{"id":"https://openalex.org/W2140503409","doi":"https://doi.org/10.1371/journal.pcbi.1000424","title":"A Quick Guide to Organizing Computational Biology Projects","display_name":"A Quick Guide to Organizing Computational Biology Projects","publication_year":2009,"publication_date":"2009-07-30","ids":{"openalex":"https://openalex.org/W2140503409","doi":"https://doi.org/10.1371/journal.pcbi.1000424","mag":"2140503409","pmid":"https://pubmed.ncbi.nlm.nih.gov/19649301"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1000424","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1000424","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000424&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","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000424&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5057375933","display_name":"William Stafford Noble","orcid":"https://orcid.org/0000-0001-7283-4715"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"William Stafford Noble","raw_affiliation_strings":["Department of Genome Sciences, School of Medicine, University of Washington, Seattle, Washington, United States of America. william-noble@u.washington.edu","Department of Genome Sciences, School of Medicine, University of Washington, Seattle, Washington, United States of America","Department of Computer Science and Engineering, University of Washington, Seattle, Washington, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Genome Sciences, School of Medicine, University of Washington, Seattle, Washington, United States of America. william-noble@u.washington.edu","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Department of Genome Sciences, School of Medicine, University of Washington, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Department of Computer Science and Engineering, University of Washington, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I201448701"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5057375933"],"corresponding_institution_ids":["https://openalex.org/I201448701"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":0.672,"has_fulltext":true,"cited_by_count":92,"citation_normalized_percentile":{"value":0.70052393,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"5","issue":"7","first_page":"e1000424","last_page":"e1000424"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.9993000030517578,"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/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.9993000030517578,"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":0.9919999837875366,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9837999939918518,"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/computational-biology","display_name":"Computational biology","score":0.4609644114971161},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4290216863155365},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.4276221990585327},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.41029655933380127}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4609644114971161},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4290216863155365},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.4276221990585327},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.41029655933380127}],"mesh":[{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012107","descriptor_name":"Research Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012107","descriptor_name":"Research Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012107","descriptor_name":"Research Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","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},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1371/journal.pcbi.1000424","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1000424","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000424&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:19649301","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19649301","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:RePEc:plo:pcbi00:1000424","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000424","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:5e60ff739c26412bb42b544c3432fa40","is_oa":true,"landing_page_url":"https://doaj.org/article/5e60ff739c26412bb42b544c3432fa40","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"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 5, Iss 7, p e1000424 (2009)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2709440","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2709440","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1000424","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1000424","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000424&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":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2140503409.pdf","grobid_xml":"https://content.openalex.org/works/W2140503409.grobid-xml"},"referenced_works_count":7,"referenced_works":["https://openalex.org/W2028031755","https://openalex.org/W2035198538","https://openalex.org/W2036212683","https://openalex.org/W2074531772","https://openalex.org/W2130018897","https://openalex.org/W2142188478","https://openalex.org/W4244938140"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2082860237","https://openalex.org/W2119695867","https://openalex.org/W2130076355","https://openalex.org/W1990804418","https://openalex.org/W1993764875","https://openalex.org/W2788277189","https://openalex.org/W2013243191","https://openalex.org/W2151865869","https://openalex.org/W2117258802"],"abstract_inverted_index":{"Most":[0],"bioinformatics":[1,21,177],"coursework":[2],"focuses":[3],"on":[4,64,122],"algorithms,":[5],"with":[6,47,82,180,186],"perhaps":[7],"some":[8],"components":[9],"devoted":[10],"to":[11,18,38,91,110,145],"learning":[12,16,69],"programming":[13],"skills":[14],"and":[15,57,67,130,132,167],"how":[17,109],"use":[19],"existing":[20],"software.":[22],"Unfortunately,":[23],"for":[24,29,96],"students":[25],"who":[26],"are":[27,61,137,160,163],"preparing":[28],"a":[30],"research":[31,148],"career,":[32],"this":[33,68,88],"type":[34],"of":[35,41,87,176],"curriculum":[36],"fails":[37],"address":[39],"many":[40],"the":[42,53,65,155,165],"day-to-day":[43],"organizational":[44,141],"challenges":[45],"associated":[46],"performing":[48],"computational":[49,59,99],"experiments.":[50,100],"In":[51],"practice,":[52],"principles":[54,166],"behind":[55],"organizing":[56,128],"documenting":[58,133],"experiments":[60],"often":[62],"learned":[63],"fly,":[66],"is":[70,90],"strongly":[71],"influenced":[72],"by":[73,79],"personal":[74],"predilections":[75],"as":[76,78,108,127],"well":[77],"chance":[80],"interactions":[81],"collaborators":[83],"or":[84,115],"colleagues.\r\n\r\nThe":[85],"purpose":[86],"article":[89],"describe":[92,104],"one":[93],"good":[94],"strategy":[95],"carrying":[97],"out":[98],"I":[101,119,150,157,170,188],"will":[102,120],"not":[103,152],"profound":[105],"issues":[106,125,136],"such":[107,126],"formulate":[111],"hypotheses,":[112],"design":[113],"experiments,":[114],"draw":[116],"conclusions.":[117],"Rather,":[118],"focus":[121],"relatively":[123],"mundane":[124],"files":[129],"directories":[131],"progress.":[134,149],"These":[135,162],"important":[138],"because":[139],"poor":[140],"choices":[142],"can":[143],"lead":[144],"significantly":[146],"slower":[147],"do":[151],"claim":[153],"that":[154,169],"strategies":[156],"outline":[158],"here":[159],"optimal.":[161],"simply":[164],"practices":[168],"have":[171,189],"developed":[172],"over":[173],"12":[174],"years":[175],"research,":[178],"augmented":[179],"various":[181],"suggestions":[182],"from":[183],"other":[184],"researchers":[185],"whom":[187],"discussed":[190],"these":[191],"issues.":[192]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":10},{"year":2020,"cited_by_count":11},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":9},{"year":2017,"cited_by_count":7},{"year":2016,"cited_by_count":10},{"year":2015,"cited_by_count":12},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":3}],"updated_date":"2026-03-22T08:09:32.410652","created_date":"2025-10-10T00:00:00"}