{"id":"https://openalex.org/W2784181309","doi":"https://doi.org/10.1093/bib/bby001","title":"Characteristics and evolution of the ecosystem of software tools supporting research in molecular biology","display_name":"Characteristics and evolution of the ecosystem of software tools supporting research in molecular biology","publication_year":2018,"publication_date":"2018-01-09","ids":{"openalex":"https://openalex.org/W2784181309","doi":"https://doi.org/10.1093/bib/bby001","mag":"2784181309","pmid":"https://pubmed.ncbi.nlm.nih.gov/29351590"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bby001","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bby001","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5062274087","display_name":"Florencio Pazos","orcid":"https://orcid.org/0000-0002-2646-6226"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Florencio Pazos","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5030602787","display_name":"M\u00f3nica Chagoyen","orcid":"https://orcid.org/0000-0001-6911-1591"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Monica Chagoyen","raw_affiliation_strings":[],"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5062274087"],"corresponding_institution_ids":[],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":0.9953,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.85482172,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"20","issue":"4","first_page":"1329","last_page":"1336"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.9883999824523926,"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"}},"topics":[{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.9883999824523926,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9682999849319458,"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/T11407","display_name":"Innovative Microfluidic and Catalytic Techniques Innovation","score":0.9628000259399414,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/server","display_name":"Server","score":0.7855764627456665},{"id":"https://openalex.org/keywords/popularity","display_name":"Popularity","score":0.6713156700134277},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6600247621536255},{"id":"https://openalex.org/keywords/citation","display_name":"Citation","score":0.6068416237831116},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.5508796572685242},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.5406664609909058},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.523030161857605},{"id":"https://openalex.org/keywords/scale","display_name":"Scale (ratio)","score":0.5015652179718018},{"id":"https://openalex.org/keywords/web-server","display_name":"Web server","score":0.45583581924438477},{"id":"https://openalex.org/keywords/interconnectivity","display_name":"Interconnectivity","score":0.44138845801353455},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.26639193296432495},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.13220152258872986},{"id":"https://openalex.org/keywords/geography","display_name":"Geography","score":0.1039612889289856}],"concepts":[{"id":"https://openalex.org/C93996380","wikidata":"https://www.wikidata.org/wiki/Q44127","display_name":"Server","level":2,"score":0.7855764627456665},{"id":"https://openalex.org/C2780586970","wikidata":"https://www.wikidata.org/wiki/Q1357284","display_name":"Popularity","level":2,"score":0.6713156700134277},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6600247621536255},{"id":"https://openalex.org/C2778805511","wikidata":"https://www.wikidata.org/wiki/Q1713","display_name":"Citation","level":2,"score":0.6068416237831116},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.5508796572685242},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.5406664609909058},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.523030161857605},{"id":"https://openalex.org/C2778755073","wikidata":"https://www.wikidata.org/wiki/Q10858537","display_name":"Scale (ratio)","level":2,"score":0.5015652179718018},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.45583581924438477},{"id":"https://openalex.org/C25516864","wikidata":"https://www.wikidata.org/wiki/Q1665949","display_name":"Interconnectivity","level":2,"score":0.44138845801353455},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.26639193296432495},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.13220152258872986},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.1039612889289856},{"id":"https://openalex.org/C58640448","wikidata":"https://www.wikidata.org/wiki/Q42515","display_name":"Cartography","level":1,"score":0.0},{"id":"https://openalex.org/C15744967","wikidata":"https://www.wikidata.org/wiki/Q9418","display_name":"Psychology","level":0,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C77805123","wikidata":"https://www.wikidata.org/wiki/Q161272","display_name":"Social psychology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D008967","descriptor_name":"Molecular Biology","qualifier_ui":"Q000639","qualifier_name":"trends","is_major_topic":false},{"descriptor_ui":"D008967","descriptor_name":"Molecular Biology","qualifier_ui":"Q000639","qualifier_name":"trends","is_major_topic":false},{"descriptor_ui":"D008967","descriptor_name":"Molecular Biology","qualifier_ui":"Q000639","qualifier_name":"trends","is_major_topic":false},{"descriptor_ui":"D008967","descriptor_name":"Molecular Biology","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D008967","descriptor_name":"Molecular Biology","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D008967","descriptor_name":"Molecular Biology","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D010506","descriptor_name":"Periodicals as Topic","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D010506","descriptor_name":"Periodicals as Topic","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D010506","descriptor_name":"Periodicals as Topic","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":"Q000639","qualifier_name":"trends","is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":"Q000639","qualifier_name":"trends","is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":"Q000639","qualifier_name":"trends","is_major_topic":true},{"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},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000639","qualifier_name":"trends","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000639","qualifier_name":"trends","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000639","qualifier_name":"trends","is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bby001","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bby001","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:29351590","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29351590","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":"Briefings in bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320321837","display_name":"Ministerio de Econom\u00eda y Competitividad","ror":"https://ror.org/034900433"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":20,"referenced_works":["https://openalex.org/W1974165330","https://openalex.org/W2010371279","https://openalex.org/W2027383523","https://openalex.org/W2081930221","https://openalex.org/W2089012022","https://openalex.org/W2110256992","https://openalex.org/W2111023940","https://openalex.org/W2140462113","https://openalex.org/W2147081522","https://openalex.org/W2152208870","https://openalex.org/W2154139219","https://openalex.org/W2171895522","https://openalex.org/W2525035644","https://openalex.org/W2592562685","https://openalex.org/W2605996289","https://openalex.org/W2608032751","https://openalex.org/W2916751937","https://openalex.org/W3091826846","https://openalex.org/W4210702584","https://openalex.org/W4229527776"],"related_works":["https://openalex.org/W2521851057","https://openalex.org/W2377883426","https://openalex.org/W2114232805","https://openalex.org/W2356158875","https://openalex.org/W3091839635","https://openalex.org/W2382865804","https://openalex.org/W1580807987","https://openalex.org/W1543753733","https://openalex.org/W2225080631","https://openalex.org/W2907557917"],"abstract_inverted_index":{"Daily":[0],"work":[1],"in":[2,116,175],"molecular":[3,117],"biology":[4],"presently":[5],"depends":[6],"on":[7],"a":[8,96,189],"large":[9],"number":[10],"of":[11,18,21,28,34,62,68,74,99,139,151,164,184,192,221],"computational":[12],"tools.":[13],"An":[14],"in-depth,":[15],"large-scale":[16,97],"study":[17],"that":[19,42,161,208],"'ecosystem'":[20],"Web":[22,103],"tools,":[23],"its":[24,51],"characteristics,":[25],"interconnectivity,":[26],"patterns":[27,183],"usage/citation,":[29],"temporal":[30,137,182],"evolution":[31,138],"and":[32,45,55,135,169,186,205],"rate":[33,191],"decay":[35],"is":[36,65,166,188,196],"crucial":[37],"for":[38,46,111],"understanding":[39],"the":[40,59,82,106,128,136,149,172,202,206,218],"forces":[41],"shape":[43],"it":[44],"informing":[47],"initiatives":[48,215],"aimed":[49,216],"at":[50,217],"funding,":[52],"long-term":[53,60,219],"maintenance":[54,61,220],"improvement.":[56],"In":[57,91],"particular,":[58],"these":[63,121,140,146,152,222],"tools":[64,84,165],"compromised":[66],"because":[67],"their":[69,125,132],"specific":[70],"development":[71],"model.":[72],"Hundreds":[73],"published":[75],"studies":[76],"become":[77,89],"irreproducible":[78],"de":[79],"facto,":[80],"as":[81,201],"software":[83,114],"used":[85],"to":[86,171],"conduct":[87],"them":[88],"unavailable.":[90],"this":[92,162],"study,":[93],"we":[94,123],"present":[95,180],"survey":[98],">5400":[100],"publications":[101],"describing":[102],"servers":[104,153,179],"within":[105],"two":[107],"main":[108],"bibliographic":[109],"resources":[110],"disseminating":[112],"new":[113],"developments":[115],"biology.":[118],"For":[119],"all":[120],"servers,":[122],"studied":[124],"citation":[126,133],"patterns,":[127],"subjects":[129,174],"they":[130,155],"address,":[131],"networks":[134],"factors.":[141],"We":[142],"also":[143],"analysed":[144],"how":[145],"factors":[147,199],"affect":[148],"availability":[150],"(whether":[154],"are":[156],"alive).":[157],"Our":[158],"results":[159,212],"show":[160],"ecosystem":[163],"highly":[167],"interconnected":[168],"adapts":[170],"'trendy'":[173],"every":[176],"moment.":[177],"The":[178],"characteristic":[181],"citation/usage,":[185],"there":[187],"worrying":[190],"server":[193,203],"'death',":[194],"which":[195],"influenced":[197],"by":[198],"such":[200],"popularity":[204],"institutions":[207],"hosts":[209],"it.":[210],"These":[211],"can":[213],"inform":[214],"resources.":[223]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
