{"id":"https://openalex.org/W2167931729","doi":"https://doi.org/10.1093/bioinformatics/btp361","title":"Modeling multi-cellular behavior in epidermal tissue homeostasis via finite state machines in multi-agent systems","display_name":"Modeling multi-cellular behavior in epidermal tissue homeostasis via finite state machines in multi-agent systems","publication_year":2009,"publication_date":"2009-06-17","ids":{"openalex":"https://openalex.org/W2167931729","doi":"https://doi.org/10.1093/bioinformatics/btp361","mag":"2167931729","pmid":"https://pubmed.ncbi.nlm.nih.gov/19535533"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btp361","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp361","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/16/2057/48993254/bioinformatics_25_16_2057.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/25/16/2057/48993254/bioinformatics_25_16_2057.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5017276043","display_name":"Thomas S\u00fctterlin","orcid":"https://orcid.org/0000-0003-0126-4692"},"institutions":[{"id":"https://openalex.org/I223822909","display_name":"Heidelberg University","ror":"https://ror.org/038t36y30","country_code":"DE","type":"education","lineage":["https://openalex.org/I223822909"]},{"id":"https://openalex.org/I2802164966","display_name":"University Hospital Heidelberg","ror":"https://ror.org/013czdx64","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I2802164966"]},{"id":"https://openalex.org/I41121874","display_name":"Heilbronn University","ror":"https://ror.org/04g5gcg95","country_code":"DE","type":"education","lineage":["https://openalex.org/I41121874"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Thomas S\u00fctterlin","raw_affiliation_strings":["1 Medical Informatics Department, Institute of Medical Biometry and Informatics, University Hospital Heidelberg, Im Neuenheimer Feld 305 and Hamamatsu Tissue Imaging and Analysis Center (TIGA), BIOQUANT, University Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg and 2 Department of Informatics, Heilbronn University, Max-Planck-Str. 39, 74081 Heilbronn, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Medical Informatics Department, Institute of Medical Biometry and Informatics, University Hospital Heidelberg, Im Neuenheimer Feld 305 and Hamamatsu Tissue Imaging and Analysis Center (TIGA), BIOQUANT, University Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg and 2 Department of Informatics, Heilbronn University, Max-Planck-Str. 39, 74081 Heilbronn, Germany","institution_ids":["https://openalex.org/I223822909","https://openalex.org/I2802164966","https://openalex.org/I41121874"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007574791","display_name":"Simone Huber","orcid":null},"institutions":[{"id":"https://openalex.org/I223822909","display_name":"Heidelberg University","ror":"https://ror.org/038t36y30","country_code":"DE","type":"education","lineage":["https://openalex.org/I223822909"]},{"id":"https://openalex.org/I2802164966","display_name":"University Hospital Heidelberg","ror":"https://ror.org/013czdx64","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I2802164966"]},{"id":"https://openalex.org/I41121874","display_name":"Heilbronn University","ror":"https://ror.org/04g5gcg95","country_code":"DE","type":"education","lineage":["https://openalex.org/I41121874"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Simone Huber","raw_affiliation_strings":["1 Medical Informatics Department, Institute of Medical Biometry and Informatics, University Hospital Heidelberg, Im Neuenheimer Feld 305 and Hamamatsu Tissue Imaging and Analysis Center (TIGA), BIOQUANT, University Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg and 2 Department of Informatics, Heilbronn University, Max-Planck-Str. 39, 74081 Heilbronn, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Medical Informatics Department, Institute of Medical Biometry and Informatics, University Hospital Heidelberg, Im Neuenheimer Feld 305 and Hamamatsu Tissue Imaging and Analysis Center (TIGA), BIOQUANT, University Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg and 2 Department of Informatics, Heilbronn University, Max-Planck-Str. 39, 74081 Heilbronn, Germany","institution_ids":["https://openalex.org/I223822909","https://openalex.org/I2802164966","https://openalex.org/I41121874"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091133949","display_name":"Hartmut Dickhaus","orcid":null},"institutions":[{"id":"https://openalex.org/I223822909","display_name":"Heidelberg University","ror":"https://ror.org/038t36y30","country_code":"DE","type":"education","lineage":["https://openalex.org/I223822909"]},{"id":"https://openalex.org/I2802164966","display_name":"University Hospital Heidelberg","ror":"https://ror.org/013czdx64","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I2802164966"]},{"id":"https://openalex.org/I41121874","display_name":"Heilbronn University","ror":"https://ror.org/04g5gcg95","country_code":"DE","type":"education","lineage":["https://openalex.org/I41121874"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Hartmut Dickhaus","raw_affiliation_strings":["1 Medical Informatics Department, Institute of Medical Biometry and Informatics, University Hospital Heidelberg, Im Neuenheimer Feld 305 and Hamamatsu Tissue Imaging and Analysis Center (TIGA), BIOQUANT, University Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg and 2 Department of Informatics, Heilbronn University, Max-Planck-Str. 39, 74081 Heilbronn, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Medical Informatics Department, Institute of Medical Biometry and Informatics, University Hospital Heidelberg, Im Neuenheimer Feld 305 and Hamamatsu Tissue Imaging and Analysis Center (TIGA), BIOQUANT, University Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg and 2 Department of Informatics, Heilbronn University, Max-Planck-Str. 39, 74081 Heilbronn, Germany","institution_ids":["https://openalex.org/I223822909","https://openalex.org/I2802164966","https://openalex.org/I41121874"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5039930487","display_name":"Niels Grabe","orcid":"https://orcid.org/0000-0003-1732-3706"},"institutions":[{"id":"https://openalex.org/I223822909","display_name":"Heidelberg University","ror":"https://ror.org/038t36y30","country_code":"DE","type":"education","lineage":["https://openalex.org/I223822909"]},{"id":"https://openalex.org/I2802164966","display_name":"University Hospital Heidelberg","ror":"https://ror.org/013czdx64","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I2802164966"]},{"id":"https://openalex.org/I41121874","display_name":"Heilbronn University","ror":"https://ror.org/04g5gcg95","country_code":"DE","type":"education","lineage":["https://openalex.org/I41121874"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Niels Grabe","raw_affiliation_strings":["1 Medical Informatics Department, Institute of Medical Biometry and Informatics, University Hospital Heidelberg, Im Neuenheimer Feld 305 and Hamamatsu Tissue Imaging and Analysis Center (TIGA), BIOQUANT, University Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg and 2 Department of Informatics, Heilbronn University, Max-Planck-Str. 39, 74081 Heilbronn, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Medical Informatics Department, Institute of Medical Biometry and Informatics, University Hospital Heidelberg, Im Neuenheimer Feld 305 and Hamamatsu Tissue Imaging and Analysis Center (TIGA), BIOQUANT, University Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg and 2 Department of Informatics, Heilbronn University, Max-Planck-Str. 39, 74081 Heilbronn, Germany","institution_ids":["https://openalex.org/I223822909","https://openalex.org/I2802164966","https://openalex.org/I41121874"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5039930487"],"corresponding_institution_ids":["https://openalex.org/I223822909","https://openalex.org/I2802164966","https://openalex.org/I41121874"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.843,"has_fulltext":false,"cited_by_count":31,"citation_normalized_percentile":{"value":0.84308588,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"25","issue":"16","first_page":"2057","last_page":"2063"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11829","display_name":"Mathematical Biology Tumor Growth","score":0.8950999975204468,"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"}},"topics":[{"id":"https://openalex.org/T11829","display_name":"Mathematical Biology Tumor Growth","score":0.8950999975204468,"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"}},{"id":"https://openalex.org/T11190","display_name":"3D Printing in Biomedical Research","score":0.02280000038444996,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10379","display_name":"Cellular Mechanics and Interactions","score":0.016200000420212746,"subfield":{"id":"https://openalex.org/subfields/1307","display_name":"Cell 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/executable","display_name":"Executable","score":0.9285662770271301},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7664807438850403},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.627077579498291},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5447410941123962},{"id":"https://openalex.org/keywords/graphical-user-interface","display_name":"Graphical user interface","score":0.4356743097305298},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.41109010577201843},{"id":"https://openalex.org/keywords/distributed-computing","display_name":"Distributed computing","score":0.3668333888053894},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.3369964063167572},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.3216401934623718},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.09859216213226318}],"concepts":[{"id":"https://openalex.org/C160145156","wikidata":"https://www.wikidata.org/wiki/Q778586","display_name":"Executable","level":2,"score":0.9285662770271301},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7664807438850403},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.627077579498291},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5447410941123962},{"id":"https://openalex.org/C37789001","wikidata":"https://www.wikidata.org/wiki/Q782543","display_name":"Graphical user interface","level":2,"score":0.4356743097305298},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.41109010577201843},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.3668333888053894},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.3369964063167572},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.3216401934623718},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.09859216213226318},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D004817","descriptor_name":"Epidermis","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004817","descriptor_name":"Epidermis","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004817","descriptor_name":"Epidermis","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D006706","descriptor_name":"Homeostasis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006706","descriptor_name":"Homeostasis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006706","descriptor_name":"Homeostasis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btp361","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp361","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/16/2057/48993254/bioinformatics_25_16_2057.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:19535533","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19535533","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":"Bioinformatics (Oxford, England)","raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btp361","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp361","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/16/2057/48993254/bioinformatics_25_16_2057.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Quality Education","score":0.5699999928474426,"id":"https://metadata.un.org/sdg/4"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2167931729.pdf"},"referenced_works_count":30,"referenced_works":["https://openalex.org/W120010193","https://openalex.org/W182590847","https://openalex.org/W1537891716","https://openalex.org/W1559012732","https://openalex.org/W1586778826","https://openalex.org/W1809480526","https://openalex.org/W1986452936","https://openalex.org/W1995341919","https://openalex.org/W1996195324","https://openalex.org/W1996449803","https://openalex.org/W2012140001","https://openalex.org/W2012935013","https://openalex.org/W2025795296","https://openalex.org/W2045478141","https://openalex.org/W2058324879","https://openalex.org/W2086356330","https://openalex.org/W2096337402","https://openalex.org/W2107062718","https://openalex.org/W2109444989","https://openalex.org/W2113239343","https://openalex.org/W2114888488","https://openalex.org/W2126160338","https://openalex.org/W2131279082","https://openalex.org/W2144244247","https://openalex.org/W2149193200","https://openalex.org/W2153355648","https://openalex.org/W2334454439","https://openalex.org/W4242005639","https://openalex.org/W6676744855","https://openalex.org/W6678934100"],"related_works":["https://openalex.org/W82161441","https://openalex.org/W2169637744","https://openalex.org/W1576042299","https://openalex.org/W1990602094","https://openalex.org/W2181943964","https://openalex.org/W1528423264","https://openalex.org/W2598672065","https://openalex.org/W3120610872","https://openalex.org/W2169715360","https://openalex.org/W1638297612"],"abstract_inverted_index":{"MOTIVATION:":[0],"For":[1],"the":[2,24,56,88,92,100,106,109],"efficient":[3,73],"application":[4],"of":[5,13,27,50,62,91,108,116,124],"multi-agent":[6,47],"systems":[7],"to":[8,79],"spatial":[9],"and":[10,16,58,76,94,138],"functional":[11,95],"modeling":[12,18,44],"tissues":[14],"flexible":[15],"intuitive":[17,57],"tools":[19],"are":[20,67],"needed,":[21],"which":[22],"allow":[23],"graphical":[25,43,82],"specification":[26,61],"cellular":[28,63],"behavior":[29],"in":[30,133],"a":[31,42,112,122],"tissue":[32,51,96],"context":[33],"without":[34],"presuming":[35],"specialized":[36],"programming":[37],"skills.":[38],"RESULTS:":[39],"We":[40,104],"developed":[41],"system":[45,86],"for":[46,136],"based":[48],"simulation":[49,83],"homeostasis.":[52],"An":[53],"editor":[54],"allows":[55,87],"hierarchically":[59],"structured":[60],"behavior.":[64],"The":[65,85,128],"models":[66],"then":[68],"automatically":[69],"compiled":[70],"into":[71],"highly":[72],"source":[74],"code":[75],"dynamically":[77],"linked":[78],"an":[80],"interactive":[81],"environment.":[84],"quantitative":[89],"analysis":[90],"morphological":[93],"properties":[97],"emerging":[98],"from":[99],"cell":[101],"behavioral":[102],"model.":[103],"demonstrate":[105],"relevance":[107],"approach":[110],"using":[111],"recently":[113],"published":[114],"model":[115],"epidermal":[117],"homeostasis":[118],"as":[119,121],"well":[120],"series":[123],"cell-cycle":[125],"models.":[126],"AVAILABILITY:":[127],"complete":[129],"software":[130],"is":[131],"available":[132],"binary":[134],"executables":[135],"MS-Windows":[137],"Linux":[139],"at":[140],"tiga.uni-hd.de.":[141]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":4},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":5},{"year":2012,"cited_by_count":5}],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2025-10-10T00:00:00"}
