{"id":"https://openalex.org/W2531582823","doi":"https://doi.org/10.1093/bioinformatics/btw812","title":"SED-ML web tools: generate, modify and export standard-compliant simulation studies","display_name":"SED-ML web tools: generate, modify and export standard-compliant simulation studies","publication_year":2016,"publication_date":"2016-12-24","ids":{"openalex":"https://openalex.org/W2531582823","doi":"https://doi.org/10.1093/bioinformatics/btw812","mag":"2531582823"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btw812","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw812","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/8/1253/25150427/btw812.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/33/8/1253/25150427/btw812.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5076617999","display_name":"Frank Bergmann","orcid":"https://orcid.org/0000-0001-5553-4702"},"institutions":[{"id":"https://openalex.org/I223822909","display_name":"Heidelberg University","ror":"https://ror.org/038t36y30","country_code":"DE","type":"education","lineage":["https://openalex.org/I223822909"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Frank T Bergmann","raw_affiliation_strings":["COS/BioQUANT, Heidelberg University, Heidelberg, Germany"],"affiliations":[{"raw_affiliation_string":"COS/BioQUANT, Heidelberg University, Heidelberg, Germany","institution_ids":["https://openalex.org/I223822909"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086460310","display_name":"David Nickerson","orcid":"https://orcid.org/0000-0003-4667-9779"},"institutions":[{"id":"https://openalex.org/I154130895","display_name":"University of Auckland","ror":"https://ror.org/03b94tp07","country_code":"NZ","type":"education","lineage":["https://openalex.org/I154130895"]}],"countries":["NZ"],"is_corresponding":false,"raw_author_name":"David Nickerson","raw_affiliation_strings":["Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand"],"affiliations":[{"raw_affiliation_string":"Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand","institution_ids":["https://openalex.org/I154130895"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103188993","display_name":"Dagmar Waltemath","orcid":"https://orcid.org/0000-0002-5886-5563"},"institutions":[{"id":"https://openalex.org/I4665924","display_name":"University of Rostock","ror":"https://ror.org/03zdwsf69","country_code":"DE","type":"education","lineage":["https://openalex.org/I4665924"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Dagmar Waltemath","raw_affiliation_strings":["Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany"],"affiliations":[{"raw_affiliation_string":"Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany","institution_ids":["https://openalex.org/I4665924"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5046119695","display_name":"Martin Scharm","orcid":"https://orcid.org/0000-0003-4519-7030"},"institutions":[{"id":"https://openalex.org/I4665924","display_name":"University of Rostock","ror":"https://ror.org/03zdwsf69","country_code":"DE","type":"education","lineage":["https://openalex.org/I4665924"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Martin Scharm","raw_affiliation_strings":["Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany"],"affiliations":[{"raw_affiliation_string":"Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany","institution_ids":["https://openalex.org/I4665924"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5076617999"],"corresponding_institution_ids":["https://openalex.org/I223822909"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.8703,"has_fulltext":false,"cited_by_count":11,"citation_normalized_percentile":{"value":0.77114737,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"33","issue":"8","first_page":"1253","last_page":"1254"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9980999827384949,"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":0.9980999827384949,"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/T11195","display_name":"Simulation Techniques and Applications","score":0.9939000010490417,"subfield":{"id":"https://openalex.org/subfields/1803","display_name":"Management Science and Operations Research"},"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/T11986","display_name":"Scientific Computing and Data Management","score":0.9728999733924866,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6873617768287659},{"id":"https://openalex.org/keywords/web-application","display_name":"Web application","score":0.48651808500289917},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.32460933923721313}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6873617768287659},{"id":"https://openalex.org/C118643609","wikidata":"https://www.wikidata.org/wiki/Q189210","display_name":"Web application","level":2,"score":0.48651808500289917},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.32460933923721313}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btw812","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw812","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/8/1253/25150427/btw812.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmh:oai:europepmc.org:4828969","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5860579","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:researchspace.auckland.ac.nz:2292/43819","is_oa":false,"landing_page_url":"http://hdl.handle.net/2292/43819","pdf_url":null,"source":{"id":"https://openalex.org/S7407055463","display_name":"ResearchSpace (University of Auckland)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I154130895","host_organization_name":"University of Auckland","host_organization_lineage":["https://openalex.org/I154130895"],"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":"Journal Article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btw812","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw812","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/8/1253/25150427/btw812.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Industry, innovation and infrastructure","score":0.41999998688697815,"id":"https://metadata.un.org/sdg/9"}],"awards":[{"id":"https://openalex.org/G5646925778","display_name":null,"funder_award_id":"GM081070","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2531582823.pdf","grobid_xml":"https://content.openalex.org/works/W2531582823.grobid-xml"},"referenced_works_count":15,"referenced_works":["https://openalex.org/W2078574757","https://openalex.org/W2096951208","https://openalex.org/W2102653059","https://openalex.org/W2123783513","https://openalex.org/W2136970290","https://openalex.org/W2150908245","https://openalex.org/W2154268795","https://openalex.org/W2160751597","https://openalex.org/W2170122529","https://openalex.org/W2187364252","https://openalex.org/W2254400129","https://openalex.org/W2285930875","https://openalex.org/W2405441773","https://openalex.org/W3145460265","https://openalex.org/W4238943364"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2478288626","https://openalex.org/W2350741829","https://openalex.org/W2530322880","https://openalex.org/W1596801655"],"abstract_inverted_index":{"Abstract":[0],"Summary":[1],"The":[2,38],"Simulation":[3],"Experiment":[4],"Description":[5],"Markup":[6],"Language":[7],"(SED-ML)":[8],"is":[9],"a":[10],"standardized":[11],"format":[12],"for":[13,30],"exchanging":[14],"simulation":[15,77],"studies":[16],"independently":[17],"of":[18,53],"software":[19],"tools.":[20],"We":[21],"present":[22],"the":[23,61,65],"SED-ML":[24,36,44,70],"Web":[25,39,62],"Tools,":[26],"an":[27],"online":[28],"application":[29],"creating,":[31],"editing,":[32],"simulating":[33],"and":[34,51,57,72,80],"validating":[35],"documents.":[37],"Tools":[40,63],"implement":[41],"all":[42],"current":[43],"specifications":[45],"and,":[46],"thus,":[47],"support":[48],"complex":[49],"modifications":[50],"co-simulation":[52],"models":[54],"in":[55],"SBML":[56],"CellML":[58],"formats.":[59],"Ultimately,":[60],"lower":[64],"bar":[66],"on":[67],"working":[68],"with":[69],"documents":[71],"help":[73],"users":[74],"create":[75],"valid":[76],"descriptions.":[78],"Availability":[79],"Implementation":[81],"http://sysbioapps.dyndns.org/SED-ML_Web_Tools/.":[82]},"counts_by_year":[{"year":2024,"cited_by_count":4},{"year":2021,"cited_by_count":2},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":1}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}