{"id":"https://openalex.org/W4400104825","doi":"https://doi.org/10.1093/bib/bbae509","title":"Building multiscale models with PhysiBoSS, an agent-based modeling tool","display_name":"Building multiscale models with PhysiBoSS, an agent-based modeling tool","publication_year":2024,"publication_date":"2024-09-23","ids":{"openalex":"https://openalex.org/W4400104825","doi":"https://doi.org/10.1093/bib/bbae509","pmid":"https://pubmed.ncbi.nlm.nih.gov/38979487"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbae509","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae509","pdf_url":"https://academic.oup.com/bib/article-pdf/25/6/bbae509/59872401/bbae509.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["arxiv","crossref","datacite","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bib/article-pdf/25/6/bbae509/59872401/bbae509.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5068648735","display_name":"Marco Ruscone","orcid":"https://orcid.org/0000-0002-7607-0203"},"institutions":[{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I2746051580","display_name":"Universit\u00e9 Paris Sciences et Lettres","ror":"https://ror.org/013cjyk83","country_code":"FR","type":"education","lineage":["https://openalex.org/I2746051580"]},{"id":"https://openalex.org/I70768539","display_name":"\u00c9cole Nationale Sup\u00e9rieure des Mines de Paris","ror":"https://ror.org/04y8cs423","country_code":"FR","type":"education","lineage":["https://openalex.org/I190752583","https://openalex.org/I2746051580","https://openalex.org/I70768539"]},{"id":"https://openalex.org/I80043","display_name":"Institut Curie","ror":"https://ror.org/04t0gwh46","country_code":"FR","type":"nonprofit","lineage":["https://openalex.org/I80043"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Marco Ruscone","raw_affiliation_strings":["INSERM , U900, 26 rue d\u2019Ulm, 75005, Paris ,","Institut Curie, Universit\u00e9 PSL , 26 rue d\u2019Ulm, 75005, Paris ,","Mines ParisTech, Universit\u00e9 PSL , 60, boulevard Saint-Michel 75006 Paris ,"],"affiliations":[{"raw_affiliation_string":"INSERM , U900, 26 rue d\u2019Ulm, 75005, Paris ,","institution_ids":["https://openalex.org/I154526488"]},{"raw_affiliation_string":"Institut Curie, Universit\u00e9 PSL , 26 rue d\u2019Ulm, 75005, Paris ,","institution_ids":["https://openalex.org/I80043","https://openalex.org/I2746051580"]},{"raw_affiliation_string":"Mines ParisTech, Universit\u00e9 PSL , 60, boulevard Saint-Michel 75006 Paris ,","institution_ids":["https://openalex.org/I70768539","https://openalex.org/I2746051580"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080251805","display_name":"Andrea Checcoli","orcid":"https://orcid.org/0000-0002-8290-6310"},"institutions":[{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I39804081","display_name":"Sorbonne Universit\u00e9","ror":"https://ror.org/02en5vm52","country_code":"FR","type":"education","lineage":["https://openalex.org/I39804081"]},{"id":"https://openalex.org/I4210092322","display_name":"Centre de Recherche des Cordeliers","ror":"https://ror.org/00dmms154","country_code":"FR","type":"facility","lineage":["https://openalex.org/I154526488","https://openalex.org/I204730241","https://openalex.org/I39804081","https://openalex.org/I4210092322"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Andrea Checcoli","raw_affiliation_strings":["Centre de Recherche des Cordeliers , Sorbonne Universit\u00e9 15 rue de l'\u00c9cole de M\u00e9decine, 75006 Paris ,","INSERM , U1138, 15 rue de l'\u00c9cole de M\u00e9decine, 75006 Paris ,"],"affiliations":[{"raw_affiliation_string":"Centre de Recherche des Cordeliers , Sorbonne Universit\u00e9 15 rue de l'\u00c9cole de M\u00e9decine, 75006 Paris ,","institution_ids":["https://openalex.org/I39804081","https://openalex.org/I4210092322"]},{"raw_affiliation_string":"INSERM , U1138, 15 rue de l'\u00c9cole de M\u00e9decine, 75006 Paris ,","institution_ids":["https://openalex.org/I154526488","https://openalex.org/I4210092322"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058904152","display_name":"Randy Heiland","orcid":"https://orcid.org/0000-0002-7440-2905"},"institutions":[{"id":"https://openalex.org/I4210119109","display_name":"Indiana University Bloomington","ror":"https://ror.org/02k40bc56","country_code":"US","type":"education","lineage":["https://openalex.org/I4210119109","https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Randy Heiland","raw_affiliation_strings":["Department of Intelligent Systems Engineering, Indiana University , 700 N Woodlawn Ave, Bloomington, IN 47408 ,"],"affiliations":[{"raw_affiliation_string":"Department of Intelligent Systems Engineering, Indiana University , 700 N Woodlawn Ave, Bloomington, IN 47408 ,","institution_ids":["https://openalex.org/I4210119109"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062067186","display_name":"Emmanuel Barillot","orcid":"https://orcid.org/0000-0003-2724-2002"},"institutions":[{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I2746051580","display_name":"Universit\u00e9 Paris Sciences et Lettres","ror":"https://ror.org/013cjyk83","country_code":"FR","type":"education","lineage":["https://openalex.org/I2746051580"]},{"id":"https://openalex.org/I70768539","display_name":"\u00c9cole Nationale Sup\u00e9rieure des Mines de Paris","ror":"https://ror.org/04y8cs423","country_code":"FR","type":"education","lineage":["https://openalex.org/I190752583","https://openalex.org/I2746051580","https://openalex.org/I70768539"]},{"id":"https://openalex.org/I80043","display_name":"Institut Curie","ror":"https://ror.org/04t0gwh46","country_code":"FR","type":"nonprofit","lineage":["https://openalex.org/I80043"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Emmanuel Barillot","raw_affiliation_strings":["INSERM , U900, 26 rue d\u2019Ulm, 75005, Paris ,","Institut Curie, Universit\u00e9 PSL , 26 rue d\u2019Ulm, 75005, Paris ,","Mines ParisTech, Universit\u00e9 PSL , 60, boulevard Saint-Michel 75006 Paris ,"],"affiliations":[{"raw_affiliation_string":"INSERM , U900, 26 rue d\u2019Ulm, 75005, Paris ,","institution_ids":["https://openalex.org/I154526488"]},{"raw_affiliation_string":"Institut Curie, Universit\u00e9 PSL , 26 rue d\u2019Ulm, 75005, Paris ,","institution_ids":["https://openalex.org/I80043","https://openalex.org/I2746051580"]},{"raw_affiliation_string":"Mines ParisTech, Universit\u00e9 PSL , 60, boulevard Saint-Michel 75006 Paris ,","institution_ids":["https://openalex.org/I70768539","https://openalex.org/I2746051580"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052380564","display_name":"Paul Macklin","orcid":"https://orcid.org/0000-0002-9925-0151"},"institutions":[{"id":"https://openalex.org/I4210119109","display_name":"Indiana University Bloomington","ror":"https://ror.org/02k40bc56","country_code":"US","type":"education","lineage":["https://openalex.org/I4210119109","https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Paul Macklin","raw_affiliation_strings":["Department of Intelligent Systems Engineering, Indiana University , 700 N Woodlawn Ave, Bloomington, IN 47408 ,"],"affiliations":[{"raw_affiliation_string":"Department of Intelligent Systems Engineering, Indiana University , 700 N Woodlawn Ave, Bloomington, IN 47408 ,","institution_ids":["https://openalex.org/I4210119109"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061154457","display_name":"Laurence Calzone","orcid":"https://orcid.org/0000-0002-7835-1148"},"institutions":[{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I2746051580","display_name":"Universit\u00e9 Paris Sciences et Lettres","ror":"https://ror.org/013cjyk83","country_code":"FR","type":"education","lineage":["https://openalex.org/I2746051580"]},{"id":"https://openalex.org/I70768539","display_name":"\u00c9cole Nationale Sup\u00e9rieure des Mines de Paris","ror":"https://ror.org/04y8cs423","country_code":"FR","type":"education","lineage":["https://openalex.org/I190752583","https://openalex.org/I2746051580","https://openalex.org/I70768539"]},{"id":"https://openalex.org/I80043","display_name":"Institut Curie","ror":"https://ror.org/04t0gwh46","country_code":"FR","type":"nonprofit","lineage":["https://openalex.org/I80043"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Laurence Calzone","raw_affiliation_strings":["INSERM , U900, 26 rue d\u2019Ulm, 75005, Paris ,","Institut Curie, Universit\u00e9 PSL , 26 rue d\u2019Ulm, 75005, Paris ,","Mines ParisTech, Universit\u00e9 PSL , 60, boulevard Saint-Michel 75006 Paris ,"],"affiliations":[{"raw_affiliation_string":"INSERM , U900, 26 rue d\u2019Ulm, 75005, Paris ,","institution_ids":["https://openalex.org/I154526488"]},{"raw_affiliation_string":"Institut Curie, Universit\u00e9 PSL , 26 rue d\u2019Ulm, 75005, Paris ,","institution_ids":["https://openalex.org/I80043","https://openalex.org/I2746051580"]},{"raw_affiliation_string":"Mines ParisTech, Universit\u00e9 PSL , 60, boulevard Saint-Michel 75006 Paris ,","institution_ids":["https://openalex.org/I70768539","https://openalex.org/I2746051580"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5085105326","display_name":"Vincent No\u00ebl","orcid":"https://orcid.org/0000-0002-5387-8664"},"institutions":[{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I2746051580","display_name":"Universit\u00e9 Paris Sciences et Lettres","ror":"https://ror.org/013cjyk83","country_code":"FR","type":"education","lineage":["https://openalex.org/I2746051580"]},{"id":"https://openalex.org/I70768539","display_name":"\u00c9cole Nationale Sup\u00e9rieure des Mines de Paris","ror":"https://ror.org/04y8cs423","country_code":"FR","type":"education","lineage":["https://openalex.org/I190752583","https://openalex.org/I2746051580","https://openalex.org/I70768539"]},{"id":"https://openalex.org/I80043","display_name":"Institut Curie","ror":"https://ror.org/04t0gwh46","country_code":"FR","type":"nonprofit","lineage":["https://openalex.org/I80043"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Vincent No\u00ebl","raw_affiliation_strings":["INSERM , U900, 26 rue d\u2019Ulm, 75005, Paris ,","Institut Curie, Universit\u00e9 PSL , 26 rue d\u2019Ulm, 75005, Paris ,","Mines ParisTech, Universit\u00e9 PSL , 60, boulevard Saint-Michel 75006 Paris ,"],"affiliations":[{"raw_affiliation_string":"INSERM , U900, 26 rue d\u2019Ulm, 75005, Paris ,","institution_ids":["https://openalex.org/I154526488"]},{"raw_affiliation_string":"Institut Curie, Universit\u00e9 PSL , 26 rue d\u2019Ulm, 75005, Paris ,","institution_ids":["https://openalex.org/I80043","https://openalex.org/I2746051580"]},{"raw_affiliation_string":"Mines ParisTech, Universit\u00e9 PSL , 60, boulevard Saint-Michel 75006 Paris ,","institution_ids":["https://openalex.org/I70768539","https://openalex.org/I2746051580"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5068648735"],"corresponding_institution_ids":["https://openalex.org/I154526488","https://openalex.org/I2746051580","https://openalex.org/I70768539","https://openalex.org/I80043"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":2.7109,"has_fulltext":true,"cited_by_count":7,"citation_normalized_percentile":{"value":0.8975972,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"25","issue":"6","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":0.9939000010490417,"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":0.9939000010490417,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.982200026512146,"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":0.7815964221954346},{"id":"https://openalex.org/keywords/rotation-formalisms-in-three-dimensions","display_name":"Rotation formalisms in three dimensions","score":0.7587470412254333},{"id":"https://openalex.org/keywords/graphical-user-interface","display_name":"Graphical user interface","score":0.5536900758743286},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.5341491103172302},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.5269967913627625},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.5159650444984436},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.4917505085468292},{"id":"https://openalex.org/keywords/computational-model","display_name":"Computational model","score":0.4717876613140106},{"id":"https://openalex.org/keywords/human\u2013computer-interaction","display_name":"Human\u2013computer interaction","score":0.41150712966918945},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.35714179277420044},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.35617852210998535},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3299447298049927},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.2621375024318695}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7815964221954346},{"id":"https://openalex.org/C171018156","wikidata":"https://www.wikidata.org/wiki/Q7370306","display_name":"Rotation formalisms in three dimensions","level":2,"score":0.7587470412254333},{"id":"https://openalex.org/C37789001","wikidata":"https://www.wikidata.org/wiki/Q782543","display_name":"Graphical user interface","level":2,"score":0.5536900758743286},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5341491103172302},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.5269967913627625},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.5159650444984436},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.4917505085468292},{"id":"https://openalex.org/C66024118","wikidata":"https://www.wikidata.org/wiki/Q1122506","display_name":"Computational model","level":2,"score":0.4717876613140106},{"id":"https://openalex.org/C107457646","wikidata":"https://www.wikidata.org/wiki/Q207434","display_name":"Human\u2013computer interaction","level":1,"score":0.41150712966918945},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.35714179277420044},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.35617852210998535},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3299447298049927},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.2621375024318695},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","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/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.0},{"id":"https://openalex.org/C129307140","wikidata":"https://www.wikidata.org/wiki/Q6795880","display_name":"Maximum bubble pressure method","level":3,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"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/C157915830","wikidata":"https://www.wikidata.org/wiki/Q2928001","display_name":"Bubble","level":2,"score":0.0}],"mesh":[],"locations_count":7,"locations":[{"id":"doi:10.1093/bib/bbae509","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae509","pdf_url":"https://academic.oup.com/bib/article-pdf/25/6/bbae509/59872401/bbae509.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38979487","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38979487","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":"ArXiv","raw_type":null},{"id":"pmid:39425527","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39425527","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},{"id":"pmh:oai:arXiv.org:2406.18371","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2406.18371","pdf_url":"https://arxiv.org/pdf/2406.18371","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"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":"","raw_type":"text"},{"id":"pmh:oai:pubmedcentral.nih.gov:11230347","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11230347","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11230347/pdf/nihpp-2406.18371v1.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ArXiv","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:11489466","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11489466","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11489466/pdf/bbae509.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"},{"id":"doi:10.48550/arxiv.2406.18371","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2406.18371","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article"}],"best_oa_location":{"id":"doi:10.1093/bib/bbae509","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae509","pdf_url":"https://academic.oup.com/bib/article-pdf/25/6/bbae509/59872401/bbae509.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Quality Education","score":0.6399999856948853,"id":"https://metadata.un.org/sdg/4"}],"awards":[{"id":"https://openalex.org/G3680960908","display_name":null,"funder_award_id":"ANR-19-P3IA-000","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G443217407","display_name":null,"funder_award_id":"PRAIRIE","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G4950536974","display_name":null,"funder_award_id":"-0001","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4970889947","display_name":null,"funder_award_id":"101136379","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G5838787665","display_name":null,"funder_award_id":"ANR-19-P3IA-0001","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G626190807","display_name":null,"funder_award_id":"19-P3IA-0001","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G6934367325","display_name":null,"funder_award_id":"U01-CA232137-01","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7606248342","display_name":null,"funder_award_id":"2303695","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G8227349700","display_name":null,"funder_award_id":"1720625","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G8318064016","display_name":null,"funder_award_id":"Horizon","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G8318455765","display_name":null,"funder_award_id":"ANR-19","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G848032724","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G8697265622","display_name":"HPC/Exascale Centre of Excellence in Personalised Medicine - PerMedCoE","funder_award_id":"951773","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320316625","display_name":"Jayne Koskinas Ted Giovanis Foundation for Health and Policy","ror":null},{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320320883","display_name":"Agence Nationale de la Recherche","ror":"https://ror.org/00rbzpz17"},{"id":"https://openalex.org/F4320320893","display_name":"Institut National de la Sant\u00e9 et de la Recherche M\u00e9dicale","ror":"https://ror.org/02vjkv261"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320334322","display_name":"HORIZON EUROPE Framework Programme","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4400104825.pdf","grobid_xml":"https://content.openalex.org/works/W4400104825.grobid-xml"},"referenced_works_count":32,"referenced_works":["https://openalex.org/W115452890","https://openalex.org/W1977943543","https://openalex.org/W2091174660","https://openalex.org/W2095433609","https://openalex.org/W2100345558","https://openalex.org/W2100762957","https://openalex.org/W2125857415","https://openalex.org/W2142171814","https://openalex.org/W2157947216","https://openalex.org/W2163415630","https://openalex.org/W2272546316","https://openalex.org/W2566910492","https://openalex.org/W2593809500","https://openalex.org/W2905127429","https://openalex.org/W2911948847","https://openalex.org/W2912260118","https://openalex.org/W2921841947","https://openalex.org/W2949797623","https://openalex.org/W2951856423","https://openalex.org/W2952658094","https://openalex.org/W2984602766","https://openalex.org/W3161450531","https://openalex.org/W3164835287","https://openalex.org/W3199089929","https://openalex.org/W4220898999","https://openalex.org/W4294284617","https://openalex.org/W4310472863","https://openalex.org/W4379878722","https://openalex.org/W4386811476","https://openalex.org/W4388035307","https://openalex.org/W4399817419","https://openalex.org/W4402135155"],"related_works":["https://openalex.org/W57206970","https://openalex.org/W4235091896","https://openalex.org/W2185981755","https://openalex.org/W2023896637","https://openalex.org/W2498253392","https://openalex.org/W2996527951","https://openalex.org/W1532035848","https://openalex.org/W3034716491","https://openalex.org/W4240625990","https://openalex.org/W2022968056"],"abstract_inverted_index":{"Multiscale":[0],"models":[1,28,54,93,136,189,208,220,242],"provide":[2],"a":[3,73,95,159],"unique":[4],"tool":[5],"for":[6,179],"analyzing":[7],"complex":[8,67,97],"processes":[9,113],"that":[10,200],"study":[11],"events":[12],"occurring":[13],"at":[14,33,41,245],"different":[15],"scales":[16],"across":[17],"space":[18],"and":[19,40,48,76,80,240],"time.":[20],"In":[21],"the":[22,34,42,58,70,77,85,100,103,107,112,117,120,123,129,147,169,177,193,210,227],"context":[23],"of":[24,60,90,102,109,111,119,149,187,198],"biological":[25],"systems,":[26],"such":[27,37,139],"can":[29],"simulate":[30],"mechanisms":[31],"happening":[32],"intracellular":[35,202],"level":[36,44,108],"as":[38,140,173,175,204,237],"signaling,":[39],"extracellular":[43],"where":[45],"cells":[46],"communicate":[47],"coordinate":[49],"with":[50,158],"other":[51],"cells.":[52],"These":[53],"aim":[55],"to":[56,83,105,114,122,133,168,209,217],"understand":[57],"impact":[59],"genetic":[61],"or":[62,116,142],"environmental":[63],"deregulation":[64],"observed":[65],"in":[66,137,163],"diseases,":[68],"describe":[69],"interplay":[71],"between":[72],"pathological":[74],"tissue":[75],"immune":[78],"system,":[79],"suggest":[81],"strategies":[82],"revert":[84],"diseased":[86],"phenotypes.":[87],"The":[88,213],"construction":[89],"these":[91,135,219],"multiscale":[92,188],"remains":[94],"very":[96],"task,":[98],"including":[99],"choice":[101],"components":[104],"consider,":[106],"details":[110],"simulate,":[115],"fitting":[118],"parameters":[121],"data.":[124],"One":[125],"additional":[126],"difficulty":[127],"is":[128,235],"expert":[130],"knowledge":[131],"needed":[132],"program":[134],"languages":[138],"C++":[141],"Python,":[143],"which":[144,190],"may":[145],"discourage":[146],"participation":[148],"non-experts.":[150],"Simplifying":[151],"this":[152],"process":[153,178],"through":[154],"structured":[155],"description":[156],"formalisms-coupled":[157],"graphical":[160],"interface-is":[161],"crucial":[162],"making":[164],"modeling":[165],"more":[166,221],"accessible":[167],"broader":[170],"scientific":[171],"community,":[172],"well":[174],"streamlining":[176],"advanced":[180],"users.":[181],"This":[182],"article":[183,214],"introduces":[184],"three":[185],"examples":[186],"rely":[191],"on":[192,224],"framework":[194],"PhysiBoSS,":[195],"an":[196],"add-on":[197],"PhysiCell":[199,225,228],"includes":[201],"descriptions":[203],"continuous":[205],"time":[206],"Boolean":[207],"agent-based":[211],"approach.":[212],"demonstrates":[215],"how":[216],"construct":[218],"easily,":[222],"relying":[223],"Studio,":[226],"Graphical":[229],"User":[230],"Interface.":[231],"A":[232],"step-by-step":[233],"tutorial":[234],"provided":[236,244],"Supplementary":[238],"Material":[239],"all":[241],"are":[243],"https://physiboss.github.io/tutorial/.":[246]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":1}],"updated_date":"2026-04-13T07:58:08.660418","created_date":"2024-06-28T00:00:00"}
