{"id":"https://openalex.org/W2151991601","doi":"https://doi.org/10.1093/database/bau095","title":"WholeCellSimDB: a hybrid relational/HDF database for whole-cell model predictions","display_name":"WholeCellSimDB: a hybrid relational/HDF database for whole-cell model predictions","publication_year":2014,"publication_date":"2014-09-16","ids":{"openalex":"https://openalex.org/W2151991601","doi":"https://doi.org/10.1093/database/bau095","mag":"2151991601","pmid":"https://pubmed.ncbi.nlm.nih.gov/25231498"},"language":"en","primary_location":{"id":"doi:10.1093/database/bau095","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/bau095","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/bau095/8248106/bau095.pdf","source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Database","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/bau095/8248106/bau095.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5016750554","display_name":"Jonathan R. Karr","orcid":"https://orcid.org/0000-0002-2605-5080"},"institutions":[{"id":"https://openalex.org/I22188714","display_name":"University of Prince Edward Island","ror":"https://ror.org/02xh9x144","country_code":"CA","type":"education","lineage":["https://openalex.org/I22188714"]},{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["CA","US"],"is_corresponding":false,"raw_author_name":"J. R. Karr","raw_affiliation_strings":["Graduate Program in Biophysics, Stanford University, Stanford, CA 94305, USA, Computer Science and Information Technology, University of Prince Edward Island, Charlottetown, PE C1A 4P3, Canada and Department of Bioengineering, Stanford University, Stanford, CA 94305, USA","Graduate Program in Biophysics, Stanford University, Stanford, CA 94305, USA, 2 Computer Science and Information Technology, University of Prince Edward Island, Charlottetown, PE C1A 4P3, Canada and 3 Department of Bioengineering, Stanford University, Stanford, CA 94305, USA"],"affiliations":[{"raw_affiliation_string":"Graduate Program in Biophysics, Stanford University, Stanford, CA 94305, USA, Computer Science and Information Technology, University of Prince Edward Island, Charlottetown, PE C1A 4P3, Canada and Department of Bioengineering, Stanford University, Stanford, CA 94305, USA","institution_ids":[]},{"raw_affiliation_string":"Graduate Program in Biophysics, Stanford University, Stanford, CA 94305, USA, 2 Computer Science and Information Technology, University of Prince Edward Island, Charlottetown, PE C1A 4P3, Canada and 3 Department of Bioengineering, Stanford University, Stanford, CA 94305, USA","institution_ids":["https://openalex.org/I22188714","https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080245892","display_name":"Nicholas C. K. Phillips","orcid":null},"institutions":[{"id":"https://openalex.org/I22188714","display_name":"University of Prince Edward Island","ror":"https://ror.org/02xh9x144","country_code":"CA","type":"education","lineage":["https://openalex.org/I22188714"]},{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["CA","US"],"is_corresponding":false,"raw_author_name":"N. C. Phillips","raw_affiliation_strings":["Graduate Program in Biophysics, Stanford University, Stanford, CA 94305, USA, Computer Science and Information Technology, University of Prince Edward Island, Charlottetown, PE C1A 4P3, Canada and Department of Bioengineering, Stanford University, Stanford, CA 94305, USA","Graduate Program in Biophysics, Stanford University, Stanford, CA 94305, USA, 2 Computer Science and Information Technology, University of Prince Edward Island, Charlottetown, PE C1A 4P3, Canada and 3 Department of Bioengineering, Stanford University, Stanford, CA 94305, USA"],"affiliations":[{"raw_affiliation_string":"Graduate Program in Biophysics, Stanford University, Stanford, CA 94305, USA, Computer Science and Information Technology, University of Prince Edward Island, Charlottetown, PE C1A 4P3, Canada and Department of Bioengineering, Stanford University, Stanford, CA 94305, USA","institution_ids":[]},{"raw_affiliation_string":"Graduate Program in Biophysics, Stanford University, Stanford, CA 94305, USA, 2 Computer Science and Information Technology, University of Prince Edward Island, Charlottetown, PE C1A 4P3, Canada and 3 Department of Bioengineering, Stanford University, Stanford, CA 94305, USA","institution_ids":["https://openalex.org/I22188714","https://openalex.org/I97018004"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5064086976","display_name":"Markus W. Covert","orcid":"https://orcid.org/0000-0002-5993-8912"},"institutions":[{"id":"https://openalex.org/I22188714","display_name":"University of Prince Edward Island","ror":"https://ror.org/02xh9x144","country_code":"CA","type":"education","lineage":["https://openalex.org/I22188714"]},{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["CA","US"],"is_corresponding":true,"raw_author_name":"M. W. Covert","raw_affiliation_strings":["Graduate Program in Biophysics, Stanford University, Stanford, CA 94305, USA, Computer Science and Information Technology, University of Prince Edward Island, Charlottetown, PE C1A 4P3, Canada and Department of Bioengineering, Stanford University, Stanford, CA 94305, USA mcovert@stanford.edu","Graduate Program in Biophysics, Stanford University, Stanford, CA 94305, USA, 2 Computer Science and Information Technology, University of Prince Edward Island, Charlottetown, PE C1A 4P3, Canada and 3 Department of Bioengineering, Stanford University, Stanford, CA 94305, USA"],"affiliations":[{"raw_affiliation_string":"Graduate Program in Biophysics, Stanford University, Stanford, CA 94305, USA, Computer Science and Information Technology, University of Prince Edward Island, Charlottetown, PE C1A 4P3, Canada and Department of Bioengineering, Stanford University, Stanford, CA 94305, USA mcovert@stanford.edu","institution_ids":[]},{"raw_affiliation_string":"Graduate Program in Biophysics, Stanford University, Stanford, CA 94305, USA, 2 Computer Science and Information Technology, University of Prince Edward Island, Charlottetown, PE C1A 4P3, Canada and 3 Department of Bioengineering, Stanford University, Stanford, CA 94305, USA","institution_ids":["https://openalex.org/I22188714","https://openalex.org/I97018004"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5064086976"],"corresponding_institution_ids":["https://openalex.org/I22188714","https://openalex.org/I97018004"],"apc_list":{"value":1415,"currency":"GBP","value_usd":1735},"apc_paid":{"value":1415,"currency":"GBP","value_usd":1735},"fwci":1.8503,"has_fulltext":true,"cited_by_count":42,"citation_normalized_percentile":{"value":0.85610523,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"2014","issue":"0","first_page":"bau095","last_page":"bau095"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9972000122070312,"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":0.9972000122070312,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.982699990272522,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9767000079154968,"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":0.8749869465827942},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.7329245805740356},{"id":"https://openalex.org/keywords/json","display_name":"JSON","score":0.7301377058029175},{"id":"https://openalex.org/keywords/metadata","display_name":"Metadata","score":0.6290545463562012},{"id":"https://openalex.org/keywords/javascript","display_name":"JavaScript","score":0.5836346745491028},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.5364001989364624},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.5283865332603455},{"id":"https://openalex.org/keywords/relational-database","display_name":"Relational database","score":0.4954310655593872},{"id":"https://openalex.org/keywords/graphical-user-interface","display_name":"Graphical user interface","score":0.48742321133613586},{"id":"https://openalex.org/keywords/interoperability","display_name":"Interoperability","score":0.45239323377609253},{"id":"https://openalex.org/keywords/sql","display_name":"SQL","score":0.4268219769001007},{"id":"https://openalex.org/keywords/relational-database-management-system","display_name":"Relational database management system","score":0.4234876036643982},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.42183998227119446},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.381641685962677},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.21532869338989258}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8749869465827942},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.7329245805740356},{"id":"https://openalex.org/C2780416260","wikidata":"https://www.wikidata.org/wiki/Q2063","display_name":"JSON","level":2,"score":0.7301377058029175},{"id":"https://openalex.org/C93518851","wikidata":"https://www.wikidata.org/wiki/Q180160","display_name":"Metadata","level":2,"score":0.6290545463562012},{"id":"https://openalex.org/C544833334","wikidata":"https://www.wikidata.org/wiki/Q2005","display_name":"JavaScript","level":2,"score":0.5836346745491028},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.5364001989364624},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.5283865332603455},{"id":"https://openalex.org/C5655090","wikidata":"https://www.wikidata.org/wiki/Q192588","display_name":"Relational database","level":2,"score":0.4954310655593872},{"id":"https://openalex.org/C37789001","wikidata":"https://www.wikidata.org/wiki/Q782543","display_name":"Graphical user interface","level":2,"score":0.48742321133613586},{"id":"https://openalex.org/C20136886","wikidata":"https://www.wikidata.org/wiki/Q749647","display_name":"Interoperability","level":2,"score":0.45239323377609253},{"id":"https://openalex.org/C510870499","wikidata":"https://www.wikidata.org/wiki/Q47607","display_name":"SQL","level":2,"score":0.4268219769001007},{"id":"https://openalex.org/C24394798","wikidata":"https://www.wikidata.org/wiki/Q192588","display_name":"Relational database management system","level":3,"score":0.4234876036643982},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.42183998227119446},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.381641685962677},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.21532869338989258},{"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/C157915830","wikidata":"https://www.wikidata.org/wiki/Q2928001","display_name":"Bubble","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D002477","descriptor_name":"Cells","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D002477","descriptor_name":"Cells","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D002477","descriptor_name":"Cells","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D003585","descriptor_name":"Cell Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003585","descriptor_name":"Cell Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003585","descriptor_name":"Cell Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/database/bau095","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/bau095","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/bau095/8248106/bau095.pdf","source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Database","raw_type":"journal-article"},{"id":"pmid:25231498","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25231498","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":"Database : the journal of biological databases and curation","raw_type":null},{"id":"pmh:oai:europepmc.org:3140114","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4165886","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:10.1093/database/bau095","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/bau095","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/bau095/8248106/bau095.pdf","source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Database","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3849284313","display_name":null,"funder_award_id":"GM107615","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7170034006","display_name":null,"funder_award_id":"Pioneer","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2151991601.pdf","grobid_xml":"https://content.openalex.org/works/W2151991601.grobid-xml"},"referenced_works_count":35,"referenced_works":["https://openalex.org/W174102300","https://openalex.org/W1596530075","https://openalex.org/W1966041739","https://openalex.org/W1971060829","https://openalex.org/W1982309495","https://openalex.org/W1984493861","https://openalex.org/W1986366456","https://openalex.org/W2001811698","https://openalex.org/W2007315393","https://openalex.org/W2008199711","https://openalex.org/W2032756564","https://openalex.org/W2075283200","https://openalex.org/W2079875740","https://openalex.org/W2081781433","https://openalex.org/W2090628795","https://openalex.org/W2096525273","https://openalex.org/W2101647774","https://openalex.org/W2107572678","https://openalex.org/W2110114082","https://openalex.org/W2113777491","https://openalex.org/W2118258530","https://openalex.org/W2123783513","https://openalex.org/W2126176298","https://openalex.org/W2128601422","https://openalex.org/W2129075935","https://openalex.org/W2131848047","https://openalex.org/W2133938042","https://openalex.org/W2135971687","https://openalex.org/W2137726543","https://openalex.org/W2605068739","https://openalex.org/W3124353295","https://openalex.org/W3169916975","https://openalex.org/W4233060585","https://openalex.org/W4238718120","https://openalex.org/W4242729757"],"related_works":["https://openalex.org/W4250821095","https://openalex.org/W4301217393","https://openalex.org/W2267058868","https://openalex.org/W2922064259","https://openalex.org/W2742949799","https://openalex.org/W2799210984","https://openalex.org/W1982455124","https://openalex.org/W1987748328","https://openalex.org/W1497653608","https://openalex.org/W2015932315"],"abstract_inverted_index":{"http://www.wholecellsimdb.org":[0],"SOURCE":[1],"CODE":[2],"REPOSITORY:":[3],"URL:":[4],"http://github.com/CovertLab/WholeCellSimDB.":[5]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":8},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":6},{"year":2015,"cited_by_count":3}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
