{"id":"https://openalex.org/W2485914614","doi":"https://doi.org/10.1109/tbme.2016.2591960","title":"Guidelines for Reproducibly Building and Simulating Systems Biology Models","display_name":"Guidelines for Reproducibly Building and Simulating Systems Biology Models","publication_year":2016,"publication_date":"2016-07-18","ids":{"openalex":"https://openalex.org/W2485914614","doi":"https://doi.org/10.1109/tbme.2016.2591960","mag":"2485914614","pmid":"https://pubmed.ncbi.nlm.nih.gov/27429432"},"language":"en","primary_location":{"id":"doi:10.1109/tbme.2016.2591960","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tbme.2016.2591960","pdf_url":null,"source":{"id":"https://openalex.org/S5240358","display_name":"IEEE Transactions on Biomedical Engineering","issn_l":"0018-9294","issn":["0018-9294","1558-2531"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Biomedical Engineering","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5131863","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, WA, USA"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of Washington, Seattle, WA, USA","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066362880","display_name":"Arthur P. Goldberg","orcid":"https://orcid.org/0000-0003-2772-1484"},"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":false,"raw_author_name":"Arthur P. Goldberg","raw_affiliation_strings":["Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai"],"affiliations":[{"raw_affiliation_string":"Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai","institution_ids":["https://openalex.org/I98704320"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5016750554","display_name":"Jonathan R. Karr","orcid":"https://orcid.org/0000-0002-2605-5080"},"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":false,"raw_author_name":"Jonathan R. Karr","raw_affiliation_strings":["Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai"],"affiliations":[{"raw_affiliation_string":"Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai","institution_ids":["https://openalex.org/I98704320"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5035478017"],"corresponding_institution_ids":["https://openalex.org/I201448701"],"apc_list":null,"apc_paid":null,"fwci":2.6146,"has_fulltext":false,"cited_by_count":31,"citation_normalized_percentile":{"value":0.89860159,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"63","issue":"10","first_page":"2015","last_page":"2020"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9968000054359436,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9968000054359436,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9951000213623047,"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":0.9837999939918518,"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":0.47708186507225037},{"id":"https://openalex.org/keywords/systems-engineering","display_name":"Systems engineering","score":0.3629712164402008},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.32828736305236816},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.27585935592651367}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.47708186507225037},{"id":"https://openalex.org/C201995342","wikidata":"https://www.wikidata.org/wiki/Q682496","display_name":"Systems engineering","level":1,"score":0.3629712164402008},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.32828736305236816},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.27585935592651367}],"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":"D003584","descriptor_name":"Cytological Techniques","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003584","descriptor_name":"Cytological Techniques","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003584","descriptor_name":"Cytological Techniques","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":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":"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":"D045704","descriptor_name":"Mycoplasma genitalium","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D045704","descriptor_name":"Mycoplasma genitalium","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D045704","descriptor_name":"Mycoplasma genitalium","qualifier_ui":"Q000166","qualifier_name":"cytology","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},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1109/tbme.2016.2591960","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tbme.2016.2591960","pdf_url":null,"source":{"id":"https://openalex.org/S5240358","display_name":"IEEE Transactions on Biomedical Engineering","issn_l":"0018-9294","issn":["0018-9294","1558-2531"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Biomedical Engineering","raw_type":"journal-article"},{"id":"pmid:27429432","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27429432","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":"IEEE transactions on bio-medical engineering","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:5131863","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5131863","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"IEEE Trans Biomed Eng","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:5131863","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5131863","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"IEEE Trans Biomed Eng","raw_type":"Text"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4052807473","display_name":null,"funder_award_id":"1548123","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6178872503","display_name":null,"funder_award_id":"1355909","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7476727123","display_name":null,"funder_award_id":"R01 GM081070","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":52,"referenced_works":["https://openalex.org/W836474583","https://openalex.org/W1518437340","https://openalex.org/W1862398452","https://openalex.org/W1971000143","https://openalex.org/W1972510991","https://openalex.org/W1972571116","https://openalex.org/W1974948521","https://openalex.org/W1988888548","https://openalex.org/W2034159788","https://openalex.org/W2034256728","https://openalex.org/W2060184615","https://openalex.org/W2069157810","https://openalex.org/W2078355959","https://openalex.org/W2081781433","https://openalex.org/W2090120515","https://openalex.org/W2101647774","https://openalex.org/W2115309705","https://openalex.org/W2123184511","https://openalex.org/W2123783513","https://openalex.org/W2125615370","https://openalex.org/W2129075935","https://openalex.org/W2133938042","https://openalex.org/W2145154883","https://openalex.org/W2145435867","https://openalex.org/W2147814423","https://openalex.org/W2150386276","https://openalex.org/W2150908245","https://openalex.org/W2151952022","https://openalex.org/W2154268795","https://openalex.org/W2158794422","https://openalex.org/W2168103533","https://openalex.org/W2170122529","https://openalex.org/W2170335512","https://openalex.org/W2183271564","https://openalex.org/W2184251399","https://openalex.org/W2186373804","https://openalex.org/W2290761674","https://openalex.org/W2296636214","https://openalex.org/W2330167820","https://openalex.org/W2330740149","https://openalex.org/W2350901857","https://openalex.org/W2411390783","https://openalex.org/W2441893520","https://openalex.org/W3106335109","https://openalex.org/W4230574494","https://openalex.org/W4233630467","https://openalex.org/W4240433289","https://openalex.org/W4241340390","https://openalex.org/W4241685680","https://openalex.org/W4285719527","https://openalex.org/W6686208936","https://openalex.org/W6705588645"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2082860237","https://openalex.org/W2119695867","https://openalex.org/W2130076355","https://openalex.org/W1990804418","https://openalex.org/W1993764875","https://openalex.org/W2046158694","https://openalex.org/W2788277189","https://openalex.org/W1971568933","https://openalex.org/W2013243191"],"abstract_inverted_index":{"We":[0],"anticipate":[1],"that":[2],"these":[3],"new":[4],"standards":[5],"and":[6,14],"software":[7],"will":[8],"enable":[9],"researchers":[10],"to":[11],"reproducibly":[12],"build":[13],"simulate":[15],"more":[16],"complex":[17],"models,":[18],"including":[19],"WC":[20],"models.":[21]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":7},{"year":2019,"cited_by_count":6},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":6},{"year":2016,"cited_by_count":1}],"updated_date":"2026-04-09T08:11:56.329763","created_date":"2025-10-10T00:00:00"}
