{"id":"https://openalex.org/W2144610372","doi":"https://doi.org/10.1093/bioinformatics/btt199","title":"BioBlend: automating pipeline analyses within Galaxy and CloudMan","display_name":"BioBlend: automating pipeline analyses within Galaxy and CloudMan","publication_year":2013,"publication_date":"2013-04-28","ids":{"openalex":"https://openalex.org/W2144610372","doi":"https://doi.org/10.1093/bioinformatics/btt199","mag":"2144610372","pmid":"https://pubmed.ncbi.nlm.nih.gov/23630176"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btt199","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt199","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/13/1685/6411064/btt199.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/29/13/1685/6411064/btt199.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5013083229","display_name":"Clare Sloggett","orcid":"https://orcid.org/0000-0001-8409-6705"},"institutions":[{"id":"https://openalex.org/I347366330","display_name":"Melbourne Bioinformatics","ror":"https://ror.org/05gkzhv48","country_code":"AU","type":"education","lineage":["https://openalex.org/I347366330"]},{"id":"https://openalex.org/I165779595","display_name":"University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"Clare Sloggett","raw_affiliation_strings":["Victorian Life Sciences Computation Initiative, University of Melbourne, Melbourne, Australia","Victorian Life Sciences Computation Initiative, University of Melbourne, Melbourne, Australia#TAB#"],"affiliations":[{"raw_affiliation_string":"Victorian Life Sciences Computation Initiative, University of Melbourne, Melbourne, Australia","institution_ids":["https://openalex.org/I347366330","https://openalex.org/I165779595"]},{"raw_affiliation_string":"Victorian Life Sciences Computation Initiative, University of Melbourne, Melbourne, Australia#TAB#","institution_ids":["https://openalex.org/I347366330"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001522124","display_name":"Nuwan Goonasekera","orcid":"https://orcid.org/0000-0002-3019-2934"},"institutions":[{"id":"https://openalex.org/I347366330","display_name":"Melbourne Bioinformatics","ror":"https://ror.org/05gkzhv48","country_code":"AU","type":"education","lineage":["https://openalex.org/I347366330"]},{"id":"https://openalex.org/I165779595","display_name":"University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Nuwan Goonasekera","raw_affiliation_strings":["Victorian Life Sciences Computation Initiative (VLSCI), University of Melbourne, Melbourne, Australia, 2Victorian eResearch Strategic Initiative (VeRSI), University of Melbourne, Melbourne, Australia and 3Center for Informatics and Computing (CIR), Ruder Boskovic Institute (RBI), Zagreb, Croatia","Melbourne Bioinformatics, Melbourne, Australia"],"affiliations":[{"raw_affiliation_string":"Victorian Life Sciences Computation Initiative (VLSCI), University of Melbourne, Melbourne, Australia, 2Victorian eResearch Strategic Initiative (VeRSI), University of Melbourne, Melbourne, Australia and 3Center for Informatics and Computing (CIR), Ruder Boskovic Institute (RBI), Zagreb, Croatia","institution_ids":["https://openalex.org/I347366330","https://openalex.org/I165779595"]},{"raw_affiliation_string":"Melbourne Bioinformatics, Melbourne, Australia","institution_ids":["https://openalex.org/I347366330"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5006951727","display_name":"Enis Afgan","orcid":"https://orcid.org/0000-0003-0922-6711"},"institutions":[{"id":"https://openalex.org/I347366330","display_name":"Melbourne Bioinformatics","ror":"https://ror.org/05gkzhv48","country_code":"AU","type":"education","lineage":["https://openalex.org/I347366330"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Enis Afgan","raw_affiliation_strings":["Melbourne Bioinformatics, Melbourne, Australia"],"affiliations":[{"raw_affiliation_string":"Melbourne Bioinformatics, Melbourne, Australia","institution_ids":["https://openalex.org/I347366330"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5013083229"],"corresponding_institution_ids":["https://openalex.org/I165779595","https://openalex.org/I347366330"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":3.7245,"has_fulltext":false,"cited_by_count":102,"citation_normalized_percentile":{"value":0.93990412,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":99},"biblio":{"volume":"29","issue":"13","first_page":"1685","last_page":"1686"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9965999722480774,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9965999722480774,"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/T11986","display_name":"Scientific Computing and Data Management","score":0.9939000010490417,"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"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9904000163078308,"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":0.8569351434707642},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.8177798986434937},{"id":"https://openalex.org/keywords/mit-license","display_name":"MIT License","score":0.7654248476028442},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.7250826358795166},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.6167742013931274},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.6058413982391357},{"id":"https://openalex.org/keywords/open-source","display_name":"Open source","score":0.5818848609924316},{"id":"https://openalex.org/keywords/license","display_name":"License","score":0.5680336952209473},{"id":"https://openalex.org/keywords/scratch","display_name":"Scratch","score":0.5549589991569519},{"id":"https://openalex.org/keywords/galaxy","display_name":"Galaxy","score":0.5397610664367676},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5082942843437195},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.43757539987564087},{"id":"https://openalex.org/keywords/os-x","display_name":"OS X","score":0.43657606840133667},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.4098471403121948},{"id":"https://openalex.org/keywords/astrophysics","display_name":"Astrophysics","score":0.0948512852191925}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8569351434707642},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.8177798986434937},{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.7654248476028442},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.7250826358795166},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.6167742013931274},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.6058413982391357},{"id":"https://openalex.org/C3018397939","wikidata":"https://www.wikidata.org/wiki/Q3644502","display_name":"Open source","level":3,"score":0.5818848609924316},{"id":"https://openalex.org/C2780560020","wikidata":"https://www.wikidata.org/wiki/Q79719","display_name":"License","level":2,"score":0.5680336952209473},{"id":"https://openalex.org/C2781235140","wikidata":"https://www.wikidata.org/wiki/Q275131","display_name":"Scratch","level":2,"score":0.5549589991569519},{"id":"https://openalex.org/C98444146","wikidata":"https://www.wikidata.org/wiki/Q318","display_name":"Galaxy","level":2,"score":0.5397610664367676},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5082942843437195},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.43757539987564087},{"id":"https://openalex.org/C515153823","wikidata":"https://www.wikidata.org/wiki/Q14116","display_name":"OS X","level":3,"score":0.43657606840133667},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.4098471403121948},{"id":"https://openalex.org/C44870925","wikidata":"https://www.wikidata.org/wiki/Q37547","display_name":"Astrophysics","level":1,"score":0.0948512852191925},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0}],"mesh":[{"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":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btt199","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt199","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/13/1685/6411064/btt199.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:23630176","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23630176","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},{"id":"pmh:oai:europepmc.org:3275242","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4288140","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"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btt199","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt199","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/13/1685/6411064/btt199.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":[{"score":0.6399999856948853,"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure"}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2144610372.pdf","grobid_xml":"https://content.openalex.org/works/W2144610372.grobid-xml"},"referenced_works_count":3,"referenced_works":["https://openalex.org/W1968659469","https://openalex.org/W2001938458","https://openalex.org/W2024872854"],"related_works":["https://openalex.org/W4309247532","https://openalex.org/W632256878","https://openalex.org/W4211197663","https://openalex.org/W2491403535","https://openalex.org/W2479811461","https://openalex.org/W2113128227","https://openalex.org/W3096946169","https://openalex.org/W2104915799","https://openalex.org/W4311938462","https://openalex.org/W3123068371"],"abstract_inverted_index":{"http://bioblend.readthedocs.org/.":[0],"Automated":[1],"installation":[2],"of":[3],"BioBlend":[4],"is":[5,17,36],"available":[6,18],"via":[7],"PyPI":[8],"(e.g.":[9],"pip":[10],"install":[11],"bioblend).":[12],"Alternatively,":[13],"the":[14,20,25],"source":[15,28],"code":[16],"from":[19],"GitHub":[21],"repository":[22],"(https://github.com/afgane/bioblend)":[23],"under":[24],"MIT":[26],"open":[27],"license.":[29],"The":[30],"library":[31],"has":[32],"been":[33],"tested":[34],"and":[35,41],"working":[37],"on":[38],"Linux,":[39],"Macintosh":[40],"Windows-based":[42],"systems.":[43]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":8},{"year":2023,"cited_by_count":7},{"year":2022,"cited_by_count":11},{"year":2021,"cited_by_count":9},{"year":2020,"cited_by_count":7},{"year":2019,"cited_by_count":6},{"year":2018,"cited_by_count":9},{"year":2017,"cited_by_count":11},{"year":2016,"cited_by_count":12},{"year":2015,"cited_by_count":8},{"year":2014,"cited_by_count":5}],"updated_date":"2026-03-10T16:38:18.471706","created_date":"2025-10-10T00:00:00"}
