{"id":"https://openalex.org/W3200584885","doi":"https://doi.org/10.1007/978-3-030-85633-5_18","title":"BioFVM-X: An MPI+OpenMP 3-D Simulator for Biological Systems","display_name":"BioFVM-X: An MPI+OpenMP 3-D Simulator for Biological Systems","publication_year":2021,"publication_date":"2021-01-01","ids":{"openalex":"https://openalex.org/W3200584885","doi":"https://doi.org/10.1007/978-3-030-85633-5_18","mag":"3200584885"},"language":"en","primary_location":{"id":"doi:10.1007/978-3-030-85633-5_18","is_oa":true,"landing_page_url":"https://doi.org/10.1007/978-3-030-85633-5_18","pdf_url":"https://link.springer.com/content/pdf/10.1007%2F978-3-030-85633-5_18.pdf","source":{"id":"https://openalex.org/S106296714","display_name":"Lecture notes in computer science","issn_l":"0302-9743","issn":["0302-9743","1611-3349"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"book series"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Lecture Notes in Computer Science","raw_type":"book-chapter"},"type":"book-chapter","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://link.springer.com/content/pdf/10.1007%2F978-3-030-85633-5_18.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101994516","display_name":"Gaurav Saxena","orcid":"https://orcid.org/0000-0001-7667-5053"},"institutions":[{"id":"https://openalex.org/I2799803557","display_name":"Barcelona Supercomputing Center","ror":"https://ror.org/05sd8tv96","country_code":"ES","type":"facility","lineage":["https://openalex.org/I2799803557","https://openalex.org/I9617848"]},{"id":"https://openalex.org/I9617848","display_name":"Universitat Polit\u00e8cnica de Catalunya","ror":"https://ror.org/03mb6wj31","country_code":"ES","type":"education","lineage":["https://openalex.org/I9617848"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Gaurav Saxena","raw_affiliation_strings":["Barcelona Supercomputing Center (BSC), Barcelona, Spain"],"affiliations":[{"raw_affiliation_string":"Barcelona Supercomputing Center (BSC), Barcelona, Spain","institution_ids":["https://openalex.org/I9617848","https://openalex.org/I2799803557"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007632406","display_name":"Miguel Ponce-de-Le\u00f3n","orcid":"https://orcid.org/0000-0002-7496-844X"},"institutions":[{"id":"https://openalex.org/I2799803557","display_name":"Barcelona Supercomputing Center","ror":"https://ror.org/05sd8tv96","country_code":"ES","type":"facility","lineage":["https://openalex.org/I2799803557","https://openalex.org/I9617848"]},{"id":"https://openalex.org/I9617848","display_name":"Universitat Polit\u00e8cnica de Catalunya","ror":"https://ror.org/03mb6wj31","country_code":"ES","type":"education","lineage":["https://openalex.org/I9617848"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Miguel Ponce-de-Leon","raw_affiliation_strings":["Barcelona Supercomputing Center (BSC), Barcelona, Spain"],"affiliations":[{"raw_affiliation_string":"Barcelona Supercomputing Center (BSC), Barcelona, Spain","institution_ids":["https://openalex.org/I9617848","https://openalex.org/I2799803557"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051818233","display_name":"Arnau Montagud","orcid":null},"institutions":[{"id":"https://openalex.org/I2799803557","display_name":"Barcelona Supercomputing Center","ror":"https://ror.org/05sd8tv96","country_code":"ES","type":"facility","lineage":["https://openalex.org/I2799803557","https://openalex.org/I9617848"]},{"id":"https://openalex.org/I9617848","display_name":"Universitat Polit\u00e8cnica de Catalunya","ror":"https://ror.org/03mb6wj31","country_code":"ES","type":"education","lineage":["https://openalex.org/I9617848"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Arnau Montagud","raw_affiliation_strings":["Barcelona Supercomputing Center (BSC), Barcelona, Spain"],"affiliations":[{"raw_affiliation_string":"Barcelona Supercomputing Center (BSC), Barcelona, Spain","institution_ids":["https://openalex.org/I9617848","https://openalex.org/I2799803557"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068897597","display_name":"D. Vicente","orcid":"https://orcid.org/0000-0002-1584-1182"},"institutions":[{"id":"https://openalex.org/I2799803557","display_name":"Barcelona Supercomputing Center","ror":"https://ror.org/05sd8tv96","country_code":"ES","type":"facility","lineage":["https://openalex.org/I2799803557","https://openalex.org/I9617848"]},{"id":"https://openalex.org/I9617848","display_name":"Universitat Polit\u00e8cnica de Catalunya","ror":"https://ror.org/03mb6wj31","country_code":"ES","type":"education","lineage":["https://openalex.org/I9617848"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"David Vicente\u00a0Dorca","raw_affiliation_strings":["Barcelona Supercomputing Center (BSC), Barcelona, Spain"],"affiliations":[{"raw_affiliation_string":"Barcelona Supercomputing Center (BSC), Barcelona, Spain","institution_ids":["https://openalex.org/I9617848","https://openalex.org/I2799803557"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5015217651","display_name":"Alfonso Valencia","orcid":"https://orcid.org/0000-0002-8937-6789"},"institutions":[{"id":"https://openalex.org/I11932220","display_name":"Instituci\u00f3 Catalana de Recerca i Estudis Avan\u00e7ats","ror":"https://ror.org/0371hy230","country_code":"ES","type":"nonprofit","lineage":["https://openalex.org/I11932220"]},{"id":"https://openalex.org/I2799803557","display_name":"Barcelona Supercomputing Center","ror":"https://ror.org/05sd8tv96","country_code":"ES","type":"facility","lineage":["https://openalex.org/I2799803557","https://openalex.org/I9617848"]},{"id":"https://openalex.org/I9617848","display_name":"Universitat Polit\u00e8cnica de Catalunya","ror":"https://ror.org/03mb6wj31","country_code":"ES","type":"education","lineage":["https://openalex.org/I9617848"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Alfonso Valencia","raw_affiliation_strings":["Barcelona Supercomputing Center (BSC), Barcelona, Spain","Instituci\u00f3 Catalana de Recerca i Estudis Avan\u00e7ats (ICREA), Barcelona, Spain"],"affiliations":[{"raw_affiliation_string":"Barcelona Supercomputing Center (BSC), Barcelona, Spain","institution_ids":["https://openalex.org/I9617848","https://openalex.org/I2799803557"]},{"raw_affiliation_string":"Instituci\u00f3 Catalana de Recerca i Estudis Avan\u00e7ats (ICREA), Barcelona, Spain","institution_ids":["https://openalex.org/I11932220"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5101994516"],"corresponding_institution_ids":["https://openalex.org/I2799803557","https://openalex.org/I9617848"],"apc_list":{"value":5000,"currency":"EUR","value_usd":5392},"apc_paid":{"value":5000,"currency":"EUR","value_usd":5392},"fwci":5.0548,"has_fulltext":true,"cited_by_count":8,"citation_normalized_percentile":{"value":0.96487985,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":null,"issue":null,"first_page":"266","last_page":"279"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11829","display_name":"Mathematical Biology Tumor Growth","score":0.9998000264167786,"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":0.9998000264167786,"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/T10492","display_name":"Microtubule and mitosis dynamics","score":0.9890000224113464,"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/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.9865000247955322,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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":0.8326431512832642},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.6973624229431152},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.6605462431907654},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.6153029799461365},{"id":"https://openalex.org/keywords/limiting","display_name":"Limiting","score":0.5294964909553528},{"id":"https://openalex.org/keywords/scale","display_name":"Scale (ratio)","score":0.5049136281013489},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.4640210270881653},{"id":"https://openalex.org/keywords/supercomputer","display_name":"Supercomputer","score":0.42938661575317383},{"id":"https://openalex.org/keywords/documentation","display_name":"Documentation","score":0.4273523688316345},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4258365333080292},{"id":"https://openalex.org/keywords/solver","display_name":"Solver","score":0.4110051393508911},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3778773546218872},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.29322898387908936},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.1951199471950531},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.1643349826335907},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.0863170325756073}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8326431512832642},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.6973624229431152},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.6605462431907654},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.6153029799461365},{"id":"https://openalex.org/C188198153","wikidata":"https://www.wikidata.org/wiki/Q1613840","display_name":"Limiting","level":2,"score":0.5294964909553528},{"id":"https://openalex.org/C2778755073","wikidata":"https://www.wikidata.org/wiki/Q10858537","display_name":"Scale (ratio)","level":2,"score":0.5049136281013489},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.4640210270881653},{"id":"https://openalex.org/C83283714","wikidata":"https://www.wikidata.org/wiki/Q121117","display_name":"Supercomputer","level":2,"score":0.42938661575317383},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.4273523688316345},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4258365333080292},{"id":"https://openalex.org/C2778770139","wikidata":"https://www.wikidata.org/wiki/Q1966904","display_name":"Solver","level":2,"score":0.4110051393508911},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3778773546218872},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.29322898387908936},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.1951199471950531},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.1643349826335907},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0863170325756073},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0},{"id":"https://openalex.org/C78519656","wikidata":"https://www.wikidata.org/wiki/Q101333","display_name":"Mechanical engineering","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1007/978-3-030-85633-5_18","is_oa":true,"landing_page_url":"https://doi.org/10.1007/978-3-030-85633-5_18","pdf_url":"https://link.springer.com/content/pdf/10.1007%2F978-3-030-85633-5_18.pdf","source":{"id":"https://openalex.org/S106296714","display_name":"Lecture notes in computer science","issn_l":"0302-9743","issn":["0302-9743","1611-3349"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"book series"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Lecture Notes in Computer Science","raw_type":"book-chapter"},{"id":"pmh:oai:zenodo.org:6539558","is_oa":true,"landing_page_url":"https://zenodo.org/record/6539558","pdf_url":"https://zenodo.org/record/6539558","source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:upcommons.upc.edu:2117/351685","is_oa":true,"landing_page_url":"http://hdl.handle.net/2117/351685","pdf_url":null,"source":{"id":"https://openalex.org/S4210207057","display_name":"QRU Quaderns de Recerca en Urbanisme","issn_l":"2014-9689","issn":["2014-9689","2385-6777"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/P4310322448","host_organization_name":"Q71272178","host_organization_lineage":["https://openalex.org/P4310322448"],"host_organization_lineage_names":["Q71272178"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Conference report"}],"best_oa_location":{"id":"doi:10.1007/978-3-030-85633-5_18","is_oa":true,"landing_page_url":"https://doi.org/10.1007/978-3-030-85633-5_18","pdf_url":"https://link.springer.com/content/pdf/10.1007%2F978-3-030-85633-5_18.pdf","source":{"id":"https://openalex.org/S106296714","display_name":"Lecture notes in computer science","issn_l":"0302-9743","issn":["0302-9743","1611-3349"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"book series"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Lecture Notes in Computer Science","raw_type":"book-chapter"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","score":0.5400000214576721,"display_name":"Industry, innovation and infrastructure"}],"awards":[{"id":"https://openalex.org/G3593447409","display_name":null,"funder_award_id":"825070","funder_id":"https://openalex.org/F4320332999","funder_display_name":"Horizon 2020 Framework Programme"},{"id":"https://openalex.org/G7331901853","display_name":null,"funder_award_id":"EU H2020","funder_id":"https://openalex.org/F4320332999","funder_display_name":"Horizon 2020 Framework Programme"},{"id":"https://openalex.org/G8470257310","display_name":null,"funder_award_id":"951773","funder_id":"https://openalex.org/F4320332999","funder_display_name":"Horizon 2020 Framework Programme"}],"funders":[{"id":"https://openalex.org/F4320332999","display_name":"Horizon 2020 Framework Programme","ror":"https://ror.org/00k4n6c32"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3200584885.pdf","grobid_xml":"https://content.openalex.org/works/W3200584885.grobid-xml"},"referenced_works_count":29,"referenced_works":["https://openalex.org/W51719658","https://openalex.org/W90568776","https://openalex.org/W280536263","https://openalex.org/W1525132831","https://openalex.org/W1530872699","https://openalex.org/W1893942944","https://openalex.org/W1967961367","https://openalex.org/W1971947347","https://openalex.org/W2002785668","https://openalex.org/W2069114279","https://openalex.org/W2086611351","https://openalex.org/W2135682468","https://openalex.org/W2151137638","https://openalex.org/W2160135160","https://openalex.org/W2256248976","https://openalex.org/W2399287928","https://openalex.org/W2485631305","https://openalex.org/W2520660423","https://openalex.org/W2763262590","https://openalex.org/W2808177248","https://openalex.org/W2949797623","https://openalex.org/W2951213949","https://openalex.org/W2951378914","https://openalex.org/W2951856423","https://openalex.org/W3012553271","https://openalex.org/W3100368092","https://openalex.org/W3107663002","https://openalex.org/W4246643851","https://openalex.org/W6600252484"],"related_works":["https://openalex.org/W1582436825","https://openalex.org/W1604758548","https://openalex.org/W2804126825","https://openalex.org/W1996803181","https://openalex.org/W1549048322","https://openalex.org/W4367553810","https://openalex.org/W2104142636","https://openalex.org/W2979588510","https://openalex.org/W2731831065","https://openalex.org/W4283162424"],"abstract_inverted_index":{"Abstract":[0],"Multi-scale":[1],"simulations":[2,29],"require":[3],"parallelization":[4],"to":[5,32,73],"address":[6],"large-scale":[7,51],"problems,":[8],"such":[9],"as":[10],"real-sized":[11],"tumor":[12],"simulations.":[13],"BioFVM":[14,39,63,80],"is":[15,40],"a":[16],"software":[17],"package":[18],"that":[19],"solves":[20],"diffusive":[21],"transport":[22],"Partial":[23],"Differential":[24],"Equations":[25],"for":[26],"3-D":[27,87],"biological":[28],"successfully":[30],"applied":[31],"tissue":[33],"and":[34,81,94,109],"cancer":[35],"biology":[36],"problems.":[37],"Currently,":[38],"only":[41],"shared-memory":[42],"parallelized":[43],"using":[44],"OpenMP,":[45],"greatly":[46],"limiting":[47],"the":[48,75,114],"execution":[49],"of":[50,62,65,79],"jobs":[52],"in":[53,85],"HPC":[54],"clusters.":[55],"We":[56],"present":[57],"BioFVM-X:":[58],"an":[59],"enhanced":[60],"version":[61],"capable":[64],"running":[66],"on":[67],"multiple":[68],"nodes.":[69],"BioFVM-X":[70,105],"uses":[71],"MPI+OpenMP":[72],"parallelize":[74],"generic":[76],"core":[77],"kernels":[78],"shows":[82],"promising":[83],"scalability":[84],"large":[86],"problems":[88],"with":[89],"several":[90],"hundreds":[91],"diffusible":[92],"substrates":[93],"$$\\approx":[95],"$$":[96],"<mml:math":[97],"xmlns:mml=\"http://www.w3.org/1998/Math/MathML\">":[98],"<mml:mo>\u2248</mml:mo>":[99],"</mml:math>":[100],"0.5":[101],"billion":[102],"voxels.":[103],"The":[104],"source":[106],"code,":[107],"examples":[108],"documentation,":[110],"are":[111],"available":[112],"under":[113],"BSD":[115],"3-Clause":[116],"license":[117],"at":[118],"https://gitlab.bsc.es/gsaxena/biofvm_x":[119],".":[120]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":1}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2021-09-27T00:00:00"}