{"id":"https://openalex.org/W2112815568","doi":"https://doi.org/10.1186/1751-0473-7-11","title":"A CellML simulation compiler and code generator using ODE solving schemes","display_name":"A CellML simulation compiler and code generator using ODE solving schemes","publication_year":2012,"publication_date":"2012-10-19","ids":{"openalex":"https://openalex.org/W2112815568","doi":"https://doi.org/10.1186/1751-0473-7-11","mag":"2112815568","pmid":"https://pubmed.ncbi.nlm.nih.gov/23083065"},"language":"en","primary_location":{"id":"doi:10.1186/1751-0473-7-11","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1751-0473-7-11","pdf_url":"https://scfbm.biomedcentral.com/counter/pdf/10.1186/1751-0473-7-11","source":{"id":"https://openalex.org/S45786803","display_name":"Source Code for Biology and Medicine","issn_l":"1751-0473","issn":["1751-0473"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Source Code for Biology and Medicine","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://scfbm.biomedcentral.com/counter/pdf/10.1186/1751-0473-7-11","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5034142671","display_name":"Florencio Rusty Punzalan","orcid":"https://orcid.org/0000-0002-7100-1815"},"institutions":[{"id":"https://openalex.org/I135768898","display_name":"Ritsumeikan University","ror":"https://ror.org/0197nmd03","country_code":"JP","type":"education","lineage":["https://openalex.org/I135768898","https://openalex.org/I4390039241"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Florencio Rusty Punzalan","raw_affiliation_strings":["Graduate School of Life Sciences, Ritsumeikan University, Shiga, Japan. floren@fc.ritsumei.ac.jp","Graduate School of Life Sciences, Ritsumeikan University, Shiga, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Graduate School of Life Sciences, Ritsumeikan University, Shiga, Japan. floren@fc.ritsumei.ac.jp","institution_ids":["https://openalex.org/I135768898"]},{"raw_affiliation_string":"Graduate School of Life Sciences, Ritsumeikan University, Shiga, Japan","institution_ids":["https://openalex.org/I135768898"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024766535","display_name":"Yoshiharu Yamashita","orcid":null},"institutions":[{"id":"https://openalex.org/I135768898","display_name":"Ritsumeikan University","ror":"https://ror.org/0197nmd03","country_code":"JP","type":"education","lineage":["https://openalex.org/I135768898","https://openalex.org/I4390039241"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Yoshiharu Yamashita","raw_affiliation_strings":["Graduate School of Information Science and Engineering, Ritsumeikan University, Shiga, Japan","Ritsumeikan University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Graduate School of Information Science and Engineering, Ritsumeikan University, Shiga, Japan","institution_ids":["https://openalex.org/I135768898"]},{"raw_affiliation_string":"Ritsumeikan University","institution_ids":["https://openalex.org/I135768898"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006222369","display_name":"Naoki Soejima","orcid":null},"institutions":[{"id":"https://openalex.org/I135768898","display_name":"Ritsumeikan University","ror":"https://ror.org/0197nmd03","country_code":"JP","type":"education","lineage":["https://openalex.org/I135768898","https://openalex.org/I4390039241"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Naoki Soejima","raw_affiliation_strings":["Graduate School of Life Sciences, Ritsumeikan University, Shiga, Japan","Ritsumeikan University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Graduate School of Life Sciences, Ritsumeikan University, Shiga, Japan","institution_ids":["https://openalex.org/I135768898"]},{"raw_affiliation_string":"Ritsumeikan University","institution_ids":["https://openalex.org/I135768898"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111670096","display_name":"Masanari Kawabata","orcid":null},"institutions":[{"id":"https://openalex.org/I135768898","display_name":"Ritsumeikan University","ror":"https://ror.org/0197nmd03","country_code":"JP","type":"education","lineage":["https://openalex.org/I135768898","https://openalex.org/I4390039241"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Masanari Kawabata","raw_affiliation_strings":["Graduate School of Life Sciences, Ritsumeikan University, Shiga, Japan","Ritsumeikan University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Graduate School of Life Sciences, Ritsumeikan University, Shiga, Japan","institution_ids":["https://openalex.org/I135768898"]},{"raw_affiliation_string":"Ritsumeikan University","institution_ids":["https://openalex.org/I135768898"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032063471","display_name":"Takao Shimayoshi","orcid":"https://orcid.org/0000-0001-8187-9915"},"institutions":[{"id":"https://openalex.org/I4210094023","display_name":"Advanced Science, Technology & Management Research Institute of Kyoto","ror":"https://ror.org/00ryrev47","country_code":"JP","type":"other","lineage":["https://openalex.org/I4210094023"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Takao Shimayoshi","raw_affiliation_strings":["ASTEM Research Institute of Kyoto, Kyoto, Japan","ASTEM Research Institute of Kyoto"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"ASTEM Research Institute of Kyoto, Kyoto, Japan","institution_ids":["https://openalex.org/I4210094023"]},{"raw_affiliation_string":"ASTEM Research Institute of Kyoto","institution_ids":["https://openalex.org/I4210094023"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006111936","display_name":"Hiroaki Kuwabara","orcid":null},"institutions":[{"id":"https://openalex.org/I135768898","display_name":"Ritsumeikan University","ror":"https://ror.org/0197nmd03","country_code":"JP","type":"education","lineage":["https://openalex.org/I135768898","https://openalex.org/I4390039241"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Hiroaki Kuwabara","raw_affiliation_strings":["Graduate School of Information Science and Engineering, Ritsumeikan University, Shiga, Japan","Ritsumeikan University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Graduate School of Information Science and Engineering, Ritsumeikan University, Shiga, Japan","institution_ids":["https://openalex.org/I135768898"]},{"raw_affiliation_string":"Ritsumeikan University","institution_ids":["https://openalex.org/I135768898"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052110553","display_name":"Yoshitoshi Kunieda","orcid":null},"institutions":[{"id":"https://openalex.org/I135768898","display_name":"Ritsumeikan University","ror":"https://ror.org/0197nmd03","country_code":"JP","type":"education","lineage":["https://openalex.org/I135768898","https://openalex.org/I4390039241"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Yoshitoshi Kunieda","raw_affiliation_strings":["Graduate School of Information Science and Engineering, Ritsumeikan University, Shiga, Japan","Ritsumeikan University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Graduate School of Information Science and Engineering, Ritsumeikan University, Shiga, Japan","institution_ids":["https://openalex.org/I135768898"]},{"raw_affiliation_string":"Ritsumeikan University","institution_ids":["https://openalex.org/I135768898"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5078531865","display_name":"Akira Amano","orcid":"https://orcid.org/0000-0002-7704-2458"},"institutions":[{"id":"https://openalex.org/I135768898","display_name":"Ritsumeikan University","ror":"https://ror.org/0197nmd03","country_code":"JP","type":"education","lineage":["https://openalex.org/I135768898","https://openalex.org/I4390039241"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Akira Amano","raw_affiliation_strings":["Graduate School of Life Sciences, Ritsumeikan University, Shiga, Japan","Ritsumeikan University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Graduate School of Life Sciences, Ritsumeikan University, Shiga, Japan","institution_ids":["https://openalex.org/I135768898"]},{"raw_affiliation_string":"Ritsumeikan University","institution_ids":["https://openalex.org/I135768898"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":8,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.4031,"has_fulltext":true,"cited_by_count":4,"citation_normalized_percentile":{"value":0.62924334,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"7","issue":"1","first_page":"11","last_page":"11"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9995999932289124,"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":0.9995999932289124,"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/T11178","display_name":"Receptor Mechanisms and Signaling","score":0.9818999767303467,"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/T10217","display_name":"Cardiac electrophysiology and arrhythmias","score":0.9728999733924866,"subfield":{"id":"https://openalex.org/subfields/2705","display_name":"Cardiology and Cardiovascular Medicine"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/ode","display_name":"Ode","score":0.9166706800460815},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7984522581100464},{"id":"https://openalex.org/keywords/ordinary-differential-equation","display_name":"Ordinary differential equation","score":0.7399892807006836},{"id":"https://openalex.org/keywords/compiler","display_name":"Compiler","score":0.7215251922607422},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.6355891823768616},{"id":"https://openalex.org/keywords/code-generation","display_name":"Code generation","score":0.6338944435119629},{"id":"https://openalex.org/keywords/generator","display_name":"Generator (circuit theory)","score":0.5478805899620056},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.5063785314559937},{"id":"https://openalex.org/keywords/scheme","display_name":"Scheme (mathematics)","score":0.4323301911354065},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.4322333037853241},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.4306102693080902},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.4014962315559387},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.39140480756759644},{"id":"https://openalex.org/keywords/differential-equation","display_name":"Differential equation","score":0.3360450267791748},{"id":"https://openalex.org/keywords/applied-mathematics","display_name":"Applied mathematics","score":0.3236401677131653},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.15132883191108704}],"concepts":[{"id":"https://openalex.org/C34862557","wikidata":"https://www.wikidata.org/wiki/Q178985","display_name":"Ode","level":2,"score":0.9166706800460815},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7984522581100464},{"id":"https://openalex.org/C51544822","wikidata":"https://www.wikidata.org/wiki/Q465274","display_name":"Ordinary differential equation","level":3,"score":0.7399892807006836},{"id":"https://openalex.org/C169590947","wikidata":"https://www.wikidata.org/wiki/Q47506","display_name":"Compiler","level":2,"score":0.7215251922607422},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.6355891823768616},{"id":"https://openalex.org/C133162039","wikidata":"https://www.wikidata.org/wiki/Q1061077","display_name":"Code generation","level":3,"score":0.6338944435119629},{"id":"https://openalex.org/C2780992000","wikidata":"https://www.wikidata.org/wiki/Q17016113","display_name":"Generator (circuit theory)","level":3,"score":0.5478805899620056},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.5063785314559937},{"id":"https://openalex.org/C77618280","wikidata":"https://www.wikidata.org/wiki/Q1155772","display_name":"Scheme (mathematics)","level":2,"score":0.4323301911354065},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.4322333037853241},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.4306102693080902},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.4014962315559387},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.39140480756759644},{"id":"https://openalex.org/C78045399","wikidata":"https://www.wikidata.org/wiki/Q11214","display_name":"Differential equation","level":2,"score":0.3360450267791748},{"id":"https://openalex.org/C28826006","wikidata":"https://www.wikidata.org/wiki/Q33521","display_name":"Applied mathematics","level":1,"score":0.3236401677131653},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.15132883191108704},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.0},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"score":0.0},{"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/C163258240","wikidata":"https://www.wikidata.org/wiki/Q25342","display_name":"Power (physics)","level":2,"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/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1186/1751-0473-7-11","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1751-0473-7-11","pdf_url":"https://scfbm.biomedcentral.com/counter/pdf/10.1186/1751-0473-7-11","source":{"id":"https://openalex.org/S45786803","display_name":"Source Code for Biology and Medicine","issn_l":"1751-0473","issn":["1751-0473"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Source Code for Biology and Medicine","raw_type":"journal-article"},{"id":"pmid:23083065","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23083065","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":"Source code for biology and medicine","raw_type":null},{"id":"pmh:oai:europepmc.org:2770660","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3778851","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1751-0473-7-11","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1751-0473-7-11","pdf_url":"https://scfbm.biomedcentral.com/counter/pdf/10.1186/1751-0473-7-11","source":{"id":"https://openalex.org/S45786803","display_name":"Source Code for Biology and Medicine","issn_l":"1751-0473","issn":["1751-0473"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Source Code for Biology and Medicine","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320320912","display_name":"Ministry of Education, Culture, Sports, Science and Technology","ror":"https://ror.org/048rj2z13"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2112815568.pdf","grobid_xml":"https://content.openalex.org/works/W2112815568.grobid-xml"},"referenced_works_count":11,"referenced_works":["https://openalex.org/W1982174804","https://openalex.org/W2009375605","https://openalex.org/W2028146834","https://openalex.org/W2065735566","https://openalex.org/W2088653672","https://openalex.org/W2123783513","https://openalex.org/W2123892496","https://openalex.org/W2132561989","https://openalex.org/W2137273343","https://openalex.org/W2150908245","https://openalex.org/W2170122529"],"related_works":["https://openalex.org/W3082668976","https://openalex.org/W2517973022","https://openalex.org/W1543121148","https://openalex.org/W1580703421","https://openalex.org/W2996841952","https://openalex.org/W2618518959","https://openalex.org/W2231364979","https://openalex.org/W4295745414","https://openalex.org/W4288093367","https://openalex.org/W4382202915"],"abstract_inverted_index":null,"counts_by_year":[{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2013,"cited_by_count":2}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
