{"id":"https://openalex.org/W2029380217","doi":"https://doi.org/10.1186/1471-2105-10-397","title":"Bioclipse 2: A scriptable integration platform for the life sciences","display_name":"Bioclipse 2: A scriptable integration platform for the life sciences","publication_year":2009,"publication_date":"2009-12-01","ids":{"openalex":"https://openalex.org/W2029380217","doi":"https://doi.org/10.1186/1471-2105-10-397","mag":"2029380217","pmid":"https://pubmed.ncbi.nlm.nih.gov/19958528"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-10-397","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-397","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-397","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-397","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5046663348","display_name":"Ola Spjuth","orcid":"https://orcid.org/0000-0002-8083-2864"},"institutions":[{"id":"https://openalex.org/I123387679","display_name":"Uppsala University","ror":"https://ror.org/048a87296","country_code":"SE","type":"education","lineage":["https://openalex.org/I123387679"]}],"countries":["SE"],"is_corresponding":true,"raw_author_name":"Ola Spjuth","raw_affiliation_strings":["Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden. ola.spjuth@farmbio.uu.se","Department of Pharmaceutical Biosciences, Uppsala University Uppsala Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden. ola.spjuth@farmbio.uu.se","institution_ids":["https://openalex.org/I123387679"]},{"raw_affiliation_string":"Department of Pharmaceutical Biosciences, Uppsala University Uppsala Sweden","institution_ids":["https://openalex.org/I123387679"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027509528","display_name":"Jonathan Alvarsson","orcid":"https://orcid.org/0000-0002-8682-7206"},"institutions":[{"id":"https://openalex.org/I123387679","display_name":"Uppsala University","ror":"https://ror.org/048a87296","country_code":"SE","type":"education","lineage":["https://openalex.org/I123387679"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Jonathan Alvarsson","raw_affiliation_strings":["Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden","Department of Pharmaceutical Biosciences, Uppsala University Uppsala Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden","institution_ids":["https://openalex.org/I123387679"]},{"raw_affiliation_string":"Department of Pharmaceutical Biosciences, Uppsala University Uppsala Sweden","institution_ids":["https://openalex.org/I123387679"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025994042","display_name":"Arvid Berg","orcid":"https://orcid.org/0000-0001-6689-6901"},"institutions":[{"id":"https://openalex.org/I123387679","display_name":"Uppsala University","ror":"https://ror.org/048a87296","country_code":"SE","type":"education","lineage":["https://openalex.org/I123387679"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Arvid Berg","raw_affiliation_strings":["Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden","Department of Pharmaceutical Biosciences, Uppsala University Uppsala Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden","institution_ids":["https://openalex.org/I123387679"]},{"raw_affiliation_string":"Department of Pharmaceutical Biosciences, Uppsala University Uppsala Sweden","institution_ids":["https://openalex.org/I123387679"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073429275","display_name":"Martin Eklund","orcid":"https://orcid.org/0000-0001-5032-5266"},"institutions":[{"id":"https://openalex.org/I123387679","display_name":"Uppsala University","ror":"https://ror.org/048a87296","country_code":"SE","type":"education","lineage":["https://openalex.org/I123387679"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Martin Eklund","raw_affiliation_strings":["Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden","Department of Pharmaceutical Biosciences, Uppsala University Uppsala Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden","institution_ids":["https://openalex.org/I123387679"]},{"raw_affiliation_string":"Department of Pharmaceutical Biosciences, Uppsala University Uppsala Sweden","institution_ids":["https://openalex.org/I123387679"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012450310","display_name":"Stefan K\u00fchn","orcid":"https://orcid.org/0000-0002-5990-4157"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]},{"id":"https://openalex.org/I87048295","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I87048295"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Stefan Kuhn","raw_affiliation_strings":["European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK","European Bioinformatics Institute, Hinxton, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK","institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I87048295"]},{"raw_affiliation_string":"European Bioinformatics Institute, Hinxton, UK","institution_ids":["https://openalex.org/I1303153112"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037663898","display_name":"Carl M\u00e4sak","orcid":null},"institutions":[{"id":"https://openalex.org/I123387679","display_name":"Uppsala University","ror":"https://ror.org/048a87296","country_code":"SE","type":"education","lineage":["https://openalex.org/I123387679"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Carl M\u00e4sak","raw_affiliation_strings":["Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden","Department of Pharmaceutical Biosciences, Uppsala University Uppsala Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden","institution_ids":["https://openalex.org/I123387679"]},{"raw_affiliation_string":"Department of Pharmaceutical Biosciences, Uppsala University Uppsala Sweden","institution_ids":["https://openalex.org/I123387679"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032118734","display_name":"Gilleain Torrance","orcid":"https://orcid.org/0000-0002-8368-6954"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]},{"id":"https://openalex.org/I87048295","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I87048295"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Gilleain Torrance","raw_affiliation_strings":["European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK","European Bioinformatics Institute, Hinxton, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK","institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I87048295"]},{"raw_affiliation_string":"European Bioinformatics Institute, Hinxton, UK","institution_ids":["https://openalex.org/I1303153112"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000829320","display_name":"Johannes Wagener","orcid":"https://orcid.org/0000-0002-5952-9422"},"institutions":[{"id":"https://openalex.org/I8204097","display_name":"Ludwig-Maximilians-Universit\u00e4t M\u00fcnchen","ror":"https://ror.org/05591te55","country_code":"DE","type":"education","lineage":["https://openalex.org/I8204097"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Johannes Wagener","raw_affiliation_strings":["Max von Pettenkofer-Institut, Ludwig-Maximilians-Universit\u00e4t, Munich, Germany","Max von Pettenkofer Institut, Ludwig-Maximilians Universit\u00e4t, Munich, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Max von Pettenkofer-Institut, Ludwig-Maximilians-Universit\u00e4t, Munich, Germany","institution_ids":["https://openalex.org/I8204097"]},{"raw_affiliation_string":"Max von Pettenkofer Institut, Ludwig-Maximilians Universit\u00e4t, Munich, Germany","institution_ids":["https://openalex.org/I8204097"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060194743","display_name":"Egon Willighagen","orcid":"https://orcid.org/0000-0001-7542-0286"},"institutions":[{"id":"https://openalex.org/I123387679","display_name":"Uppsala University","ror":"https://ror.org/048a87296","country_code":"SE","type":"education","lineage":["https://openalex.org/I123387679"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Egon L Willighagen","raw_affiliation_strings":["Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden","Department of Pharmaceutical Biosciences, Uppsala University Uppsala Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden","institution_ids":["https://openalex.org/I123387679"]},{"raw_affiliation_string":"Department of Pharmaceutical Biosciences, Uppsala University Uppsala Sweden","institution_ids":["https://openalex.org/I123387679"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040194803","display_name":"Christoph Steinbeck","orcid":"https://orcid.org/0000-0001-6966-0814"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]},{"id":"https://openalex.org/I87048295","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I87048295"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Christoph Steinbeck","raw_affiliation_strings":["European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK","European Bioinformatics Institute, Hinxton, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK","institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I87048295"]},{"raw_affiliation_string":"European Bioinformatics Institute, Hinxton, UK","institution_ids":["https://openalex.org/I1303153112"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5081984122","display_name":"Jarl E. S. Wikberg","orcid":"https://orcid.org/0000-0003-1916-3013"},"institutions":[{"id":"https://openalex.org/I123387679","display_name":"Uppsala University","ror":"https://ror.org/048a87296","country_code":"SE","type":"education","lineage":["https://openalex.org/I123387679"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Jarl ES Wikberg","raw_affiliation_strings":["Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden","Department of Pharmaceutical Biosciences, Uppsala University Uppsala Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden","institution_ids":["https://openalex.org/I123387679"]},{"raw_affiliation_string":"Department of Pharmaceutical Biosciences, Uppsala University Uppsala Sweden","institution_ids":["https://openalex.org/I123387679"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5046663348"],"corresponding_institution_ids":["https://openalex.org/I123387679"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":11.4082,"has_fulltext":true,"cited_by_count":62,"citation_normalized_percentile":{"value":0.98080741,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"10","issue":"1","first_page":"397","last_page":"397"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.2818000018596649,"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"}},"topics":[{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.2818000018596649,"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/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.25029999017715454,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.08309999853372574,"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":0.8008159399032593},{"id":"https://openalex.org/keywords/scripting-language","display_name":"Scripting language","score":0.7220472693443298},{"id":"https://openalex.org/keywords/workbench","display_name":"Workbench","score":0.7162724733352661},{"id":"https://openalex.org/keywords/graphical-user-interface","display_name":"Graphical user interface","score":0.5633441805839539},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.5279154777526855},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.505305826663971},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.5039038062095642},{"id":"https://openalex.org/keywords/user-interface","display_name":"User interface","score":0.49548184871673584},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.4700329005718231},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.46219828724861145},{"id":"https://openalex.org/keywords/human\u2013computer-interaction","display_name":"Human\u2013computer interaction","score":0.45416221022605896},{"id":"https://openalex.org/keywords/javascript","display_name":"JavaScript","score":0.4475454092025757},{"id":"https://openalex.org/keywords/web-service","display_name":"Web service","score":0.4379523694515228},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.3837001621723175},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.2487991452217102},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.15374189615249634},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.13774198293685913},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.13653242588043213}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8008159399032593},{"id":"https://openalex.org/C61423126","wikidata":"https://www.wikidata.org/wiki/Q187432","display_name":"Scripting language","level":2,"score":0.7220472693443298},{"id":"https://openalex.org/C2779145975","wikidata":"https://www.wikidata.org/wiki/Q347690","display_name":"Workbench","level":3,"score":0.7162724733352661},{"id":"https://openalex.org/C37789001","wikidata":"https://www.wikidata.org/wiki/Q782543","display_name":"Graphical user interface","level":2,"score":0.5633441805839539},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.5279154777526855},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.505305826663971},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.5039038062095642},{"id":"https://openalex.org/C89505385","wikidata":"https://www.wikidata.org/wiki/Q47146","display_name":"User interface","level":2,"score":0.49548184871673584},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.4700329005718231},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.46219828724861145},{"id":"https://openalex.org/C107457646","wikidata":"https://www.wikidata.org/wiki/Q207434","display_name":"Human\u2013computer interaction","level":1,"score":0.45416221022605896},{"id":"https://openalex.org/C544833334","wikidata":"https://www.wikidata.org/wiki/Q2005","display_name":"JavaScript","level":2,"score":0.4475454092025757},{"id":"https://openalex.org/C35578498","wikidata":"https://www.wikidata.org/wiki/Q193424","display_name":"Web service","level":2,"score":0.4379523694515228},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.3837001621723175},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.2487991452217102},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.15374189615249634},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.13774198293685913},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.13653242588043213},{"id":"https://openalex.org/C157915830","wikidata":"https://www.wikidata.org/wiki/Q2928001","display_name":"Bubble","level":2,"score":0.0},{"id":"https://openalex.org/C129307140","wikidata":"https://www.wikidata.org/wiki/Q6795880","display_name":"Maximum bubble pressure method","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001690","descriptor_name":"Biological Science Disciplines","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001690","descriptor_name":"Biological Science Disciplines","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001690","descriptor_name":"Biological Science Disciplines","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":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":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":7,"locations":[{"id":"doi:10.1186/1471-2105-10-397","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-397","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-397","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:19958528","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19958528","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:cris.maastrichtuniversity.nl:openaire/58e65826-0a79-46bf-acf8-a72dde7d4a05","is_oa":true,"landing_page_url":"https://cris.maastrichtuniversity.nl/en/publications/58e65826-0a79-46bf-acf8-a72dde7d4a05","pdf_url":null,"source":{"id":"https://openalex.org/S4306402616","display_name":"Research Publications (Maastricht University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I34352273","host_organization_name":"Maastricht University","host_organization_lineage":["https://openalex.org/I34352273"],"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":"Spjuth, O, Alvarsson, J, Berg, A, Eklund, M, Kuhn, S, Masak, C, Torrance, G, Wagener, J, Willighagen, E L, Steinbeck, C & Wikberg, J E S 2009, 'Bioclipse 2 : A scriptable integration platform for the life sciences', BMC Bioinformatics, vol. 10, 397. https://doi.org/10.1186/1471-2105-10-397","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:DiVA.org:uu-109304","is_oa":true,"landing_page_url":"http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-109304","pdf_url":null,"source":{"id":"https://openalex.org/S4306402042","display_name":"Uppsala University Publications (Uppsala University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I123387679","host_organization_name":"Uppsala University","host_organization_lineage":["https://openalex.org/I123387679"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:doaj.org/article:8b991d275a4f41d6b7758df8fe84ef93","is_oa":false,"landing_page_url":"https://doaj.org/article/8b991d275a4f41d6b7758df8fe84ef93","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 10, Iss 1, p 397 (2009)","raw_type":"article"},{"id":"pmh:oai:epub.ub.uni-muenchen.de:23565","is_oa":false,"landing_page_url":"http://nbn-resolving.de/urn:nbn:de:bvb:19-epub-23565-2","pdf_url":null,"source":{"id":"https://openalex.org/S4306401845","display_name":"Open access LMU (Ludwid Maxmilian's Universitat Munchen)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I8204097","host_organization_name":"Ludwig-Maximilians-Universit\u00e4t M\u00fcnchen","host_organization_lineage":["https://openalex.org/I8204097"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"doc-type:article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2799422","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2799422","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":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-10-397","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-397","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-397","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/12","score":0.47999998927116394,"display_name":"Responsible consumption and production"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320324119","display_name":"Uppsala Universitet","ror":"https://ror.org/048a87296"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2029380217.pdf","grobid_xml":"https://content.openalex.org/works/W2029380217.grobid-xml"},"referenced_works_count":20,"referenced_works":["https://openalex.org/W10705947","https://openalex.org/W1575370537","https://openalex.org/W1590240800","https://openalex.org/W1828735316","https://openalex.org/W1976149536","https://openalex.org/W1999145583","https://openalex.org/W2049961577","https://openalex.org/W2058673890","https://openalex.org/W2064270057","https://openalex.org/W2072537419","https://openalex.org/W2098889731","https://openalex.org/W2100827887","https://openalex.org/W2121936656","https://openalex.org/W2143543488","https://openalex.org/W2143614763","https://openalex.org/W2147231162","https://openalex.org/W2148797284","https://openalex.org/W2159675211","https://openalex.org/W2168103533","https://openalex.org/W2206991991"],"related_works":["https://openalex.org/W4247806713","https://openalex.org/W4378700020","https://openalex.org/W2208447305","https://openalex.org/W2390396596","https://openalex.org/W3180179400","https://openalex.org/W2118366689","https://openalex.org/W2154998455","https://openalex.org/W2116888309","https://openalex.org/W2477652530","https://openalex.org/W2039055059"],"abstract_inverted_index":{"BACKGROUND:":[0],"Contemporary":[1],"biological":[2],"research":[3,98],"integrates":[4],"neighboring":[5],"scientific":[6],"domains":[7],"to":[8,28,32,34,151,226,273],"answer":[9],"complex":[10,154],"questions":[11],"in":[12,96,156,282],"fields":[13,158],"such":[14],"as":[15,132,134,164,231,233],"systems":[16],"biology":[17],"and":[18,60,69,86,99,108,140,161,193,215,242,252,284,292],"drug":[19],"discovery.":[20],"This":[21],"calls":[22],"for":[23,48,67,73,113,120,125,138,179,197,239,250],"tools":[24,149,238],"that":[25,128,207,269],"are":[26,294],"intuitive":[27,71,237],"use,":[29],"yet":[30],"flexible":[31,265],"adapt":[33],"new":[35,228],"tasks.":[36],"RESULTS:":[37],"Bioclipse":[38,114,143,171,208,247,278],"is":[39,78,145,210,256,280],"a":[40,55,62,88,117,123,135,165,181,264],"free,":[41],"open":[42,266],"source":[43,267],"workbench":[44,72],"with":[45,147],"advanced":[46,103,148,214],"features":[47],"the":[49,82,94,106,109,157,191,243,259],"life":[50],"sciences.":[51],"Version":[52],"2.0":[53],"constitutes":[54],"complete":[56],"rewrite":[57],"of":[58,105,159,190,203,275],"Bioclipse,":[59],"delivers":[61],"stable,":[63],"scalable":[64],"integration":[65],"platform":[66,219],"developers":[68],"an":[70,213],"end":[74,240],"users.":[75],"All":[76],"functionality":[77],"available":[79,296],"both":[80],"from":[81,87],"graphical":[83,136],"user":[84,183],"interface":[85],"built-in":[89],"novel":[90],"domain-specific":[91],"language,":[92],"supporting":[93],"scientist":[95],"interdisciplinary":[97,251],"reproducible":[100],"analyses":[101],"through":[102],"visualization":[104],"inputs":[107],"results.":[110],"New":[111],"components":[112],"2":[115,144,172,209,248,255,279],"include":[116],"rewritten":[118],"editor":[119,137],"chemical":[121],"structures,":[122],"table":[124],"multiple":[126],"molecules":[127],"supports":[129],"gigabyte-sized":[130],"files,":[131],"well":[133,232],"sequences":[139],"alignments.":[141],"CONCLUSION:":[142],"equipped":[146],"required":[150],"carry":[152],"out":[153],"analysis":[155],"bio-":[160],"cheminformatics.":[162],"Developed":[163],"Rich":[166],"Client":[167],"based":[168,211],"on":[169,174,212,286],"Eclipse,":[170],"leverages":[173],"today's":[175],"powerful":[176],"desktop":[177],"computers":[178],"providing":[180],"responsive":[182],"interface,":[184],"but":[185],"also":[186],"takes":[187],"full":[188],"advantage":[189],"Web":[192],"networked":[194],"(Web/Cloud)":[195],"services":[196],"more":[198],"demanding":[199],"calculations":[200],"or":[201],"retrieval":[202],"data.":[204],"The":[205,236],"fact":[206],"widely":[216],"used":[217],"service":[218],"ensures":[220],"wide":[221],"extensibility,":[222],"making":[223],"it":[224],"easy":[225],"add":[227],"algorithms,":[229],"visualizations,":[230],"scripting":[234],"commands.":[235],"users":[241],"extensible":[244],"architecture":[245],"make":[246],"ideal":[249],"integrative":[253],"research.Bioclipse":[254],"released":[257],"under":[258],"Eclipse":[260],"Public":[261],"License":[262],"(EPL),":[263],"license":[268],"allows":[270],"additional":[271],"plugins":[272],"be":[274],"any":[276],"license.":[277],"implemented":[281],"Java":[283],"supported":[285],"all":[287],"major":[288],"platforms;":[289],"Source":[290],"code":[291],"binaries":[293],"freely":[295],"at":[297],"http://www.bioclipse.net.":[298]},"counts_by_year":[{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":3},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":7},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":7},{"year":2012,"cited_by_count":10}],"updated_date":"2026-07-02T09:51:11.867554","created_date":"2025-10-10T00:00:00"}
