{"id":"https://openalex.org/W4390099002","doi":"https://doi.org/10.1093/bioinformatics/btad773","title":"CellularPotts.jl: simulating multiscale cellular models in Julia","display_name":"CellularPotts.jl: simulating multiscale cellular models in Julia","publication_year":2023,"publication_date":"2023-12-22","ids":{"openalex":"https://openalex.org/W4390099002","doi":"https://doi.org/10.1093/bioinformatics/btad773","pmid":"https://pubmed.ncbi.nlm.nih.gov/38134421"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btad773","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad773","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad773/54762916/btad773.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad773/54762916/btad773.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5077176967","display_name":"Robert W. Gregg","orcid":"https://orcid.org/0000-0002-2930-621X"},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]},{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Robert W Gregg","raw_affiliation_strings":["Department of Biomedical Informatics, University of Pittsburgh , Pittsburgh, PA 15206, United States","Department of Computational and Systems Biology, University of Pittsburgh , Pittsburgh, PA 15213, United States","Department of Epidemiology, University of Florida , Gainesville, FL 32603, United States","University of Pittsburgh Department of Biomedical Informatics, , Pittsburgh, PA USA","University of Pittsburgh Department of Computational and Systems Biology, , Pittsburgh, PA USA","University of Florida Department of Epidemiology, , Gainesville, FL USA"],"raw_orcid":"https://orcid.org/0000-0002-2930-621X","affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, University of Pittsburgh , Pittsburgh, PA 15206, United States","institution_ids":["https://openalex.org/I170201317"]},{"raw_affiliation_string":"Department of Computational and Systems Biology, University of Pittsburgh , Pittsburgh, PA 15213, United States","institution_ids":["https://openalex.org/I170201317"]},{"raw_affiliation_string":"Department of Epidemiology, University of Florida , Gainesville, FL 32603, United States","institution_ids":["https://openalex.org/I33213144"]},{"raw_affiliation_string":"University of Pittsburgh Department of Biomedical Informatics, , Pittsburgh, PA USA","institution_ids":["https://openalex.org/I170201317"]},{"raw_affiliation_string":"University of Pittsburgh Department of Computational and Systems Biology, , Pittsburgh, PA USA","institution_ids":["https://openalex.org/I170201317"]},{"raw_affiliation_string":"University of Florida Department of Epidemiology, , Gainesville, FL USA","institution_ids":["https://openalex.org/I33213144"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5042618575","display_name":"Panayiotis V. Benos","orcid":"https://orcid.org/0000-0003-3172-3132"},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]},{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Panayiotis V Benos","raw_affiliation_strings":["Department of Biomedical Informatics, University of Pittsburgh , Pittsburgh, PA 15206, United States","Department of Computational and Systems Biology, University of Pittsburgh , Pittsburgh, PA 15213, United States","Department of Epidemiology, University of Florida , Gainesville, FL 32603, United States","University of Florida Department of Epidemiology, , Gainesville, FL USA","University of Pittsburgh Department of Computational and Systems Biology, , Pittsburgh, PA USA","University of Pittsburgh Department of Biomedical Informatics, , Pittsburgh, PA USA"],"raw_orcid":"https://orcid.org/0000-0003-3172-3132","affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, University of Pittsburgh , Pittsburgh, PA 15206, United States","institution_ids":["https://openalex.org/I170201317"]},{"raw_affiliation_string":"Department of Computational and Systems Biology, University of Pittsburgh , Pittsburgh, PA 15213, United States","institution_ids":["https://openalex.org/I170201317"]},{"raw_affiliation_string":"Department of Epidemiology, University of Florida , Gainesville, FL 32603, United States","institution_ids":["https://openalex.org/I33213144"]},{"raw_affiliation_string":"University of Florida Department of Epidemiology, , Gainesville, FL USA","institution_ids":["https://openalex.org/I33213144"]},{"raw_affiliation_string":"University of Pittsburgh Department of Computational and Systems Biology, , Pittsburgh, PA USA","institution_ids":["https://openalex.org/I170201317"]},{"raw_affiliation_string":"University of Pittsburgh Department of Biomedical Informatics, , Pittsburgh, PA USA","institution_ids":["https://openalex.org/I170201317"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5077176967"],"corresponding_institution_ids":["https://openalex.org/I170201317","https://openalex.org/I33213144"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.2003,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.50420492,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":95},"biblio":{"volume":"40","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11829","display_name":"Mathematical Biology Tumor Growth","score":0.630299985408783,"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":0.630299985408783,"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/T10379","display_name":"Cellular Mechanics and Interactions","score":0.17409999668598175,"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"}},{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.043800000101327896,"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":0.7401125431060791},{"id":"https://openalex.org/keywords/mit-license","display_name":"MIT License","score":0.5850780010223389},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5665525794029236},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.5067847371101379},{"id":"https://openalex.org/keywords/table","display_name":"Table (database)","score":0.4757363796234131},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.4682748317718506},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.4362941086292267},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.340706467628479},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.27318739891052246},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.23986560106277466}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7401125431060791},{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.5850780010223389},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5665525794029236},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.5067847371101379},{"id":"https://openalex.org/C45235069","wikidata":"https://www.wikidata.org/wiki/Q278425","display_name":"Table (database)","level":2,"score":0.4757363796234131},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.4682748317718506},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.4362941086292267},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.340706467628479},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.27318739891052246},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.23986560106277466},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D002468","descriptor_name":"Cell Physiological Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002468","descriptor_name":"Cell Physiological Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002468","descriptor_name":"Cell Physiological Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002468","descriptor_name":"Cell Physiological Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002468","descriptor_name":"Cell Physiological Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002468","descriptor_name":"Cell Physiological Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002468","descriptor_name":"Cell Physiological Phenomena","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":"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":"D008954","descriptor_name":"Models, Biological","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":"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":"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}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btad773","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad773","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad773/54762916/btad773.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38134421","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38134421","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},{"id":"pmh:oai:pubmedcentral.nih.gov:10781660","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10781660","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10781660/pdf/btad773.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btad773","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad773","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad773/54762916/btad773.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1449305495","display_name":null,"funder_award_id":"T15 LM007059","funder_id":"https://openalex.org/F4320337372","funder_display_name":"U.S. National Library of Medicine"},{"id":"https://openalex.org/G1490118717","display_name":null,"funder_award_id":"R01 HL159805","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"},{"id":"https://openalex.org/G6376775872","display_name":null,"funder_award_id":"T15LM007059","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7735959302","display_name":null,"funder_award_id":"R01HL159805","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8027025126","display_name":null,"funder_award_id":"R01HL127349","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G806062132","display_name":null,"funder_award_id":"R01 HL127349","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337338","display_name":"National Heart, Lung, and Blood Institute","ror":"https://ror.org/012pb6c26"},{"id":"https://openalex.org/F4320337372","display_name":"U.S. National Library of Medicine","ror":"https://ror.org/0060t0j89"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4390099002.pdf"},"referenced_works_count":13,"referenced_works":["https://openalex.org/W115452890","https://openalex.org/W2002055996","https://openalex.org/W2002785668","https://openalex.org/W2041619208","https://openalex.org/W2058162908","https://openalex.org/W2070232376","https://openalex.org/W2089362240","https://openalex.org/W2100345558","https://openalex.org/W2511630048","https://openalex.org/W2619381903","https://openalex.org/W2995369486","https://openalex.org/W3146965333","https://openalex.org/W3160630995"],"related_works":["https://openalex.org/W4309247532","https://openalex.org/W3081644756","https://openalex.org/W3096946169","https://openalex.org/W2113128227","https://openalex.org/W2144610372","https://openalex.org/W4312114021","https://openalex.org/W4311938462","https://openalex.org/W2121840477","https://openalex.org/W2515936044","https://openalex.org/W3123068371"],"abstract_inverted_index":{"SUMMARY:":[0],"CellularPotts.jl":[1,170],"is":[2,27,172,179],"a":[3,107,112,124,149],"software":[4],"package":[5,97,171],"written":[6],"in":[7,120,164],"Julia":[8],"to":[9,37,56,66,102,117,140,145],"simulate":[10,57],"biological":[11,34],"cellular":[12,58,153],"processes":[13,26],"such":[14],"as":[15],"division,":[16],"adhesion,":[17],"and":[18,22,46,60,123,155,178],"signaling.":[19],"Accurately":[20],"modeling":[21],"predicting":[23],"these":[24],"simple":[25],"crucial":[28],"because":[29,79],"they":[30,80],"facilitate":[31],"more":[32],"complex":[33],"phenomena":[35],"related":[36],"important":[38],"disease":[39],"states":[40],"like":[41],"tumor":[42],"growth,":[43],"wound":[44],"healing,":[45],"infection.":[47],"Here":[48],"we":[49],"take":[50],"advantage":[51],"of":[52,95,126,159,186,192],"Cellular":[53],"Potts":[54],"Modeling":[55],"interactions":[59],"combine":[61],"them":[62],"with":[63],"differential":[64],"equations":[65],"model":[67,105,127],"dynamic":[68],"cell":[69,86,131],"signaling":[70],"patterns.":[71],"These":[72],"models":[73],"are":[74],"advantageous":[75],"over":[76,138],"other":[77],"approaches":[78],"retain":[81],"spatial":[82],"information":[83],"about":[84],"each":[85],"while":[87],"remaining":[88],"computationally":[89],"efficient":[90],"at":[91,181,190,198],"larger":[92],"scales.":[93],"Users":[94],"this":[96],"define":[98],"three":[99],"key":[100],"inputs":[101],"create":[103],"valid":[104],"definitions:":[106],"2-":[108],"or":[109],"3-dimensional":[110],"space,":[111,122],"table":[113],"describing":[114],"the":[115,160,175,187],"cells":[116],"be":[118,136,196],"positioned":[119],"that":[121,129],"list":[125],"penalties":[128],"dictate":[130],"behaviors.":[132],"Models":[133],"can":[134,194],"then":[135],"evolved":[137],"time":[139,191],"collect":[141],"statistics,":[142],"simulated":[143],"repeatedly":[144],"investigate":[146],"how":[147],"changing":[148],"specific":[150],"property":[151],"impacts":[152],"behavior,":[154],"visualized":[156],"using":[157],"any":[158],"available":[161,180],"plotting":[162],"libraries":[163],"Julia.":[165],"AVAILABILITY":[166],"AND":[167],"IMPLEMENTATION:":[168],"The":[169],"released":[173],"under":[174],"MIT":[176],"license":[177],"https://github.com/RobertGregg/CellularPotts.jl.":[182],"An":[183],"archived":[184],"version":[185],"code":[188],"(v0.3.2)":[189],"submission":[193],"also":[195],"found":[197],"https://doi.org/10.5281/zenodo.10407783.":[199]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-07-13T07:31:44.756512","created_date":"2025-10-10T00:00:00"}
