{"id":"https://openalex.org/W2557994837","doi":"https://doi.org/10.1371/journal.pcbi.1004947","title":"Ten Simple Rules for Taking Advantage of Git and GitHub","display_name":"Ten Simple Rules for Taking Advantage of Git and GitHub","publication_year":2016,"publication_date":"2016-07-14","ids":{"openalex":"https://openalex.org/W2557994837","doi":"https://doi.org/10.1371/journal.pcbi.1004947","mag":"2557994837","pmid":"https://pubmed.ncbi.nlm.nih.gov/27415786"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1004947","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1004947","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004947&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","datacite","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004947&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5037412788","display_name":"Yasset Perez-Riverol","orcid":null},"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":true,"raw_author_name":"Yasset Perez-Riverol","raw_affiliation_strings":["European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom","institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I87048295"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064560423","display_name":"Laurent Gatto","orcid":"https://orcid.org/0000-0002-1520-2268"},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Laurent Gatto","raw_affiliation_strings":["Computational Proteomics Unit, Cambridge Systems Biology Centre, University of Cambridge, Cambridge, United Kingdom"],"raw_orcid":"https://orcid.org/0000-0002-1520-2268","affiliations":[{"raw_affiliation_string":"Computational Proteomics Unit, Cambridge Systems Biology Centre, University of Cambridge, Cambridge, United Kingdom","institution_ids":["https://openalex.org/I241749"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100431163","display_name":"Rui Wang","orcid":"https://orcid.org/0000-0001-9048-2979"},"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":"Rui Wang","raw_affiliation_strings":["European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom","institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I87048295"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053274567","display_name":"Timo Sachsenberg","orcid":"https://orcid.org/0000-0002-2833-6070"},"institutions":[{"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":"Timo Sachsenberg","raw_affiliation_strings":["Applied Bioinformatics and Department of Computer Science, University of T\u00fcbingen, T\u00fcbingen, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Applied Bioinformatics and Department of Computer Science, University of T\u00fcbingen, T\u00fcbingen, Germany","institution_ids":["https://openalex.org/I8087733"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034680534","display_name":"Julian Uszkoreit","orcid":"https://orcid.org/0000-0001-7522-4007"},"institutions":[{"id":"https://openalex.org/I904495901","display_name":"Ruhr University Bochum","ror":"https://ror.org/04tsk2644","country_code":"DE","type":"education","lineage":["https://openalex.org/I904495901"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Julian Uszkoreit","raw_affiliation_strings":["Medizinisches Proteom-Center, Ruhr-Universit\u00e4t Bochum, Bochum, Germany"],"raw_orcid":"https://orcid.org/0000-0001-7522-4007","affiliations":[{"raw_affiliation_string":"Medizinisches Proteom-Center, Ruhr-Universit\u00e4t Bochum, Bochum, Germany","institution_ids":["https://openalex.org/I904495901"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020657222","display_name":"Felipe da Veiga Leprevost","orcid":"https://orcid.org/0000-0002-8228-5374"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]},{"id":"https://openalex.org/I4210111179","display_name":"Michigan United","ror":"https://ror.org/0291ys696","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210111179"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Felipe da Veiga Leprevost","raw_affiliation_strings":["Department of Pathology, University of Michigan, Ann Arbor, Michigan, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-8228-5374","affiliations":[{"raw_affiliation_string":"Department of Pathology, University of Michigan, Ann Arbor, Michigan, United States of America","institution_ids":["https://openalex.org/I27837315","https://openalex.org/I4210111179"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081126095","display_name":"Christian Fufezan","orcid":"https://orcid.org/0000-0002-7048-6822"},"institutions":[{"id":"https://openalex.org/I22465464","display_name":"University of M\u00fcnster","ror":"https://ror.org/00pd74e08","country_code":"DE","type":"education","lineage":["https://openalex.org/I22465464"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Christian Fufezan","raw_affiliation_strings":["Institute of Plant Biology and Biotechnology, University of M\u00fcnster, M\u00fcnster, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Plant Biology and Biotechnology, University of M\u00fcnster, M\u00fcnster, Germany","institution_ids":["https://openalex.org/I22465464"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080538573","display_name":"Tobias Ternent","orcid":"https://orcid.org/0000-0003-0279-7335"},"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":"Tobias Ternent","raw_affiliation_strings":["European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom"],"raw_orcid":"https://orcid.org/0000-0003-0279-7335","affiliations":[{"raw_affiliation_string":"European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom","institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I87048295"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004633766","display_name":"Stephen J. Eglen","orcid":"https://orcid.org/0000-0001-8607-8025"},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Stephen J. Eglen","raw_affiliation_strings":["Centre for Mathematical Sciences, University of Cambridge, Cambridge, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Mathematical Sciences, University of Cambridge, Cambridge, United Kingdom","institution_ids":["https://openalex.org/I241749"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061630529","display_name":"Daniel S. Katz","orcid":"https://orcid.org/0000-0001-5934-7525"},"institutions":[{"id":"https://openalex.org/I157725225","display_name":"University of Illinois Urbana-Champaign","ror":"https://ror.org/047426m28","country_code":"US","type":"education","lineage":["https://openalex.org/I157725225"]},{"id":"https://openalex.org/I4210135837","display_name":"National Center for Supercomputing Applications","ror":"https://ror.org/03r10zj06","country_code":"US","type":"facility","lineage":["https://openalex.org/I157725225","https://openalex.org/I4210135837"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Daniel S. Katz","raw_affiliation_strings":["National Center for Supercomputing Applications and Graduate School of Library and Information Science, University of Illinois, Urbana, Illinois, United States of America"],"raw_orcid":"https://orcid.org/0000-0001-5934-7525","affiliations":[{"raw_affiliation_string":"National Center for Supercomputing Applications and Graduate School of Library and Information Science, University of Illinois, Urbana, Illinois, United States of America","institution_ids":["https://openalex.org/I4210135837","https://openalex.org/I157725225"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086791063","display_name":"Tom Pollard","orcid":null},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tom J. Pollard","raw_affiliation_strings":["MIT Laboratory for Computational Physiology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-5676-7898","affiliations":[{"raw_affiliation_string":"MIT Laboratory for Computational Physiology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101451426","display_name":"Alexander Konovalov","orcid":"https://orcid.org/0000-0001-5299-3292"},"institutions":[{"id":"https://openalex.org/I16835326","display_name":"University of St Andrews","ror":"https://ror.org/02wn5qz54","country_code":"GB","type":"education","lineage":["https://openalex.org/I16835326"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Alexander Konovalov","raw_affiliation_strings":["Centre for Interdisciplinary Research in Computational Algebra, University of St Andrews, St Andrews, United Kingdom"],"raw_orcid":"https://orcid.org/0000-0001-5299-3292","affiliations":[{"raw_affiliation_string":"Centre for Interdisciplinary Research in Computational Algebra, University of St Andrews, St Andrews, United Kingdom","institution_ids":["https://openalex.org/I16835326"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062202807","display_name":"Robert M Flight","orcid":"https://orcid.org/0000-0001-8141-7788"},"institutions":[{"id":"https://openalex.org/I143302722","display_name":"University of Kentucky","ror":"https://ror.org/02k3smh20","country_code":"US","type":"education","lineage":["https://openalex.org/I143302722"]},{"id":"https://openalex.org/I2802239656","display_name":"Markey Cancer Center","ror":"https://ror.org/01dhvva97","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1285210727","https://openalex.org/I2802239656"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Robert M. Flight","raw_affiliation_strings":["Department of Molecular Biology and Biochemistry, Markey Cancer Center, Resource Center for Stable Isotope-Resolved Metabolomics, University of Kentucky, Lexington, Kentucky, United States of America"],"raw_orcid":"https://orcid.org/0000-0001-8141-7788","affiliations":[{"raw_affiliation_string":"Department of Molecular Biology and Biochemistry, Markey Cancer Center, Resource Center for Stable Isotope-Resolved Metabolomics, University of Kentucky, Lexington, Kentucky, United States of America","institution_ids":["https://openalex.org/I2802239656","https://openalex.org/I143302722"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018360029","display_name":"Kai Blin","orcid":"https://orcid.org/0000-0003-3764-6051"},"institutions":[{"id":"https://openalex.org/I2801134892","display_name":"Novo Nordisk Foundation","ror":"https://ror.org/04txyc737","country_code":"DK","type":"facility","lineage":["https://openalex.org/I2801134892"]},{"id":"https://openalex.org/I96673099","display_name":"Technical University of Denmark","ror":"https://ror.org/04qtj9h94","country_code":"DK","type":"education","lineage":["https://openalex.org/I96673099"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"Kai Blin","raw_affiliation_strings":["The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, H\u00f8rsholm, Denmark"],"raw_orcid":"https://orcid.org/0000-0003-3764-6051","affiliations":[{"raw_affiliation_string":"The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, H\u00f8rsholm, Denmark","institution_ids":["https://openalex.org/I2801134892","https://openalex.org/I96673099"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5044603792","display_name":"Juan Antonio Vizca\u00edno","orcid":"https://orcid.org/0000-0002-3905-4335"},"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":true,"raw_author_name":"Juan Antonio Vizca\u00edno","raw_affiliation_strings":["European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom"],"raw_orcid":"https://orcid.org/0000-0002-3905-4335","affiliations":[{"raw_affiliation_string":"European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom","institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I87048295"]}]}],"institutions":[],"countries_distinct_count":4,"institutions_distinct_count":15,"corresponding_author_ids":["https://openalex.org/A5037412788","https://openalex.org/A5044603792"],"corresponding_institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I87048295"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.18007772,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"12","issue":"7","first_page":"e1004947","last_page":"e1004947"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11891","display_name":"Big Data and Business Intelligence","score":0.48420000076293945,"subfield":{"id":"https://openalex.org/subfields/1404","display_name":"Management Information Systems"},"field":{"id":"https://openalex.org/fields/14","display_name":"Business, Management and Accounting"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},"topics":[{"id":"https://openalex.org/T11891","display_name":"Big Data and Business Intelligence","score":0.48420000076293945,"subfield":{"id":"https://openalex.org/subfields/1404","display_name":"Management Information Systems"},"field":{"id":"https://openalex.org/fields/14","display_name":"Business, Management and Accounting"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},{"id":"https://openalex.org/T10273","display_name":"IoT and Edge/Fog Computing","score":0.4284999966621399,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.3885999917984009,"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/simple","display_name":"Simple (philosophy)","score":0.6780197620391846},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5531474947929382},{"id":"https://openalex.org/keywords/epistemology","display_name":"Epistemology","score":0.1569787859916687},{"id":"https://openalex.org/keywords/philosophy","display_name":"Philosophy","score":0.12751638889312744}],"concepts":[{"id":"https://openalex.org/C2780586882","wikidata":"https://www.wikidata.org/wiki/Q7520643","display_name":"Simple (philosophy)","level":2,"score":0.6780197620391846},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5531474947929382},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.1569787859916687},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.12751638889312744}],"mesh":[{"descriptor_ui":"D017408","descriptor_name":"Guidelines as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017408","descriptor_name":"Guidelines as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017408","descriptor_name":"Guidelines as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017408","descriptor_name":"Guidelines as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017408","descriptor_name":"Guidelines as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":12,"locations":[{"id":"doi:10.1371/journal.pcbi.1004947","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1004947","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004947&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:27415786","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27415786","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:research-repository.st-andrews.ac.uk:10023/9146","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1004947,","pdf_url":"http://biorxiv.org/content/early/2016/05/06/048744","source":{"id":"https://openalex.org/S4306400230","display_name":"St Andrews Research Repository (St Andrews Research Repository)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I16835326","host_organization_name":"University of St Andrews","host_organization_lineage":["https://openalex.org/I16835326"],"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":"Journal article"},{"id":"pmh:oai:uknowledge.uky.edu:biochem_facpub-1103","is_oa":true,"landing_page_url":"https://uknowledge.uky.edu/biochem_facpub/103","pdf_url":null,"source":{"id":"https://openalex.org/S4306402622","display_name":"UKnowledge (University of Kentucky)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I143302722","host_organization_name":"University of Kentucky","host_organization_lineage":["https://openalex.org/I143302722"],"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":"Molecular and Cellular Biochemistry Faculty Publications","raw_type":"text"},{"id":"pmh:oai:RePEc:plo:pcbi00:1004947","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004947","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:cf71e88e54c44aec8a4ecd4ca3b2f1fc","is_oa":true,"landing_page_url":"https://doaj.org/article/cf71e88e54c44aec8a4ecd4ca3b2f1fc","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 12, Iss 7, p e1004947 (2016)","raw_type":"article"},{"id":"pmh:oai:dspace.mit.edu:1721.1/105446","is_oa":true,"landing_page_url":"http://hdl.handle.net/1721.1/105446","pdf_url":null,"source":{"id":"https://openalex.org/S4306400425","display_name":"DSpace@MIT (Massachusetts Institute of Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I63966007","host_organization_name":"Massachusetts Institute of Technology","host_organization_lineage":["https://openalex.org/I63966007"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLOS","raw_type":"http://purl.org/eprint/type/JournalArticle"},{"id":"pmh:oai:europepmc.org:3938005","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4945047","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:pure.atira.dk:publications/75f2c16b-64b2-4cf3-9ce3-92f804ee590b","is_oa":true,"landing_page_url":"https://orbit.dtu.dk/en/publications/75f2c16b-64b2-4cf3-9ce3-92f804ee590b","pdf_url":null,"source":{"id":"https://openalex.org/S4306400705","display_name":"Technical University of Denmark, DTU Orbit (Technical University of Denmark, DTU)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I96673099","host_organization_name":"Technical University of Denmark","host_organization_lineage":["https://openalex.org/I96673099"],"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":"Perez-Riverol , Y , Gatto , L , Wang , R , Sachsenberg , T , Uszkoreit , J , Leprevost , F D V , Fufezan , C , Ternent , T , Eglen , S J , Katz , D S , Pollard , T J , Konovalov , A , Flight , R M , Blin , K &amp; Vizca\u00edno , J A 2016 , ' Ten Simple Rules for Taking Advantage of Git and GitHub ' , P L o S Computational Biology (Online) , vol. 12 , no. 7 , e1004947 . https://doi.org/10.1371/journal.pcbi.1004947","raw_type":"article"},{"id":"pmh:oai:www.repository.cam.ac.uk:1810/256458","is_oa":true,"landing_page_url":"https://www.repository.cam.ac.uk/handle/1810/256458","pdf_url":null,"source":{"id":"https://openalex.org/S4306401777","display_name":"Apollo (University of Cambridge)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I241749","host_organization_name":"University of Cambridge","host_organization_lineage":["https://openalex.org/I241749"],"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":null,"raw_type":"Article"},{"id":"mag:2557994837","is_oa":false,"landing_page_url":"https://dspace.mit.edu/handle/1721.1/105446","pdf_url":null,"source":null,"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":null},{"id":"doi:10.17863/cam.402","is_oa":true,"landing_page_url":"https://doi.org/10.17863/cam.402","pdf_url":null,"source":{"id":"https://openalex.org/S7407050737","display_name":"Apollo","issn_l":null,"issn":[],"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","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article-journal"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1004947","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1004947","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004947&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":[],"awards":[{"id":"https://openalex.org/G1423456925","display_name":null,"funder_award_id":"A 534A","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G1443135587","display_name":null,"funder_award_id":"WT101477MA","funder_id":"https://openalex.org/F4320311904","funder_display_name":"Wellcome Trust"},{"id":"https://openalex.org/G1521975359","display_name":null,"funder_award_id":"R01-GM-094231","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G1986666941","display_name":"PROCESS - Proteomics data Collection, Software and Standards to support open access and long term management of data","funder_award_id":"BB/K01997X/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G2627982309","display_name":null,"funder_award_id":"BB/K01997X/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G3198396954","display_name":null,"funder_award_id":"BB/K020145/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G443606298","display_name":null,"funder_award_id":"BB/L024225/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G4522999067","display_name":null,"funder_award_id":"BB/L002817/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G4609934237","display_name":"CAREER:  Developing Biochemoinformatics Tools for Large-Scale Metabolomics Applications","funder_award_id":"1252893","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G5046430597","display_name":null,"funder_award_id":"WT101477MA","funder_id":"https://openalex.org/F4320307874","funder_display_name":"Wellcome"},{"id":"https://openalex.org/G5727345831","display_name":null,"funder_award_id":"BB/I00095X/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G640079941","display_name":"ProteoGenomics: Dynamic Linkage of Genomes and Proteomes through Ensembl and ProteomeXchange","funder_award_id":"BB/L024225/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G6539226222","display_name":null,"funder_award_id":"BB/I000909/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G678811400","display_name":null,"funder_award_id":"EP/M022641/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G7330173492","display_name":"An Integrated Open Source Software Resource for Quantitative Proteomics","funder_award_id":"BB/I00095X/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G8002632484","display_name":"CoDiMa (CCP in the area of Computational Discrete Mathematics)","funder_award_id":"EP/M022641/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G8092777680","display_name":"A SPATIO-TEMPORAL MAP OF THE DEVELOPMENTAL FLY INTERACTOME","funder_award_id":"BB/L002817/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"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/F4320321114","display_name":"Bundesministerium f\u00fcr Bildung und Forschung","ror":"https://ror.org/04pz7b180"},{"id":"https://openalex.org/F4320322436","display_name":"Novo Nordisk","ror":"https://ror.org/0435rc536"},{"id":"https://openalex.org/F4320330124","display_name":"German Network for Bioinformatics Infrastructure","ror":null},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320334627","display_name":"Engineering and Physical Sciences Research Council","ror":"https://ror.org/0439y7842"},{"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/W2557994837.pdf","grobid_xml":"https://content.openalex.org/works/W2557994837.grobid-xml"},"referenced_works_count":22,"referenced_works":["https://openalex.org/W183866246","https://openalex.org/W1863361676","https://openalex.org/W1964721736","https://openalex.org/W1968993977","https://openalex.org/W2023010129","https://openalex.org/W2026532911","https://openalex.org/W2052388444","https://openalex.org/W2073022274","https://openalex.org/W2097888424","https://openalex.org/W2106839391","https://openalex.org/W2108234281","https://openalex.org/W2114850508","https://openalex.org/W2129390057","https://openalex.org/W2136482257","https://openalex.org/W2140503409","https://openalex.org/W2151577432","https://openalex.org/W2270443308","https://openalex.org/W2582743722","https://openalex.org/W4231676257","https://openalex.org/W4250273625","https://openalex.org/W6635661929","https://openalex.org/W6893467813"],"related_works":[],"abstract_inverted_index":{"Bioinformatics":[0],"is":[1,10,40,97],"a":[2,147,153],"broad":[3],"discipline":[4],"in":[5,25],"which":[6],"one":[7],"common":[8],"denominator":[9],"the":[11,32,43,46,50,62,100,128,142,160],"need":[12],"to":[13,22,81],"produce":[14],"and/or":[15],"use":[16],"software":[17,59,89,123],"that":[18,42,151],"can":[19],"be":[20,65],"applied":[21],"biological":[23],"data":[24,51],"different":[26,136],"contexts.":[27],"To":[28],"enable":[29,127],"and":[30,34,49,78,90,112,130,155,164,184,196],"ensure":[31],"replicability":[33],"traceability":[35],"of":[36,86,102,132,145],"scientific":[37,44],"claims,":[38],"it":[39],"essential":[41,120],"publication,":[45],"corresponding":[47],"datasets,":[48],"analysis":[52,63],"are":[53,118],"made":[54],"publicly":[55],"available":[56,88],"[1,2].":[57],"All":[58],"used":[60],"for":[61,70,121,158,168,176,182,194],"should":[64],"either":[66],"carefully":[67],"documented":[68],"(e.g.,":[69],"commercial":[71],"software)":[72],"or,":[73],"better":[74],"yet,":[75],"openly":[76,87],"shared":[77],"directly":[79],"accessible":[80],"others":[82],"[3,4].":[83],"The":[84],"rise":[85],"source":[91,161],"code":[92,104],"alongside":[93],"concomitant":[94],"collaborative":[95,122],"development":[96],"facilitated":[98],"by":[99],"existence":[101],"several":[103],"repository":[105],"services":[106],"such":[107],"as":[108,186,188],"SourceForge,":[109],"Bitbucket,":[110],"GitLab,":[111],"GitHub,":[113,146],"among":[114],"others.":[115],"These":[116],"resources":[117],"also":[119,172],"projects":[124],"because":[125],"they":[126],"organization":[129],"sharing":[131],"programming":[133],"tasks":[134],"between":[135],"remote":[137],"contributors.":[138],"Here,":[139],"we":[140],"introduce":[141],"main":[143],"features":[144],"popular":[148],"web-based":[149],"platform":[150],"offers":[152,173],"free":[154,189],"integrated":[156],"environment":[157],"hosting":[159],"code,":[162],"documentation,":[163],"project-related":[165],"web":[166],"content":[167],"open-source":[169],"projects.":[170],"GitHub":[171],"paid":[174],"plans":[175,190],"private":[177,192],"repositories":[178,193],"(see":[179],"Box":[180],"1)":[181],"individuals":[183],"businesses":[185],"well":[187],"including":[191],"research":[195],"educational":[197],"use.":[198]},"counts_by_year":[],"updated_date":"2026-06-22T08:00:12.763002","created_date":"2025-10-10T00:00:00"}
