{"id":"https://openalex.org/W2138326194","doi":"https://doi.org/10.1093/bioinformatics/bts432","title":"CySBML: a Cytoscape plugin for SBML","display_name":"CySBML: a Cytoscape plugin for SBML","publication_year":2012,"publication_date":"2012-07-05","ids":{"openalex":"https://openalex.org/W2138326194","doi":"https://doi.org/10.1093/bioinformatics/bts432","mag":"2138326194","pmid":"https://pubmed.ncbi.nlm.nih.gov/22772946"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bts432","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts432","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/18/2402/48883805/bioinformatics_28_18_2402.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","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/28/18/2402/48883805/bioinformatics_28_18_2402.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5012727458","display_name":"Matthias K\u00f6nig","orcid":"https://orcid.org/0000-0003-1725-179X"},"institutions":[{"id":"https://openalex.org/I7877124","display_name":"Charit\u00e9 - Universit\u00e4tsmedizin Berlin","ror":"https://ror.org/001w7jn25","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I7877124"]},{"id":"https://openalex.org/I8087733","display_name":"University of T\u00fcbingen","ror":"https://ror.org/03a1kwz48","country_code":"DE","type":"education","lineage":["https://openalex.org/I8087733"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Matthias K\u00f6nig","raw_affiliation_strings":["1 Department of Biochemistry, University Medicine Charit\u00e9 Berlin, 13347, Berlin and 2Department Cognitive Systems, Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, 72076, T\u00fcbingen, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Biochemistry, University Medicine Charit\u00e9 Berlin, 13347, Berlin and 2Department Cognitive Systems, Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, 72076, T\u00fcbingen, Germany","institution_ids":["https://openalex.org/I8087733","https://openalex.org/I7877124"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065854572","display_name":"Andreas Dr\u00e4ger","orcid":"https://orcid.org/0000-0002-1240-5553"},"institutions":[{"id":"https://openalex.org/I7877124","display_name":"Charit\u00e9 - Universit\u00e4tsmedizin Berlin","ror":"https://ror.org/001w7jn25","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I7877124"]},{"id":"https://openalex.org/I8087733","display_name":"University of T\u00fcbingen","ror":"https://ror.org/03a1kwz48","country_code":"DE","type":"education","lineage":["https://openalex.org/I8087733"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Andreas Dr\u00e4ger","raw_affiliation_strings":["1 Department of Biochemistry, University Medicine Charit\u00e9 Berlin, 13347, Berlin and 2Department Cognitive Systems, Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, 72076, T\u00fcbingen, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Biochemistry, University Medicine Charit\u00e9 Berlin, 13347, Berlin and 2Department Cognitive Systems, Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, 72076, T\u00fcbingen, Germany","institution_ids":["https://openalex.org/I8087733","https://openalex.org/I7877124"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5078409502","display_name":"Hermann\u2212Georg Holzh\u00fctter","orcid":"https://orcid.org/0000-0002-5054-6023"},"institutions":[{"id":"https://openalex.org/I7877124","display_name":"Charit\u00e9 - Universit\u00e4tsmedizin Berlin","ror":"https://ror.org/001w7jn25","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I7877124"]},{"id":"https://openalex.org/I8087733","display_name":"University of T\u00fcbingen","ror":"https://ror.org/03a1kwz48","country_code":"DE","type":"education","lineage":["https://openalex.org/I8087733"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Hermann-Georg Holzh\u00fctter","raw_affiliation_strings":["1 Department of Biochemistry, University Medicine Charit\u00e9 Berlin, 13347, Berlin and 2Department Cognitive Systems, Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, 72076, T\u00fcbingen, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Biochemistry, University Medicine Charit\u00e9 Berlin, 13347, Berlin and 2Department Cognitive Systems, Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, 72076, T\u00fcbingen, Germany","institution_ids":["https://openalex.org/I8087733","https://openalex.org/I7877124"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.2094,"has_fulltext":false,"cited_by_count":57,"citation_normalized_percentile":{"value":0.78497767,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"28","issue":"18","first_page":"2402","last_page":"2403"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.6025999784469604,"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":0.6025999784469604,"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.1404000073671341,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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":0.03539999946951866,"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/sbml","display_name":"SBML","score":0.9602937698364258},{"id":"https://openalex.org/keywords/plug-in","display_name":"Plug-in","score":0.8757447004318237},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6269766092300415},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.5039951205253601},{"id":"https://openalex.org/keywords/markup-language","display_name":"Markup language","score":0.38221123814582825},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.367669939994812},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3605855703353882},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2038639783859253},{"id":"https://openalex.org/keywords/xml","display_name":"XML","score":0.08191627264022827}],"concepts":[{"id":"https://openalex.org/C87186988","wikidata":"https://www.wikidata.org/wiki/Q452197","display_name":"SBML","level":4,"score":0.9602937698364258},{"id":"https://openalex.org/C4924752","wikidata":"https://www.wikidata.org/wiki/Q184148","display_name":"Plug-in","level":2,"score":0.8757447004318237},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6269766092300415},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.5039951205253601},{"id":"https://openalex.org/C45874996","wikidata":"https://www.wikidata.org/wiki/Q37045","display_name":"Markup language","level":3,"score":0.38221123814582825},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.367669939994812},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3605855703353882},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2038639783859253},{"id":"https://openalex.org/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"score":0.08191627264022827}],"mesh":[{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/bts432","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts432","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/18/2402/48883805/bioinformatics_28_18_2402.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":"pmid:22772946","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22772946","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":"Bioinformatics (Oxford, England)","raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bts432","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts432","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/18/2402/48883805/bioinformatics_28_18_2402.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":[{"id":"https://metadata.un.org/sdg/9","score":0.44999998807907104,"display_name":"Industry, innovation and infrastructure"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":12,"referenced_works":["https://openalex.org/W1964246733","https://openalex.org/W2001758733","https://openalex.org/W2102057828","https://openalex.org/W2114124738","https://openalex.org/W2135290856","https://openalex.org/W2144656637","https://openalex.org/W2145435867","https://openalex.org/W2150599425","https://openalex.org/W2150908245","https://openalex.org/W2159675211","https://openalex.org/W2162144833","https://openalex.org/W3215028400"],"related_works":["https://openalex.org/W2082621456","https://openalex.org/W2150908245","https://openalex.org/W2981332207","https://openalex.org/W2211443823","https://openalex.org/W2040642413","https://openalex.org/W3048335229","https://openalex.org/W2146744007","https://openalex.org/W2100525485","https://openalex.org/W2890725831","https://openalex.org/W3041939341"],"abstract_inverted_index":{"SUMMARY:":[0],"CySBML":[1,48],"is":[2],"a":[3],"plugin":[4,71],"designed":[5],"to":[6,40,54],"work":[7],"with":[8],"Systems":[9],"Biology":[10],"Markup":[11],"Language":[12],"(SBML)":[13],"in":[14,32],"Cytoscape":[15,70],"having":[16],"the":[17,24,69],"following":[18],"features:":[19],"SBML":[20,25,37,46,56],"import,":[21],"support":[22],"of":[23],"layout":[26],"and":[27,42,45,87],"qualitative":[28],"model":[29],"packages,":[30],"navigation":[31],"network":[33],"layouts":[34],"based":[35],"on":[36],"structure,":[38],"access":[39],"MIRIAM":[41],"SBO-based":[43],"annotations":[44],"validation.":[47],"includes":[49],"an":[50],"importer":[51],"for":[52,65,74,92],"BioModels":[53],"load":[55],"from":[57],"standard":[58],"repositories.":[59],"AVAILABILITY":[60],"AND":[61],"IMPLEMENTATION:":[62],"Freely":[63],"available":[64,91],"non-commercial":[66],"purposes":[67],"through":[68],"manager":[72],"or":[73],"download":[75,93],"at":[76,94],"http://sourceforge.net/projects/cysbml/.":[77],"CONTACT:":[78],"cysbml-team@lists.sourceforge.net":[79],"SUPPLEMENTARY":[80],"INFORMATION:":[81],"Tutorial,":[82],"usage":[83],"guide,":[84],"installation":[85],"instructions":[86],"additional":[88],"figures":[89],"are":[90],"http://www.charite.de/sysbio/people/koenig/software/cysbml/.":[95]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":10},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":5},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":6},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":7},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":6}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
