{"id":"https://openalex.org/W2057414058","doi":"https://doi.org/10.1093/bib/bbr035","title":"A toolbox for developing bioinformatics software","display_name":"A toolbox for developing bioinformatics software","publication_year":2011,"publication_date":"2011-07-29","ids":{"openalex":"https://openalex.org/W2057414058","doi":"https://doi.org/10.1093/bib/bbr035","mag":"2057414058","pmid":"https://pubmed.ncbi.nlm.nih.gov/21803787"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbr035","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbr035","pdf_url":"https://academic.oup.com/bib/article-pdf/13/2/244/704110/bbr035.pdf","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":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bib/article-pdf/13/2/244/704110/bbr035.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5058131399","display_name":"Kristian Rother","orcid":null},"institutions":[{"id":"https://openalex.org/I59411706","display_name":"Adam Mickiewicz University in Pozna\u0144","ror":"https://ror.org/04g6bbq64","country_code":"PL","type":"education","lineage":["https://openalex.org/I59411706"]}],"countries":["PL"],"is_corresponding":true,"raw_author_name":"K. Rother","raw_affiliation_strings":["Laboratory of Structural Bioinformatics, Institute of Molecular Biology and Biotechnology, Collegium Biologicum, Adam Mickiewicz University, ul. Umultowska 89, 61-614 Poznan, Poland. krother@genesilico.pl"],"affiliations":[{"raw_affiliation_string":"Laboratory of Structural Bioinformatics, Institute of Molecular Biology and Biotechnology, Collegium Biologicum, Adam Mickiewicz University, ul. Umultowska 89, 61-614 Poznan, Poland. krother@genesilico.pl","institution_ids":["https://openalex.org/I59411706"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014742875","display_name":"Wojciech Potrzebowski","orcid":"https://orcid.org/0000-0002-7789-6779"},"institutions":[{"id":"https://openalex.org/I4210136583","display_name":"Institute of Molecular Biology and Biotechnology","ror":"https://ror.org/03zrdpv47","country_code":"BG","type":"facility","lineage":["https://openalex.org/I4210136583"]}],"countries":["BG"],"is_corresponding":false,"raw_author_name":"W. Potrzebowski","raw_affiliation_strings":["Collegium Biologicum, Adam Mickiewicz University, ul. Umultowska 89, 61-614 Poznan, Poland","Laboratory of Structural Bioinformatics, Institute of Molecular Biology and Biotechnology,"],"affiliations":[{"raw_affiliation_string":"Collegium Biologicum, Adam Mickiewicz University, ul. Umultowska 89, 61-614 Poznan, Poland","institution_ids":[]},{"raw_affiliation_string":"Laboratory of Structural Bioinformatics, Institute of Molecular Biology and Biotechnology,","institution_ids":["https://openalex.org/I4210136583"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062033787","display_name":"T. Puton","orcid":null},"institutions":[{"id":"https://openalex.org/I4210136583","display_name":"Institute of Molecular Biology and Biotechnology","ror":"https://ror.org/03zrdpv47","country_code":"BG","type":"facility","lineage":["https://openalex.org/I4210136583"]}],"countries":["BG"],"is_corresponding":false,"raw_author_name":"T. Puton","raw_affiliation_strings":["Collegium Biologicum, Adam Mickiewicz University, ul. Umultowska 89, 61-614 Poznan, Poland","Laboratory of Structural Bioinformatics, Institute of Molecular Biology and Biotechnology,"],"affiliations":[{"raw_affiliation_string":"Collegium Biologicum, Adam Mickiewicz University, ul. Umultowska 89, 61-614 Poznan, Poland","institution_ids":[]},{"raw_affiliation_string":"Laboratory of Structural Bioinformatics, Institute of Molecular Biology and Biotechnology,","institution_ids":["https://openalex.org/I4210136583"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078300601","display_name":"M. Rother","orcid":null},"institutions":[{"id":"https://openalex.org/I4210136583","display_name":"Institute of Molecular Biology and Biotechnology","ror":"https://ror.org/03zrdpv47","country_code":"BG","type":"facility","lineage":["https://openalex.org/I4210136583"]}],"countries":["BG"],"is_corresponding":false,"raw_author_name":"M. Rother","raw_affiliation_strings":["Collegium Biologicum, Adam Mickiewicz University, ul. Umultowska 89, 61-614 Poznan, Poland","Laboratory of Structural Bioinformatics, Institute of Molecular Biology and Biotechnology,"],"affiliations":[{"raw_affiliation_string":"Collegium Biologicum, Adam Mickiewicz University, ul. Umultowska 89, 61-614 Poznan, Poland","institution_ids":[]},{"raw_affiliation_string":"Laboratory of Structural Bioinformatics, Institute of Molecular Biology and Biotechnology,","institution_ids":["https://openalex.org/I4210136583"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041419710","display_name":"Ewa Wywia\u0142","orcid":null},"institutions":[{"id":"https://openalex.org/I4210136583","display_name":"Institute of Molecular Biology and Biotechnology","ror":"https://ror.org/03zrdpv47","country_code":"BG","type":"facility","lineage":["https://openalex.org/I4210136583"]}],"countries":["BG"],"is_corresponding":false,"raw_author_name":"E. Wywial","raw_affiliation_strings":["Collegium Biologicum, Adam Mickiewicz University, ul. Umultowska 89, 61-614 Poznan, Poland","Laboratory of Structural Bioinformatics, Institute of Molecular Biology and Biotechnology,"],"affiliations":[{"raw_affiliation_string":"Collegium Biologicum, Adam Mickiewicz University, ul. Umultowska 89, 61-614 Poznan, Poland","institution_ids":[]},{"raw_affiliation_string":"Laboratory of Structural Bioinformatics, Institute of Molecular Biology and Biotechnology,","institution_ids":["https://openalex.org/I4210136583"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5003280938","display_name":"Janusz M. Bujnicki","orcid":"https://orcid.org/0000-0002-6633-165X"},"institutions":[{"id":"https://openalex.org/I4210136583","display_name":"Institute of Molecular Biology and Biotechnology","ror":"https://ror.org/03zrdpv47","country_code":"BG","type":"facility","lineage":["https://openalex.org/I4210136583"]}],"countries":["BG"],"is_corresponding":false,"raw_author_name":"J. M. Bujnicki","raw_affiliation_strings":["Collegium Biologicum, Adam Mickiewicz University, ul. Umultowska 89, 61-614 Poznan, Poland","Laboratory of Structural Bioinformatics, Institute of Molecular Biology and Biotechnology,"],"affiliations":[{"raw_affiliation_string":"Collegium Biologicum, Adam Mickiewicz University, ul. Umultowska 89, 61-614 Poznan, Poland","institution_ids":[]},{"raw_affiliation_string":"Laboratory of Structural Bioinformatics, Institute of Molecular Biology and Biotechnology,","institution_ids":["https://openalex.org/I4210136583"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5058131399"],"corresponding_institution_ids":["https://openalex.org/I59411706"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":1.6009,"has_fulltext":true,"cited_by_count":23,"citation_normalized_percentile":{"value":0.82602043,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"13","issue":"2","first_page":"244","last_page":"257"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.9890000224113464,"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":0.9890000224113464,"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":0.9872000217437744,"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/T10260","display_name":"Software Engineering Research","score":0.9807999730110168,"subfield":{"id":"https://openalex.org/subfields/1710","display_name":"Information Systems"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7339182496070862},{"id":"https://openalex.org/keywords/toolbox","display_name":"Toolbox","score":0.7261034846305847},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.7033992409706116},{"id":"https://openalex.org/keywords/software-development","display_name":"Software development","score":0.6119011640548706},{"id":"https://openalex.org/keywords/maintainability","display_name":"Maintainability","score":0.6077684164047241},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5401604771614075},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.4583640992641449},{"id":"https://openalex.org/keywords/software-development-process","display_name":"Software development process","score":0.416349321603775},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.41332685947418213},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.14013203978538513}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7339182496070862},{"id":"https://openalex.org/C2777655017","wikidata":"https://www.wikidata.org/wiki/Q1501161","display_name":"Toolbox","level":2,"score":0.7261034846305847},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.7033992409706116},{"id":"https://openalex.org/C529173508","wikidata":"https://www.wikidata.org/wiki/Q638608","display_name":"Software development","level":3,"score":0.6119011640548706},{"id":"https://openalex.org/C160713754","wikidata":"https://www.wikidata.org/wiki/Q1389965","display_name":"Maintainability","level":2,"score":0.6077684164047241},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5401604771614075},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.4583640992641449},{"id":"https://openalex.org/C180152950","wikidata":"https://www.wikidata.org/wiki/Q2904257","display_name":"Software development process","level":4,"score":0.416349321603775},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.41332685947418213},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.14013203978538513}],"mesh":[{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"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":4,"locations":[{"id":"doi:10.1093/bib/bbr035","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbr035","pdf_url":"https://academic.oup.com/bib/article-pdf/13/2/244/704110/bbr035.pdf","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:21803787","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21803787","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},{"id":"pmh:oai:europepmc.org:2582129","is_oa":false,"landing_page_url":"http://europepmc.org/articles/PMC3294241","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":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:3294241","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3294241","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbr035","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbr035","pdf_url":"https://academic.oup.com/bib/article-pdf/13/2/244/704110/bbr035.pdf","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"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","score":0.5699999928474426,"display_name":"Industry, innovation and infrastructure"}],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2057414058.pdf","grobid_xml":"https://content.openalex.org/works/W2057414058.grobid-xml"},"referenced_works_count":54,"referenced_works":["https://openalex.org/W48540783","https://openalex.org/W255996521","https://openalex.org/W1484115408","https://openalex.org/W1493688518","https://openalex.org/W1508730334","https://openalex.org/W1511496623","https://openalex.org/W1529465401","https://openalex.org/W1586436801","https://openalex.org/W1649645444","https://openalex.org/W1982680051","https://openalex.org/W1995164506","https://openalex.org/W2005568256","https://openalex.org/W2006661775","https://openalex.org/W2006874588","https://openalex.org/W2020517116","https://openalex.org/W2035198538","https://openalex.org/W2055623935","https://openalex.org/W2064463982","https://openalex.org/W2067763964","https://openalex.org/W2072876893","https://openalex.org/W2079320648","https://openalex.org/W2079890844","https://openalex.org/W2081683425","https://openalex.org/W2082176153","https://openalex.org/W2085822559","https://openalex.org/W2097049539","https://openalex.org/W2100827887","https://openalex.org/W2102516324","https://openalex.org/W2108862685","https://openalex.org/W2108997067","https://openalex.org/W2110992797","https://openalex.org/W2114850508","https://openalex.org/W2116423958","https://openalex.org/W2120787570","https://openalex.org/W2121054327","https://openalex.org/W2123586642","https://openalex.org/W2128044898","https://openalex.org/W2129005287","https://openalex.org/W2141829611","https://openalex.org/W2143980572","https://openalex.org/W2147397672","https://openalex.org/W2148906281","https://openalex.org/W2150934173","https://openalex.org/W2151651919","https://openalex.org/W2170030776","https://openalex.org/W2267596186","https://openalex.org/W2500633667","https://openalex.org/W2616313643","https://openalex.org/W2752455916","https://openalex.org/W2917136151","https://openalex.org/W2973456924","https://openalex.org/W2983995785","https://openalex.org/W3143245542","https://openalex.org/W4205516218"],"related_works":["https://openalex.org/W4230627789","https://openalex.org/W168761233","https://openalex.org/W3105511281","https://openalex.org/W2476117260","https://openalex.org/W983931886","https://openalex.org/W2472680075","https://openalex.org/W2088382486","https://openalex.org/W4292756589","https://openalex.org/W1845068655","https://openalex.org/W3121161786"],"abstract_inverted_index":{"Creating":[0],"useful":[1,78,140],"software":[2,13,35,59,69,112],"is":[3,19,38],"a":[4,64,81,108],"major":[5],"activity":[6],"of":[7,66,86,97,117,131,150],"many":[8,125,142],"scientists,":[9],"including":[10],"bioinformaticians.":[11],"Nevertheless,":[12],"development":[14,36,70],"in":[15,71,121],"an":[16,72],"academic":[17,73],"setting":[18],"often":[20],"unsystematic,":[21],"which":[22],"can":[23],"lead":[24],"to":[25,40,79,91,127,138,147],"problems":[26],"associated":[27],"with":[28],"maintenance":[29],"and":[30,42,61,90,95,123,146],"long-term":[31],"availibility.":[32],"Unfortunately,":[33],"well-documented":[34],"methodology":[37],"difficult":[39],"adopt,":[41],"technical":[43],"measures":[44],"that":[45,106],"directly":[46],"improve":[47],"bioinformatic":[48],"programming":[49,144],"have":[50,56,62],"not":[51],"been":[52],"described":[53],"comprehensively.":[54],"We":[55,75,114,134],"examined":[57],"22":[58,119],"projects":[60,120,145],"identified":[63],"set":[65],"practices":[67],"for":[68,141],"environment.":[74],"found":[76],"them":[77],"plan":[80],"project,":[82],"support":[83],"the":[84,98,118,129,148],"involvement":[85],"experts":[87],"(e.g.":[88],"experimentalists),":[89],"promote":[92],"higher":[93],"quality":[94],"maintainability":[96],"resulting":[99],"programs.":[100],"This":[101],"article":[102],"describes":[103],"12":[104],"techniques":[105],"facilitate":[107],"quick":[109],"start":[110],"into":[111],"engineering.":[113],"describe":[115],"3":[116],"detail":[122],"give":[124],"examples":[126],"illustrate":[128],"usage":[130],"particular":[132],"techniques.":[133],"expect":[135],"this":[136],"toolbox":[137],"be":[139],"bioinformatics":[143],"training":[149],"scientific":[151],"programmers.":[152]},"counts_by_year":[{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":2},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":7}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}
