{"id":"https://openalex.org/W2807821194","doi":"https://doi.org/10.1371/journal.pcbi.1006220","title":"Tellurium notebooks\u2014An environment for reproducible dynamical modeling in systems biology","display_name":"Tellurium notebooks\u2014An environment for reproducible dynamical modeling in systems biology","publication_year":2018,"publication_date":"2018-06-15","ids":{"openalex":"https://openalex.org/W2807821194","doi":"https://doi.org/10.1371/journal.pcbi.1006220","mag":"2807821194","pmid":"https://pubmed.ncbi.nlm.nih.gov/29906293"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1006220","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1006220","pdf_url":"https://storage.googleapis.com/plos-corpus-prod/10.1371/journal.pcbi.1006220/2/pcbi.1006220.pdf?X-Goog-Algorithm=GOOG4-RSA-SHA256&X-Goog-Credential=wombat-sa%40plos-prod.iam.gserviceaccount.com%2F20210215%2Fauto%2Fstorage%2Fgoog4_request&X-Goog-Date=20210215T183309Z&X-Goog-Expires=3600&X-Goog-SignedHeaders=host&X-Goog-Signature=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","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://storage.googleapis.com/plos-corpus-prod/10.1371/journal.pcbi.1006220/2/pcbi.1006220.pdf?X-Goog-Algorithm=GOOG4-RSA-SHA256&X-Goog-Credential=wombat-sa%40plos-prod.iam.gserviceaccount.com%2F20210215%2Fauto%2Fstorage%2Fgoog4_request&X-Goog-Date=20210215T183309Z&X-Goog-Expires=3600&X-Goog-SignedHeaders=host&X-Goog-Signature=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","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5035478017","display_name":"Kyle Medley","orcid":"https://orcid.org/0000-0002-9135-0844"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"J. Kyle Medley","raw_affiliation_strings":["Department of Bioengineering, University of Washington, Seattle, Washington, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-9135-0844","affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of Washington, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009998609","display_name":"Kiri Choi","orcid":"https://orcid.org/0000-0002-0156-8410"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Kiri Choi","raw_affiliation_strings":["Department of Bioengineering, University of Washington, Seattle, Washington, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-0156-8410","affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of Washington, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012727458","display_name":"Matthias K\u00f6nig","orcid":"https://orcid.org/0000-0003-1725-179X"},"institutions":[{"id":"https://openalex.org/I39343248","display_name":"Humboldt-Universit\u00e4t zu Berlin","ror":"https://ror.org/01hcx6992","country_code":"DE","type":"education","lineage":["https://openalex.org/I39343248"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Matthias K\u00f6nig","raw_affiliation_strings":["Institute for Theoretical Biology, Humboldt University of Berlin, Berlin, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Theoretical Biology, Humboldt University of Berlin, Berlin, Germany","institution_ids":["https://openalex.org/I39343248"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067339679","display_name":"Lucian P. Smith","orcid":"https://orcid.org/0000-0001-7002-6386"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Lucian Smith","raw_affiliation_strings":["Department of Bioengineering, University of Washington, Seattle, Washington, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of Washington, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030469432","display_name":"Stanley Gu","orcid":null},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Stanley Gu","raw_affiliation_strings":["Department of Bioengineering, University of Washington, Seattle, Washington, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of Washington, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111881591","display_name":"Joseph L. Hellerstein","orcid":null},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Joseph Hellerstein","raw_affiliation_strings":["eScience Institute, University of Washington, Seattle, Washington, United States of America"],"raw_orcid":"https://orcid.org/0000-0003-1725-179X","affiliations":[{"raw_affiliation_string":"eScience Institute, University of Washington, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058017696","display_name":"Stuart C. Sealfon","orcid":"https://orcid.org/0000-0001-5791-1217"},"institutions":[{"id":"https://openalex.org/I98704320","display_name":"Icahn School of Medicine at Mount Sinai","ror":"https://ror.org/04a9tmd77","country_code":"US","type":"education","lineage":["https://openalex.org/I1320796813","https://openalex.org/I98704320"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Stuart C. Sealfon","raw_affiliation_strings":["Department of Neurology and Center for Advanced Research on Diagnostic Assays Icahn School of Medicine at Mount Sinai, New York, New York, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Neurology and Center for Advanced Research on Diagnostic Assays Icahn School of Medicine at Mount Sinai, New York, New York, United States of America","institution_ids":["https://openalex.org/I98704320"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5044484291","display_name":"Herbert M. Sauro","orcid":"https://orcid.org/0000-0002-3659-6817"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Herbert M. Sauro","raw_affiliation_strings":["Department of Bioengineering, University of Washington, Seattle, Washington, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-3659-6817","affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of Washington, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I201448701"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5009998609","https://openalex.org/A5012727458","https://openalex.org/A5030469432","https://openalex.org/A5035478017","https://openalex.org/A5044484291","https://openalex.org/A5058017696","https://openalex.org/A5067339679","https://openalex.org/A5111881591"],"corresponding_institution_ids":["https://openalex.org/I201448701","https://openalex.org/I39343248","https://openalex.org/I98704320"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":2.8868,"has_fulltext":false,"cited_by_count":60,"citation_normalized_percentile":{"value":0.91928827,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"14","issue":"6","first_page":"e1006220","last_page":"e1006220"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9987999796867371,"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":0.9987999796867371,"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/T11986","display_name":"Scientific Computing and Data Management","score":0.9950000047683716,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},{"id":"https://openalex.org/T11764","display_name":"Evolution and Genetic Dynamics","score":0.993399977684021,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/python","display_name":"Python (programming language)","score":0.8970299959182739},{"id":"https://openalex.org/keywords/reuse","display_name":"Reuse","score":0.8417230248451233},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7654134035110474},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5763568878173828},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.4967980682849884},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.32414180040359497},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.19409394264221191},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.10445275902748108}],"concepts":[{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.8970299959182739},{"id":"https://openalex.org/C206588197","wikidata":"https://www.wikidata.org/wiki/Q846574","display_name":"Reuse","level":2,"score":0.8417230248451233},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7654134035110474},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5763568878173828},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.4967980682849884},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.32414180040359497},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.19409394264221191},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.10445275902748108},{"id":"https://openalex.org/C548081761","wikidata":"https://www.wikidata.org/wiki/Q180388","display_name":"Waste management","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000295","qualifier_name":"instrumentation","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000295","qualifier_name":"instrumentation","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000295","qualifier_name":"instrumentation","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":7,"locations":[{"id":"doi:10.1371/journal.pcbi.1006220","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1006220","pdf_url":"https://storage.googleapis.com/plos-corpus-prod/10.1371/journal.pcbi.1006220/2/pcbi.1006220.pdf?X-Goog-Algorithm=GOOG4-RSA-SHA256&X-Goog-Credential=wombat-sa%40plos-prod.iam.gserviceaccount.com%2F20210215%2Fauto%2Fstorage%2Fgoog4_request&X-Goog-Date=20210215T183309Z&X-Goog-Expires=3600&X-Goog-SignedHeaders=host&X-Goog-Signature=550f8be51305cb41666622b5990fc72fe8c3f2c5b544c09849570aa5036ecf73b4322d0f20fd926031c9dfa86aa066f271f155d4d9e72573ec5f2f9b0e2cafb76a936642c56d82c5551840aadced939bc92942f268723e45808c8098698ee8a6c1bfb35173eaee41ebbc6746d17ad3c749603ecf2266757603fddc1a9161a0d5f49271e6b22f72ae8e0d7541affef3a54104e0f377fec20685cc4659edb9d4be305339004f6748cb04a2c2639f80c10407d9fb83de35d59c939d6132a8efae5599e7c7c3612b8d2066a1b2bd2ed6f7b122f1c2e49859cce0a09272bd8bbcfe7e7a6079263b2003a03562038ed88f85823d6c23e6ca7bf84d6a4012383bd24666","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:29906293","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29906293","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:RePEc:plo:pcbi00:1006220","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006220","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":null,"raw_type":"article"},{"id":"pmh:oai:europepmc.org:4985734","is_oa":true,"landing_page_url":"http://europepmc.org/pmc/articles/PMC6021116","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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:6021116","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6021116","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:154705802d6649ccbea844e4c4f26440","is_oa":true,"landing_page_url":"https://doaj.org/article/154705802d6649ccbea844e4c4f26440","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 14, Iss 6, p e1006220 (2018)","raw_type":"article"},{"id":"pmh:oai:figshare.com:article/6553430","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/Tellurium_notebooks_An_environment_for_reproducible_dynamical_modeling_in_systems_biology/6553430","pdf_url":null,"source":{"id":"https://openalex.org/S4306402621","display_name":"INDIGO (University of Illinois at Chicago)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I39422238","host_organization_name":"University of Illinois Chicago","host_organization_lineage":["https://openalex.org/I39422238"],"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":"Dataset"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1006220","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1006220","pdf_url":"https://storage.googleapis.com/plos-corpus-prod/10.1371/journal.pcbi.1006220/2/pcbi.1006220.pdf?X-Goog-Algorithm=GOOG4-RSA-SHA256&X-Goog-Credential=wombat-sa%40plos-prod.iam.gserviceaccount.com%2F20210215%2Fauto%2Fstorage%2Fgoog4_request&X-Goog-Date=20210215T183309Z&X-Goog-Expires=3600&X-Goog-SignedHeaders=host&X-Goog-Signature=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","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2150262284","display_name":null,"funder_award_id":"HHSN266200500021C","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G3345066367","display_name":null,"funder_award_id":"GM081070-01","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4125070280","display_name":null,"funder_award_id":"U19 AI117873","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G4796235692","display_name":null,"funder_award_id":"U19 AI117873","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5475673595","display_name":null,"funder_award_id":"U01 HL122199","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"},{"id":"https://openalex.org/G5539405233","display_name":null,"funder_award_id":"GM123032-01A1","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5708185203","display_name":null,"funder_award_id":"2013-10-29","funder_id":"https://openalex.org/F4320306151","funder_display_name":"Alfred P. Sloan Foundation"},{"id":"https://openalex.org/G6957213843","display_name":null,"funder_award_id":"HHSN266200500026C","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G8352764473","display_name":null,"funder_award_id":"031L0054","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G8633427868","display_name":null,"funder_award_id":"U01HL122199-02","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"}],"funders":[{"id":"https://openalex.org/F4320306151","display_name":"Alfred P. Sloan Foundation","ror":"https://ror.org/052csg198"},{"id":"https://openalex.org/F4320306202","display_name":"Gordon and Betty Moore Foundation","ror":"https://ror.org/006wxqw41"},{"id":"https://openalex.org/F4320321114","display_name":"Bundesministerium f\u00fcr Bildung und Forschung","ror":"https://ror.org/04pz7b180"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320332178","display_name":"National Institute of Standards and Technology","ror":"https://ror.org/05xpvk416"},{"id":"https://openalex.org/F4320337338","display_name":"National Heart, Lung, and Blood Institute","ror":"https://ror.org/012pb6c26"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":83,"referenced_works":["https://openalex.org/W96334552","https://openalex.org/W115452890","https://openalex.org/W1596279130","https://openalex.org/W1645305843","https://openalex.org/W1974143589","https://openalex.org/W2008985174","https://openalex.org/W2010985163","https://openalex.org/W2034375827","https://openalex.org/W2036318837","https://openalex.org/W2038264484","https://openalex.org/W2044889656","https://openalex.org/W2048465561","https://openalex.org/W2051959027","https://openalex.org/W2063731290","https://openalex.org/W2067833766","https://openalex.org/W2070441922","https://openalex.org/W2078734278","https://openalex.org/W2081781433","https://openalex.org/W2092077482","https://openalex.org/W2096492216","https://openalex.org/W2096951208","https://openalex.org/W2097240335","https://openalex.org/W2097319997","https://openalex.org/W2102653059","https://openalex.org/W2106320930","https://openalex.org/W2107062718","https://openalex.org/W2107974267","https://openalex.org/W2114124738","https://openalex.org/W2117364474","https://openalex.org/W2119510512","https://openalex.org/W2123783513","https://openalex.org/W2125615370","https://openalex.org/W2126987356","https://openalex.org/W2132817950","https://openalex.org/W2133938042","https://openalex.org/W2136482257","https://openalex.org/W2136970290","https://openalex.org/W2145154883","https://openalex.org/W2145435867","https://openalex.org/W2150908245","https://openalex.org/W2152922122","https://openalex.org/W2153100796","https://openalex.org/W2155418451","https://openalex.org/W2160751597","https://openalex.org/W2163493106","https://openalex.org/W2168103533","https://openalex.org/W2170032647","https://openalex.org/W2170122529","https://openalex.org/W2173310660","https://openalex.org/W2183271564","https://openalex.org/W2247294682","https://openalex.org/W2258281343","https://openalex.org/W2285930875","https://openalex.org/W2320969362","https://openalex.org/W2345593393","https://openalex.org/W2413797628","https://openalex.org/W2419000639","https://openalex.org/W2474648852","https://openalex.org/W2485914614","https://openalex.org/W2499888240","https://openalex.org/W2513008430","https://openalex.org/W2525009482","https://openalex.org/W2526123986","https://openalex.org/W2531582823","https://openalex.org/W2560096094","https://openalex.org/W2560264276","https://openalex.org/W2580869787","https://openalex.org/W2586192494","https://openalex.org/W2607963885","https://openalex.org/W2747676177","https://openalex.org/W2791048175","https://openalex.org/W2793993424","https://openalex.org/W2950427239","https://openalex.org/W2951092176","https://openalex.org/W2981018396","https://openalex.org/W3145460265","https://openalex.org/W4240433289","https://openalex.org/W4241340390","https://openalex.org/W4253238405","https://openalex.org/W4386772731","https://openalex.org/W4399649310","https://openalex.org/W6877696872","https://openalex.org/W6999788484"],"related_works":["https://openalex.org/W2341492732","https://openalex.org/W3187193180","https://openalex.org/W106542691","https://openalex.org/W1699080303","https://openalex.org/W4297799326","https://openalex.org/W3116064965","https://openalex.org/W4287027380","https://openalex.org/W3193760048","https://openalex.org/W4285822516","https://openalex.org/W2505261959"],"abstract_inverted_index":{"The":[0],"considerable":[1],"difficulty":[2],"encountered":[3],"in":[4,80],"reproducing":[5],"the":[6,69,141,161,167,181],"results":[7],"of":[8,17,160,183,193,199,202],"published":[9],"dynamical":[10,46],"models":[11,47,50,95,163,194],"limits":[12],"validation,":[13],"exploration":[14],"and":[15,40,48,62,84,91,105,130,164,170,186,191,209],"reuse":[16,192],"this":[18,26],"increasingly":[19],"large":[20],"biomedical":[21],"research":[22],"resource.":[23],"To":[24],"address":[25],"problem,":[27],"we":[28],"have":[29],"developed":[30],"Tellurium":[31,108,136,203],"Notebook,":[32,109],"a":[33,54,110],"software":[34],"system":[35],"for":[36,76],"model":[37,74,78,102,206],"authoring,":[38],"simulation,":[39],"teaching":[41],"that":[42],"facilitates":[43],"building":[44],"reproducible":[45],"reusing":[49],"by":[51,123,144],"1)":[52],"providing":[53],"notebook":[55,147],"environment":[56],"which":[57],"allows":[58,189],"models,":[59],"Python":[60],"code,":[61],"narrative":[63],"to":[64,88,99,116,138,156,172],"be":[65],"intermixed,":[66],"2)":[67],"supporting":[68],"COMBINE":[70,127],"archive":[71],"format":[72,83],"during":[73],"development":[75,190],"capturing":[77],"information":[79],"an":[81],"exchangeable":[82],"3)":[85],"enabling":[86],"users":[87,155],"easily":[89],"simulate":[90],"edit":[92,157],"public":[93,97],"COMBINE-compliant":[94],"from":[96],"repositories":[98],"facilitate":[100],"studying":[101],"dynamics,":[103],"variants":[104],"test":[106],"cases.":[107],"Python-based":[111],"Jupyter-like":[112],"environment,":[113],"is":[114],"designed":[115],"seamlessly":[117],"inter-operate":[118],"with":[119],"these":[120],"community":[121],"standards":[122,128],"automating":[124],"conversion":[125],"between":[126],"formulations":[129],"corresponding":[131],"in-line,":[132,169],"human-readable":[133],"representations.":[134],"Thus,":[135],"brings":[137],"systems":[139,148],"biology":[140],"strategy":[142],"used":[143],"other":[145],"literate":[146],"such":[149],"as":[150],"Mathematica.":[151],"These":[152],"capabilities":[153],"allow":[154],"every":[158],"aspect":[159],"standards-compliant":[162],"simulations,":[165],"run":[166],"simulations":[168],"re-export":[171],"standard":[173],"formats.":[174],"We":[175],"provide":[176],"several":[177],"use":[178],"cases":[179],"illustrating":[180],"advantages":[182],"our":[184],"approach":[185],"how":[187],"it":[188],"without":[195],"requiring":[196],"technical":[197],"knowledge":[198],"standards.":[200],"Adoption":[201],"should":[204],"accelerate":[205],"development,":[207],"reproducibility":[208],"reuse.":[210]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":8},{"year":2023,"cited_by_count":7},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":10},{"year":2020,"cited_by_count":11},{"year":2019,"cited_by_count":9},{"year":2018,"cited_by_count":2}],"updated_date":"2026-07-08T08:33:18.762332","created_date":"2025-10-10T00:00:00"}
