{"id":"https://openalex.org/W2584007713","doi":"https://doi.org/10.1371/journal.pcbi.1005351","title":"ASPASIA: A toolkit for evaluating the effects of biological interventions on SBML model behaviour","display_name":"ASPASIA: A toolkit for evaluating the effects of biological interventions on SBML model behaviour","publication_year":2017,"publication_date":"2017-02-03","ids":{"openalex":"https://openalex.org/W2584007713","doi":"https://doi.org/10.1371/journal.pcbi.1005351","mag":"2584007713","pmid":"https://pubmed.ncbi.nlm.nih.gov/28158307"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1005351","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1005351","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1005351&type=printable","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://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1005351&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5074373302","display_name":"Stephanie Evans","orcid":"https://orcid.org/0000-0002-2345-5249"},"institutions":[{"id":"https://openalex.org/I52099693","display_name":"University of York","ror":"https://ror.org/04m01e293","country_code":"GB","type":"education","lineage":["https://openalex.org/I52099693"]},{"id":"https://openalex.org/I69768126","display_name":"Hull York Medical School","ror":"https://ror.org/0003e4m70","country_code":"GB","type":"education","lineage":["https://openalex.org/I69768126"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Stephanie Evans","raw_affiliation_strings":["Centre for Immunology and Infection, Department of Biology and Hull York Medical School, University of York, York, United Kingdom","Department of Electronics, University of York, York, United Kingdom","York Computational Immunology Lab, University of York, York, United Kingdom"],"raw_orcid":"https://orcid.org/0000-0002-2345-5249","affiliations":[{"raw_affiliation_string":"Centre for Immunology and Infection, Department of Biology and Hull York Medical School, University of York, York, United Kingdom","institution_ids":["https://openalex.org/I69768126","https://openalex.org/I52099693"]},{"raw_affiliation_string":"Department of Electronics, University of York, York, United Kingdom","institution_ids":["https://openalex.org/I52099693"]},{"raw_affiliation_string":"York Computational Immunology Lab, University of York, York, United Kingdom","institution_ids":["https://openalex.org/I52099693"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024360871","display_name":"Kieran Alden","orcid":"https://orcid.org/0000-0003-4411-1776"},"institutions":[{"id":"https://openalex.org/I52099693","display_name":"University of York","ror":"https://ror.org/04m01e293","country_code":"GB","type":"education","lineage":["https://openalex.org/I52099693"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Kieran Alden","raw_affiliation_strings":["Department of Electronics, University of York, York, United Kingdom","York Computational Immunology Lab, University of York, York, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electronics, University of York, York, United Kingdom","institution_ids":["https://openalex.org/I52099693"]},{"raw_affiliation_string":"York Computational Immunology Lab, University of York, York, United Kingdom","institution_ids":["https://openalex.org/I52099693"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069575948","display_name":"L. Cucurull-Sanchez","orcid":"https://orcid.org/0000-0002-2397-6490"},"institutions":[{"id":"https://openalex.org/I2800110054","display_name":"Age UK","ror":"https://ror.org/050x9d346","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I2800110054"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Lourdes Cucurull-Sanchez","raw_affiliation_strings":["GSK Medicines Research Centre, Stevenage, United Kingdom"],"raw_orcid":"https://orcid.org/0000-0002-2397-6490","affiliations":[{"raw_affiliation_string":"GSK Medicines Research Centre, Stevenage, United Kingdom","institution_ids":["https://openalex.org/I2800110054"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026727801","display_name":"Christopher Larminie","orcid":"https://orcid.org/0000-0003-4986-1824"},"institutions":[{"id":"https://openalex.org/I2800110054","display_name":"Age UK","ror":"https://ror.org/050x9d346","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I2800110054"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Christopher Larminie","raw_affiliation_strings":["GSK Medicines Research Centre, Stevenage, United Kingdom"],"raw_orcid":"https://orcid.org/0000-0003-4986-1824","affiliations":[{"raw_affiliation_string":"GSK Medicines Research Centre, Stevenage, United Kingdom","institution_ids":["https://openalex.org/I2800110054"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048352835","display_name":"Mark Coles","orcid":"https://orcid.org/0000-0001-8079-9358"},"institutions":[{"id":"https://openalex.org/I52099693","display_name":"University of York","ror":"https://ror.org/04m01e293","country_code":"GB","type":"education","lineage":["https://openalex.org/I52099693"]},{"id":"https://openalex.org/I69768126","display_name":"Hull York Medical School","ror":"https://ror.org/0003e4m70","country_code":"GB","type":"education","lineage":["https://openalex.org/I69768126"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Mark C. Coles","raw_affiliation_strings":["Centre for Immunology and Infection, Department of Biology and Hull York Medical School, University of York, York, United Kingdom","York Computational Immunology Lab, University of York, York, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Immunology and Infection, Department of Biology and Hull York Medical School, University of York, York, United Kingdom","institution_ids":["https://openalex.org/I69768126","https://openalex.org/I52099693"]},{"raw_affiliation_string":"York Computational Immunology Lab, University of York, York, United Kingdom","institution_ids":["https://openalex.org/I52099693"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007182284","display_name":"Marika C. Kullberg","orcid":null},"institutions":[{"id":"https://openalex.org/I52099693","display_name":"University of York","ror":"https://ror.org/04m01e293","country_code":"GB","type":"education","lineage":["https://openalex.org/I52099693"]},{"id":"https://openalex.org/I69768126","display_name":"Hull York Medical School","ror":"https://ror.org/0003e4m70","country_code":"GB","type":"education","lineage":["https://openalex.org/I69768126"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Marika C. Kullberg","raw_affiliation_strings":["Centre for Immunology and Infection, Department of Biology and Hull York Medical School, University of York, York, United Kingdom","York Computational Immunology Lab, University of York, York, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Immunology and Infection, Department of Biology and Hull York Medical School, University of York, York, United Kingdom","institution_ids":["https://openalex.org/I69768126","https://openalex.org/I52099693"]},{"raw_affiliation_string":"York Computational Immunology Lab, University of York, York, United Kingdom","institution_ids":["https://openalex.org/I52099693"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5080582720","display_name":"Jon Timmis","orcid":"https://orcid.org/0000-0003-1055-0471"},"institutions":[{"id":"https://openalex.org/I52099693","display_name":"University of York","ror":"https://ror.org/04m01e293","country_code":"GB","type":"education","lineage":["https://openalex.org/I52099693"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Jon Timmis","raw_affiliation_strings":["Department of Electronics, University of York, York, United Kingdom","York Computational Immunology Lab, University of York, York, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electronics, University of York, York, United Kingdom","institution_ids":["https://openalex.org/I52099693"]},{"raw_affiliation_string":"York Computational Immunology Lab, University of York, York, United Kingdom","institution_ids":["https://openalex.org/I52099693"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5007182284","https://openalex.org/A5024360871"],"corresponding_institution_ids":["https://openalex.org/I52099693","https://openalex.org/I69768126"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2123,"currency":"EUR","value_usd":2289},"fwci":0.3364,"has_fulltext":true,"cited_by_count":5,"citation_normalized_percentile":{"value":0.58842801,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":95},"biblio":{"volume":"13","issue":"2","first_page":"e1005351","last_page":"e1005351"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9998999834060669,"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":0.9998999834060669,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.993399977684021,"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":0.9864000082015991,"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/sbml","display_name":"SBML","score":0.9941020607948303},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.69489985704422},{"id":"https://openalex.org/keywords/markup-language","display_name":"Markup language","score":0.6749436855316162},{"id":"https://openalex.org/keywords/solver","display_name":"Solver","score":0.5696008801460266},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.5418096780776978},{"id":"https://openalex.org/keywords/computational-model","display_name":"Computational model","score":0.48427051305770874},{"id":"https://openalex.org/keywords/sensitivity","display_name":"Sensitivity (control systems)","score":0.4389493465423584},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.42674311995506287},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3427530527114868},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.26805320382118225},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.26007941365242004},{"id":"https://openalex.org/keywords/simulation","display_name":"Simulation","score":0.2530916929244995},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.22745797038078308},{"id":"https://openalex.org/keywords/xml","display_name":"XML","score":0.11506670713424683},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.08716455101966858}],"concepts":[{"id":"https://openalex.org/C87186988","wikidata":"https://www.wikidata.org/wiki/Q452197","display_name":"SBML","level":4,"score":0.9941020607948303},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.69489985704422},{"id":"https://openalex.org/C45874996","wikidata":"https://www.wikidata.org/wiki/Q37045","display_name":"Markup language","level":3,"score":0.6749436855316162},{"id":"https://openalex.org/C2778770139","wikidata":"https://www.wikidata.org/wiki/Q1966904","display_name":"Solver","level":2,"score":0.5696008801460266},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.5418096780776978},{"id":"https://openalex.org/C66024118","wikidata":"https://www.wikidata.org/wiki/Q1122506","display_name":"Computational model","level":2,"score":0.48427051305770874},{"id":"https://openalex.org/C21200559","wikidata":"https://www.wikidata.org/wiki/Q7451068","display_name":"Sensitivity (control systems)","level":2,"score":0.4389493465423584},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.42674311995506287},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3427530527114868},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.26805320382118225},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.26007941365242004},{"id":"https://openalex.org/C44154836","wikidata":"https://www.wikidata.org/wiki/Q45045","display_name":"Simulation","level":1,"score":0.2530916929244995},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.22745797038078308},{"id":"https://openalex.org/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"score":0.11506670713424683},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.08716455101966858},{"id":"https://openalex.org/C24326235","wikidata":"https://www.wikidata.org/wiki/Q126095","display_name":"Electronic engineering","level":1,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"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":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","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":"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":9,"locations":[{"id":"doi:10.1371/journal.pcbi.1005351","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1005351","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1005351&type=printable","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:28158307","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28158307","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:eprints.whiterose.ac.uk:112730","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4306400854","display_name":"White Rose Research Online (University of Leeds, The University of Sheffield, University of York)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2800616092","host_organization_name":"White Rose University Consortium","host_organization_lineage":["https://openalex.org/I2800616092"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"PeerReviewed"},{"id":"pmh:oai:sure.sunderland.ac.uk:10847","is_oa":false,"landing_page_url":"http://sure.sunderland.ac.uk/view/creators/Evans=3AStephanie=3A=3A.html>,","pdf_url":null,"source":{"id":"https://openalex.org/S4306402295","display_name":"Sunderland Repository (University of Sunderland)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I5728261","host_organization_name":"University of Sunderland","host_organization_lineage":["https://openalex.org/I5728261"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"PeerReviewed"},{"id":"pmh:oai:RePEc:plo:pcbi00:1005351","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005351","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},{"id":"pmh:oai:doaj.org/article:3c1ae83685e248029bd5fb56d064a54a","is_oa":true,"landing_page_url":"https://doaj.org/article/3c1ae83685e248029bd5fb56d064a54a","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 13, Iss 2, p e1005351 (2017)","raw_type":"article"},{"id":"pmh:oai:figshare.com:article/4619767","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/ASPASIA_A_toolkit_for_evaluating_the_effects_of_biological_interventions_on_SBML_model_behaviour/4619767","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"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"},{"id":"pmh:oai:ora.ox.ac.uk:uuid:9572a716-e758-4750-9224-a48044e3b42c","is_oa":true,"landing_page_url":"https://ora.ox.ac.uk/objects/uuid:9572a716-e758-4750-9224-a48044e3b42c","pdf_url":null,"source":{"id":"https://openalex.org/S4306402636","display_name":"Oxford University Research Archive (ORA) (University of Oxford)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I40120149","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/I40120149"],"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":"Journal article"},{"id":"pmh:oai:pubmedcentral.nih.gov:5315406","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5315406","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1005351","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1005351","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1005351&type=printable","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":[{"display_name":"Partnerships for the goals","score":0.4300000071525574,"id":"https://metadata.un.org/sdg/17"}],"awards":[{"id":"https://openalex.org/G5573745944","display_name":"Institutional Strategic Support Fund 2011/12.","funder_award_id":"097829","funder_id":"https://openalex.org/F4320311904","funder_display_name":"Wellcome Trust"},{"id":"https://openalex.org/G573911661","display_name":null,"funder_award_id":"097829","funder_id":"https://openalex.org/F4320307874","funder_display_name":"Wellcome"},{"id":"https://openalex.org/G8243662396","display_name":"Systems biology approach to understand inflammation mechanisms active in in the gastrointestinal tract","funder_award_id":"BB/K501487/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"}],"funders":[{"id":"https://openalex.org/F4320307874","display_name":"Wellcome","ror":"https://ror.org/029chgv08"},{"id":"https://openalex.org/F4320311904","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08"},{"id":"https://openalex.org/F4320320005","display_name":"Royal Academy of Engineering","ror":"https://ror.org/0526snb40"},{"id":"https://openalex.org/F4320320006","display_name":"Royal Society","ror":"https://ror.org/03wnrjx87"},{"id":"https://openalex.org/F4320332167","display_name":"Directorate for Biological Sciences","ror":"https://ror.org/001xhss06"},{"id":"https://openalex.org/F4320334629","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2584007713.pdf","grobid_xml":"https://content.openalex.org/works/W2584007713.grobid-xml"},"referenced_works_count":26,"referenced_works":["https://openalex.org/W221263235","https://openalex.org/W1786929561","https://openalex.org/W1922774027","https://openalex.org/W1979034309","https://openalex.org/W2016803695","https://openalex.org/W2017893786","https://openalex.org/W2038669746","https://openalex.org/W2051148575","https://openalex.org/W2064625208","https://openalex.org/W2071019594","https://openalex.org/W2071471925","https://openalex.org/W2072449713","https://openalex.org/W2095649879","https://openalex.org/W2104759754","https://openalex.org/W2105379381","https://openalex.org/W2114355189","https://openalex.org/W2117344541","https://openalex.org/W2123783513","https://openalex.org/W2128330762","https://openalex.org/W2132635773","https://openalex.org/W2150908245","https://openalex.org/W2152803686","https://openalex.org/W2154387393","https://openalex.org/W2156730317","https://openalex.org/W4206280824","https://openalex.org/W4237151101"],"related_works":["https://openalex.org/W2150908245","https://openalex.org/W2735157934","https://openalex.org/W3091139413","https://openalex.org/W2152827261","https://openalex.org/W2792182172","https://openalex.org/W4225469991","https://openalex.org/W2465447782","https://openalex.org/W4281744058","https://openalex.org/W4295136412","https://openalex.org/W2013641696"],"abstract_inverted_index":{"A":[0],"calibrated":[1],"computational":[2],"model":[3,32,38,55,203],"reflects":[4],"behaviours":[5],"that":[6,29,85,209,251],"are":[7,152],"expected":[8],"or":[9],"observed":[10],"in":[11,90,106,193,198],"a":[12,16,37,40,48,80,87,133,147],"complex":[13],"system,":[14],"providing":[15],"baseline":[17],"upon":[18],"which":[19,187],"sensitivity":[20,158,164],"analysis":[21,159],"techniques":[22],"can":[23,113,143,240,265],"be":[24,58,130,144,191,241,266],"used":[25],"to":[26,129,165,228,243,247],"analyse":[27],"pathways":[28],"may":[30,57,190],"impact":[31,96],"responses.":[33],"However,":[34],"calibration":[35],"of":[36,149,172,204,211,220,231],"where":[39,146],"behaviour":[41,102],"depends":[42],"on":[43,60,100,255],"an":[44,97,123,201,235],"intervention":[45,67,98,252],"introduced":[46],"after":[47],"defined":[49],"time":[50,65],"point":[51],"is":[52,68,226],"difficult,":[53],"as":[54,122],"responses":[56],"dependent":[59],"the":[61,64,66,95,162,166,170,184,212,221,249,261],"conditions":[62],"at":[63],"applied.":[69],"We":[70],"present":[71],"ASPASIA":[72,112,197],"(Automated":[73],"Simulation":[74],"Parameter":[75],"Alteration":[76],"and":[77,115,156],"SensItivity":[78],"Analysis),":[79],"cross-platform,":[81],"open-source":[82],"Java":[83],"toolkit":[84],"addresses":[86],"key":[88],"deficiency":[89],"software":[91],"tools":[92],"for":[93,103],"understanding":[94],"has":[99,136,179],"system":[101,256],"models":[104,117,142,246],"specified":[105],"Systems":[107],"Biology":[108],"Markup":[109],"Language":[110],"(SBML).":[111],"generate":[114],"modify":[116],"using":[118,154,196],"SBML":[119,141,202],"solver":[120],"output":[121],"initial":[124],"parameter":[125,150],"set,":[126],"allowing":[127],"interventions":[128],"applied":[131,242],"once":[132],"steady":[134],"state":[135],"been":[137],"reached.":[138],"Additionally,":[139],"multiple":[140],"generated":[145,180],"subset":[148],"values":[151],"perturbed":[153],"local":[155],"global":[157],"techniques,":[160],"revealing":[161],"model's":[163],"intervention.":[167],"To":[168],"illustrate":[169],"capabilities":[171],"ASPASIA,":[173,258],"we":[174,207],"demonstrate":[175],"how":[176],"this":[177],"tool":[178],"novel":[181],"hypotheses":[182],"regarding":[183],"mechanisms":[185],"by":[186],"Th17-cell":[188,205],"plasticity":[189],"controlled":[192],"vivo.":[194],"By":[195],"conjunction":[199],"with":[200],"polarisation,":[206],"predict":[208,248],"promotion":[210],"Th1-associated":[213],"transcription":[214,223],"factor":[215,224],"T-bet,":[216],"rather":[217],"than":[218],"inhibition":[219],"Th17-associated":[222],"ROR\u03b3t,":[225],"sufficient":[227],"drive":[229],"switching":[230],"Th17":[232],"cells":[233],"towards":[234],"IFN-\u03b3-producing":[236],"phenotype.":[237],"Our":[238],"approach":[239],"all":[244],"SBML-encoded":[245],"effect":[250],"strategies":[253],"have":[254],"behaviour.":[257],"released":[259],"under":[260],"Artistic":[262],"License":[263],"(2.0),":[264],"downloaded":[267],"from":[268],"http://www.york.ac.uk/ycil/software.":[269]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":1}],"updated_date":"2026-05-09T13:55:54.758798","created_date":"2025-10-10T00:00:00"}