"Stefan Leye","orcid":null},"institutions":[{"id":"https://openalex.org/I4210147717","display_name":"Advanced Simulation & Design (Germany)","ror":"https://ror.org/0533m8w24","country_code":"DE","type":"company","lineage":["https://openalex.org/I4210147717"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"S. Leye","raw_affiliation_strings":["Stefan Leye holds a diploma in Computer Science from the University of Rostock and pursues a PhD at the Modeling and Simulation Group at the University of Rostock. His research interests lie in experiment design, validation, optimization and simulation algorithms"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Stefan Leye holds a diploma in Computer Science from the University of Rostock and pursues a PhD at the Modeling and Simulation Group at the University of Rostock. His research interests lie in experiment design, validation, optimization and simulation algorithms","institution_ids":["https://openalex.org/I4210147717"]}]},{"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/I4210151178","display_name":"System Simulation (United Kingdom)","ror":"https://ror.org/04gf6zh40","country_code":"GB","type":"company","lineage":["https://openalex.org/I4210151178"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"A. M. Uhrmacher","raw_affiliation_strings":["Adelinde M. Uhrmacher is a Professor in the Department of Computer Science at the University of Rostock and head of the Modeling and Simulation Group. Her research interests lie in modeling and simulation methodologies and their applications"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Adelinde M. Uhrmacher is a Professor in the Department of Computer Science at the University of Rostock and head of the Modeling and Simulation Group. Her research interests lie in modeling and simulation methodologies and their applications","institution_ids":["https://openalex.org/I4210151178"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":3.2219,"has_fulltext":false,"cited_by_count":43,"citation_normalized_percentile":{"value":0.92475914,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"11","issue":"3","first_page":"290","last_page":"300"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9991999864578247,"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":0.9991999864578247,"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/T11195","display_name":"Simulation Techniques and Applications","score":0.9958999752998352,"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/T11986","display_name":"Scientific Computing and Data Management","score":0.9926000237464905,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/reuse","display_name":"Reuse","score":0.7922221422195435},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7175263166427612},{"id":"https://openalex.org/keywords/complement","display_name":"Complement (music)","score":0.703872799873352},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3437594175338745},{"id":"https://openalex.org/keywords/systems-engineering","display_name":"Systems engineering","score":0.34177470207214355},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.15362030267715454},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.08901265263557434},{"id":"https://openalex.org/keywords/ecology","display_name":"Ecology","score":0.08312281966209412}],"concepts":[{"id":"https://openalex.org/C206588197","wikidata":"https://www.wikidata.org/wiki/Q846574","display_name":"Reuse","level":2,"score":0.7922221422195435},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7175263166427612},{"id":"https://openalex.org/C112313634","wikidata":"https://www.wikidata.org/wiki/Q7886648","display_name":"Complement (music)","level":5,"score":0.703872799873352},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3437594175338745},{"id":"https://openalex.org/C201995342","wikidata":"https://www.wikidata.org/wiki/Q682496","display_name":"Systems engineering","level":1,"score":0.34177470207214355},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.15362030267715454},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.08901265263557434},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.08312281966209412},{"id":"https://openalex.org/C188082640","wikidata":"https://www.wikidata.org/wiki/Q1780899","display_name":"Complementation","level":4,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001695","descriptor_name":"Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D001695","descriptor_name":"Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D001695","descriptor_name":"Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012985","descriptor_name":"Software Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012985","descriptor_name":"Software Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012985","descriptor_name":"Software Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018511","descriptor_name":"Systems Integration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018511","descriptor_name":"Systems Integration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018511","descriptor_name":"Systems Integration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbp067","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbp067","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:20118105","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20118105","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":57,"referenced_works":["https://openalex.org/W1495775210","https://openalex.org/W1496706822","https://openalex.org/W1516206624","https://openalex.org/W1527989821","https://openalex.org/W1543889792","https://openalex.org/W1595516773","https://openalex.org/W1606860353","https://openalex.org/W1667887397","https://openalex.org/W1964104034","https://openalex.org/W1964514022","https://openalex.org/W1968226729","https://openalex.org/W1978486653","https://openalex.org/W1984227316","https://openalex.org/W1990752200","https://openalex.org/W1998498767","https://openalex.org/W2002752105","https://openalex.org/W2006901874","https://openalex.org/W2007524983","https://openalex.org/W2043991659","https://openalex.org/W2044859335","https://openalex.org/W2052571303","https://openalex.org/W2063580982","https://openalex.org/W2084421093","https://openalex.org/W2086444832","https://openalex.org/W2095595785","https://openalex.org/W2102606643","https://openalex.org/W2107109814","https://openalex.org/W2107892091","https://openalex.org/W2108010457","https://openalex.org/W2108706121","https://openalex.org/W2113952037","https://openalex.org/W2114804859","https://openalex.org/W2118036437","https://openalex.org/W2120105248","https://openalex.org/W2121525062","https://openalex.org/W2121917352","https://openalex.org/W2123483967","https://openalex.org/W2123524009","https://openalex.org/W2124116278","https://openalex.org/W2125784747","https://openalex.org/W2133551843","https://openalex.org/W2143762317","https://openalex.org/W2147419311","https://openalex.org/W2149502453","https://openalex.org/W2150306925","https://openalex.org/W2150908245","https://openalex.org/W2153180943","https://openalex.org/W2155260680","https://openalex.org/W2158323882","https://openalex.org/W2168321020","https://openalex.org/W2284263109","https://openalex.org/W2341880139","https://openalex.org/W2517931055","https://openalex.org/W2608641272","https://openalex.org/W2622427009","https://openalex.org/W2790581848","https://openalex.org/W3148930403"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2000444236","https://openalex.org/W2390279801","https://openalex.org/W2384475851","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2353602216","https://openalex.org/W2382566571","https://openalex.org/W2382290278"],"abstract_inverted_index":{"Dry-lab":[0],"experimentation":[1,72],"is":[2,14],"being":[3],"increasingly":[4],"used":[5],"to":[6,53],"complement":[7],"wet-lab":[8],"experimentation.":[9],"However,":[10],"conducting":[11],"dry-lab":[12],"experiments":[13],"a":[15,27],"challenging":[16],"endeavor":[17],"that":[18,46],"requires":[19],"the":[20,36,62,65,68,80],"combination":[21],"of":[22,40,59,67],"diverse":[23],"techniques.":[24,42],"JAMES":[25],"II,":[26],"plug-in-based":[28],"open":[29],"source":[30],"modeling":[31],"and":[32,38,56,64,74],"simulation":[33,69],"framework,":[34],"facilitates":[35],"exploitation":[37],"configuration":[39],"these":[41],"The":[43],"different":[44],"aspects":[45],"form":[47],"an":[48],"experiment":[49],"are":[50,77],"made":[51],"explicit":[52],"facilitate":[54],"repeatability":[55],"reuse.":[57],"Each":[58],"those":[60],"influences":[61],"performance":[63],"quality":[66],"experiment.":[70],"Common":[71],"pitfalls":[73],"current":[75],"challenges":[76],"discussed":[78],"along":[79],"way.":[81]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":4},{"year":2014,"cited_by_count":5},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":10}],"updated_date":"2026-06-16T07:32:37.131356","created_date":"2025-10-10T00:00:00"}
