{"id":"https://openalex.org/W1972830673","doi":"https://doi.org/10.1109/biovis.2012.6378597","title":"Visualizing cells and their connectivity graphs for CompuCell3D","display_name":"Visualizing cells and their connectivity graphs for CompuCell3D","publication_year":2012,"publication_date":"2012-10-01","ids":{"openalex":"https://openalex.org/W1972830673","doi":"https://doi.org/10.1109/biovis.2012.6378597","mag":"1972830673"},"language":"en","primary_location":{"id":"doi:10.1109/biovis.2012.6378597","is_oa":false,"landing_page_url":"https://doi.org/10.1109/biovis.2012.6378597","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2012 IEEE Symposium on Biological Data Visualization (BioVis)","raw_type":"proceedings-article"},"type":"article","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/A5058904152","display_name":"Randy Heiland","orcid":"https://orcid.org/0000-0002-7440-2905"},"institutions":[{"id":"https://openalex.org/I901403493","display_name":"NuVasive (United States)","ror":"https://ror.org/036dqy506","country_code":"US","type":"company","lineage":["https://openalex.org/I901403493"]},{"id":"https://openalex.org/I592451","display_name":"Indiana University","ror":"https://ror.org/01kg8sb98","country_code":"US","type":"education","lineage":["https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Randy Heiland","raw_affiliation_strings":["CREST, Pervasive Technology Institute, Indiana University, USA","CREST, Pervasive, Technology Institute, Indiana University"],"affiliations":[{"raw_affiliation_string":"CREST, Pervasive Technology Institute, Indiana University, USA","institution_ids":["https://openalex.org/I901403493","https://openalex.org/I592451"]},{"raw_affiliation_string":"CREST, Pervasive, Technology Institute, Indiana University","institution_ids":["https://openalex.org/I592451"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032411137","display_name":"Abbas Shirinifard","orcid":"https://orcid.org/0000-0002-4517-6080"},"institutions":[{"id":"https://openalex.org/I4210151352","display_name":"Biocom","ror":"https://ror.org/03ymdxs56","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210151352"]},{"id":"https://openalex.org/I592451","display_name":"Indiana University","ror":"https://ror.org/01kg8sb98","country_code":"US","type":"education","lineage":["https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Abbas Shirinifard","raw_affiliation_strings":["Biocomplexity Institute, Indiana University, USA","Biocomplexity Institute Indiana University"],"affiliations":[{"raw_affiliation_string":"Biocomplexity Institute, Indiana University, USA","institution_ids":["https://openalex.org/I4210151352","https://openalex.org/I592451"]},{"raw_affiliation_string":"Biocomplexity Institute Indiana University","institution_ids":["https://openalex.org/I4210151352","https://openalex.org/I592451"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5109469196","display_name":"Maciek Swat","orcid":null},"institutions":[{"id":"https://openalex.org/I4210151352","display_name":"Biocom","ror":"https://ror.org/03ymdxs56","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210151352"]},{"id":"https://openalex.org/I592451","display_name":"Indiana University","ror":"https://ror.org/01kg8sb98","country_code":"US","type":"education","lineage":["https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Maciek Swat","raw_affiliation_strings":["Biocomplexity Institute, Indiana University, USA","Biocomplexity Institute Indiana University"],"affiliations":[{"raw_affiliation_string":"Biocomplexity Institute, Indiana University, USA","institution_ids":["https://openalex.org/I4210151352","https://openalex.org/I592451"]},{"raw_affiliation_string":"Biocomplexity Institute Indiana University","institution_ids":["https://openalex.org/I4210151352","https://openalex.org/I592451"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024115480","display_name":"Gilberto L. Thomas","orcid":"https://orcid.org/0000-0003-0317-6186"},"institutions":[{"id":"https://openalex.org/I592451","display_name":"Indiana University","ror":"https://ror.org/01kg8sb98","country_code":"US","type":"education","lineage":["https://openalex.org/I592451"]},{"id":"https://openalex.org/I4210151352","display_name":"Biocom","ror":"https://ror.org/03ymdxs56","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210151352"]},{"id":"https://openalex.org/I130442723","display_name":"Universidade Federal do Rio Grande do Sul","ror":"https://ror.org/041yk2d64","country_code":"BR","type":"education","lineage":["https://openalex.org/I130442723"]}],"countries":["BR","US"],"is_corresponding":false,"raw_author_name":"Gilberto L. Thomas","raw_affiliation_strings":["Biocomplexity Institute, Indiana University, USA","Instituto de Fisica Universidade Federal do Rio Grande do Sul"],"affiliations":[{"raw_affiliation_string":"Biocomplexity Institute, Indiana University, USA","institution_ids":["https://openalex.org/I4210151352","https://openalex.org/I592451"]},{"raw_affiliation_string":"Instituto de Fisica Universidade Federal do Rio Grande do Sul","institution_ids":["https://openalex.org/I130442723"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066360902","display_name":"James P. Sluka","orcid":"https://orcid.org/0000-0002-5901-1404"},"institutions":[{"id":"https://openalex.org/I592451","display_name":"Indiana University","ror":"https://ror.org/01kg8sb98","country_code":"US","type":"education","lineage":["https://openalex.org/I592451"]},{"id":"https://openalex.org/I4210151352","display_name":"Biocom","ror":"https://ror.org/03ymdxs56","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210151352"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"James Sluka","raw_affiliation_strings":["Biocomplexity Institute, Indiana University, USA","Biocomplexity Institute Indiana University"],"affiliations":[{"raw_affiliation_string":"Biocomplexity Institute, Indiana University, USA","institution_ids":["https://openalex.org/I4210151352","https://openalex.org/I592451"]},{"raw_affiliation_string":"Biocomplexity Institute Indiana University","institution_ids":["https://openalex.org/I4210151352","https://openalex.org/I592451"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074260102","display_name":"Andrew Lumsdaine","orcid":"https://orcid.org/0000-0002-9153-6622"},"institutions":[{"id":"https://openalex.org/I130442723","display_name":"Universidade Federal do Rio Grande do Sul","ror":"https://ror.org/041yk2d64","country_code":"BR","type":"education","lineage":["https://openalex.org/I130442723"]},{"id":"https://openalex.org/I592451","display_name":"Indiana University","ror":"https://ror.org/01kg8sb98","country_code":"US","type":"education","lineage":["https://openalex.org/I592451"]}],"countries":["BR","US"],"is_corresponding":false,"raw_author_name":"Andrew Lumsdaine","raw_affiliation_strings":["Instituto de Fisica, Universidade Federal do Rio Grande do Sul, Brazil","CREST, Pervasive, Technology Institute, Indiana University"],"affiliations":[{"raw_affiliation_string":"Instituto de Fisica, Universidade Federal do Rio Grande do Sul, Brazil","institution_ids":["https://openalex.org/I130442723"]},{"raw_affiliation_string":"CREST, Pervasive, Technology Institute, Indiana University","institution_ids":["https://openalex.org/I592451"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017523715","display_name":"Benjamin Zaitlen","orcid":null},"institutions":[{"id":"https://openalex.org/I592451","display_name":"Indiana University","ror":"https://ror.org/01kg8sb98","country_code":"US","type":"education","lineage":["https://openalex.org/I592451"]},{"id":"https://openalex.org/I901403493","display_name":"NuVasive (United States)","ror":"https://ror.org/036dqy506","country_code":"US","type":"company","lineage":["https://openalex.org/I901403493"]},{"id":"https://openalex.org/I4210151352","display_name":"Biocom","ror":"https://ror.org/03ymdxs56","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210151352"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Benjamin Zaitlen","raw_affiliation_strings":["CREST, Pervasive Technology Institute, Indiana University, USA","Biocomplexity Institute Indiana University"],"affiliations":[{"raw_affiliation_string":"CREST, Pervasive Technology Institute, Indiana University, USA","institution_ids":["https://openalex.org/I901403493","https://openalex.org/I592451"]},{"raw_affiliation_string":"Biocomplexity Institute Indiana University","institution_ids":["https://openalex.org/I4210151352","https://openalex.org/I592451"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5032161283","display_name":"James A. Glazier","orcid":"https://orcid.org/0000-0003-3634-190X"},"institutions":[{"id":"https://openalex.org/I592451","display_name":"Indiana University","ror":"https://ror.org/01kg8sb98","country_code":"US","type":"education","lineage":["https://openalex.org/I592451"]},{"id":"https://openalex.org/I4210151352","display_name":"Biocom","ror":"https://ror.org/03ymdxs56","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210151352"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"James A. Glazier","raw_affiliation_strings":["Department of Physics, Biocomplexity Institute, Indiana University, USA","Department of Physics, Biocomplexity Institute, Indiana University"],"affiliations":[{"raw_affiliation_string":"Department of Physics, Biocomplexity Institute, Indiana University, USA","institution_ids":["https://openalex.org/I4210151352","https://openalex.org/I592451"]},{"raw_affiliation_string":"Department of Physics, Biocomplexity Institute, Indiana University","institution_ids":["https://openalex.org/I4210151352","https://openalex.org/I592451"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5058904152"],"corresponding_institution_ids":["https://openalex.org/I592451","https://openalex.org/I901403493"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.05203087,"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":"85","last_page":"90"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9819999933242798,"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":0.9819999933242798,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9643999934196472,"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.9610000252723694,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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":0.8537502884864807},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.8403885364532471},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.5466982126235962},{"id":"https://openalex.org/keywords/open-source","display_name":"Open source","score":0.5330781936645508},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.4287523329257965},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.4131145477294922},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.3649689555168152},{"id":"https://openalex.org/keywords/human\u2013computer-interaction","display_name":"Human\u2013computer interaction","score":0.3445446491241455},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3403865098953247},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.32532042264938354},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.20945453643798828}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8537502884864807},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.8403885364532471},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.5466982126235962},{"id":"https://openalex.org/C3018397939","wikidata":"https://www.wikidata.org/wiki/Q3644502","display_name":"Open source","level":3,"score":0.5330781936645508},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4287523329257965},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.4131145477294922},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.3649689555168152},{"id":"https://openalex.org/C107457646","wikidata":"https://www.wikidata.org/wiki/Q207434","display_name":"Human\u2013computer interaction","level":1,"score":0.3445446491241455},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3403865098953247},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.32532042264938354},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.20945453643798828},{"id":"https://openalex.org/C187736073","wikidata":"https://www.wikidata.org/wiki/Q2920921","display_name":"Management","level":1,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/biovis.2012.6378597","is_oa":false,"landing_page_url":"https://doi.org/10.1109/biovis.2012.6378597","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2012 IEEE Symposium on Biological Data Visualization (BioVis)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320309409","display_name":"Lilly Endowment","ror":"https://ror.org/00cpsd622"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":14,"referenced_works":["https://openalex.org/W1491829605","https://openalex.org/W1967026214","https://openalex.org/W2002785668","https://openalex.org/W2003933044","https://openalex.org/W2011301426","https://openalex.org/W2018337293","https://openalex.org/W2041643735","https://openalex.org/W2044719035","https://openalex.org/W2100910924","https://openalex.org/W2105135903","https://openalex.org/W2132022337","https://openalex.org/W2216895152","https://openalex.org/W2291283624","https://openalex.org/W3128894147"],"related_works":["https://openalex.org/W2341492732","https://openalex.org/W3187193180","https://openalex.org/W106542691","https://openalex.org/W1699080303","https://openalex.org/W2207495067","https://openalex.org/W1906486629","https://openalex.org/W4401741136","https://openalex.org/W2557718140","https://openalex.org/W4399490472","https://openalex.org/W67092138"],"abstract_inverted_index":{"Developing":[0],"models":[1],"that":[2,29,39],"simulate":[3],"the":[4,49,71],"behavior":[5,51],"of":[6,9,87],"different":[7],"types":[8],"interacting":[10],"biological":[11],"cells":[12],"can":[13],"be":[14],"a":[15,41,45],"very":[16],"time":[17],"consuming":[18],"and":[19,36,52,67],"error":[20],"prone":[21],"task.":[22],"CompuCell3D":[23,69],"is":[24,47,55],"an":[25],"open":[26],"source":[27],"application":[28],"addresses":[30],"this":[31],"challenge.":[32],"It":[33,57],"provides":[34],"interactive":[35],"customizable":[37],"visualizations":[38],"help":[40],"user":[42],"detect":[43],"when":[44,53],"model":[46],"producing":[48],"desired":[50],"it":[54],"failing.":[56],"also":[58],"allows":[59,76],"for":[60,65,77,83],"high":[61],"quality":[62],"image":[63],"generation":[64],"publications":[66],"presentations.":[68],"uses":[70],"Python":[72],"programming":[73],"language":[74],"which":[75],"easy":[78],"extensions.":[79],"Examples":[80],"are":[81],"provided":[82],"performing":[84],"graph":[85],"analyses":[86],"cell":[88],"connectivity.":[89]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2016,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
