{"id":"https://openalex.org/W2951604286","doi":"https://doi.org/10.1186/s12918-017-0423-3","title":"SBpipe: a collection of pipelines for automating repetitive simulation and analysis tasks","display_name":"SBpipe: a collection of pipelines for automating repetitive simulation and analysis tasks","publication_year":2017,"publication_date":"2017-04-10","ids":{"openalex":"https://openalex.org/W2951604286","doi":"https://doi.org/10.1186/s12918-017-0423-3","mag":"2951604286","pmid":"https://pubmed.ncbi.nlm.nih.gov/28395655"},"language":"en","primary_location":{"id":"doi:10.1186/s12918-017-0423-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12918-017-0423-3","pdf_url":"https://bmcsystbiol.biomedcentral.com/track/pdf/10.1186/s12918-017-0423-3","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Systems Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://bmcsystbiol.biomedcentral.com/track/pdf/10.1186/s12918-017-0423-3","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5015476957","display_name":"Piero Dalle Pezze","orcid":"https://orcid.org/0000-0003-1695-6763"},"institutions":[{"id":"https://openalex.org/I1302113299","display_name":"Babraham Institute","ror":"https://ror.org/01d5qpn59","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1302113299","https://openalex.org/I2799693246","https://openalex.org/I4210087105"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Piero Dalle Pezze","raw_affiliation_strings":["The Babraham Institute, Babraham Campus, Cambridge, CB22 3AT, UK. piero.dallepezze@babraham.ac.uk","The Babraham Institute, Babraham Campus, Cambridge, CB22 3AT, UK"],"raw_orcid":"https://orcid.org/0000-0003-1695-6763","affiliations":[{"raw_affiliation_string":"The Babraham Institute, Babraham Campus, Cambridge, CB22 3AT, UK. piero.dallepezze@babraham.ac.uk","institution_ids":["https://openalex.org/I1302113299"]},{"raw_affiliation_string":"The Babraham Institute, Babraham Campus, Cambridge, CB22 3AT, UK","institution_ids":["https://openalex.org/I1302113299"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5112438594","display_name":"Nicolas Le Nov\u00e8re","orcid":null},"institutions":[{"id":"https://openalex.org/I1302113299","display_name":"Babraham Institute","ror":"https://ror.org/01d5qpn59","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1302113299","https://openalex.org/I2799693246","https://openalex.org/I4210087105"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Nicolas Le Nov\u00e8re","raw_affiliation_strings":["The Babraham Institute, Babraham Campus, Cambridge, CB22 3AT, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Babraham Institute, Babraham Campus, Cambridge, CB22 3AT, UK","institution_ids":["https://openalex.org/I1302113299"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5015476957"],"corresponding_institution_ids":["https://openalex.org/I1302113299"],"apc_list":null,"apc_paid":null,"fwci":0.8972,"has_fulltext":true,"cited_by_count":11,"citation_normalized_percentile":{"value":0.74527117,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"11","issue":"1","first_page":"46","last_page":"46"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.3174000084400177,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.3174000084400177,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.10199999809265137,"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":0.046300001442432404,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.8918065428733826},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7812691926956177},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5953395366668701},{"id":"https://openalex.org/keywords/documentation","display_name":"Documentation","score":0.5466445684432983},{"id":"https://openalex.org/keywords/pipeline-transport","display_name":"Pipeline transport","score":0.5411907434463501},{"id":"https://openalex.org/keywords/open-source","display_name":"Open source","score":0.47745516896247864},{"id":"https://openalex.org/keywords/robustness","display_name":"Robustness (evolution)","score":0.46254608035087585},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.4550701975822449},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.4241713583469391},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.40672919154167175},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.3393624424934387},{"id":"https://openalex.org/keywords/real-time-computing","display_name":"Real-time computing","score":0.3336537480354309}],"concepts":[{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.8918065428733826},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7812691926956177},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5953395366668701},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.5466445684432983},{"id":"https://openalex.org/C175309249","wikidata":"https://www.wikidata.org/wiki/Q725864","display_name":"Pipeline transport","level":2,"score":0.5411907434463501},{"id":"https://openalex.org/C3018397939","wikidata":"https://www.wikidata.org/wiki/Q3644502","display_name":"Open source","level":3,"score":0.47745516896247864},{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.46254608035087585},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.4550701975822449},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.4241713583469391},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.40672919154167175},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.3393624424934387},{"id":"https://openalex.org/C79403827","wikidata":"https://www.wikidata.org/wiki/Q3988","display_name":"Real-time computing","level":1,"score":0.3336537480354309},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C87717796","wikidata":"https://www.wikidata.org/wiki/Q146326","display_name":"Environmental engineering","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"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":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12918-017-0423-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12918-017-0423-3","pdf_url":"https://bmcsystbiol.biomedcentral.com/track/pdf/10.1186/s12918-017-0423-3","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Systems Biology","raw_type":"journal-article"},{"id":"pmid:28395655","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28395655","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":"BMC systems biology","raw_type":null},{"id":"pmh:oai:doaj.org/article:c066ea8d983548409ba28a7662b25c12","is_oa":false,"landing_page_url":"https://doaj.org/article/c066ea8d983548409ba28a7662b25c12","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Systems Biology, Vol 11, Iss 1, Pp 1-5 (2017)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:5387271","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5387271","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Syst Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12918-017-0423-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12918-017-0423-3","pdf_url":"https://bmcsystbiol.biomedcentral.com/track/pdf/10.1186/s12918-017-0423-3","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Systems Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.5400000214576721,"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure"}],"awards":[{"id":"https://openalex.org/G5753548785","display_name":null,"funder_award_id":"BBS/E/B/000C0419","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G6705591880","display_name":"A systems approach to understanding lipid, Ca2+ and MAPK signalling networks","funder_award_id":"BBS/E/B/000C0419","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G7255661211","display_name":null,"funder_award_id":"BBS/E/B/000C0432","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"}],"funders":[{"id":"https://openalex.org/F4320334629","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2951604286.pdf","grobid_xml":"https://content.openalex.org/works/W2951604286.grobid-xml"},"referenced_works_count":16,"referenced_works":["https://openalex.org/W1965130848","https://openalex.org/W1978159157","https://openalex.org/W2003003919","https://openalex.org/W2047108386","https://openalex.org/W2100486339","https://openalex.org/W2102653059","https://openalex.org/W2107062718","https://openalex.org/W2115343689","https://openalex.org/W2136755623","https://openalex.org/W2153921000","https://openalex.org/W2472163094","https://openalex.org/W2543580944","https://openalex.org/W2610752197","https://openalex.org/W2626382019","https://openalex.org/W2765438719","https://openalex.org/W2804004722"],"related_works":["https://openalex.org/W2380602769","https://openalex.org/W2047554624","https://openalex.org/W4317425630","https://openalex.org/W2106292811","https://openalex.org/W3008399030","https://openalex.org/W3185131596","https://openalex.org/W3112960188","https://openalex.org/W2745015246","https://openalex.org/W2950999793","https://openalex.org/W2788194819"],"abstract_inverted_index":{"BACKGROUND:":[0],"The":[1,24,113,244],"rapid":[2],"growth":[3],"of":[4,7,16,28,63,94,119,136,169,219,249],"the":[5,14,61,129,143,167,207,217,256],"number":[6],"mathematical":[8],"models":[9,177],"in":[10,80,179,184,233],"Systems":[11],"Biology":[12],"fostered":[13],"development":[15,241],"many":[17],"tools":[18],"to":[19,214],"simulate":[20],"and":[21,26,36,83,107,123,172,222,225,236,242,247],"analyse":[22],"them.":[23],"reliability":[25],"precision":[27],"these":[29,54,230],"tasks":[30,79,218],"often":[31],"depend":[32],"on":[33,53,152],"multiple":[34],"repetitions":[35],"they":[37],"can":[38,50,150,175,201],"be":[39,51,202],"optimised":[40],"if":[41],"executed":[42],"as":[43,191],"pipelines.":[44],"In":[45],"addition,":[46],"new":[47],"formal":[48],"analyses":[49,102,118],"performed":[52],"repeat":[55,216,231],"sequences,":[56],"revealing":[57],"important":[58],"insights":[59],"about":[60],"accuracy":[62],"model":[64,81,96,140,170,220,240],"predictions.":[65],"RESULTS:":[66],"Here":[67],"we":[68],"introduce":[69],"SBpipe,":[70],"an":[71],"open":[72],"source":[73,245],"software":[74,199],"tool":[75],"for":[76,134,197],"automating":[77],"repetitive":[78],"building":[82,171],"simulation.":[84,173],"Using":[85],"basic":[86],"YAML":[87],"configuration":[88],"files,":[89],"SBpipe":[90,174,211],"builds":[91],"a":[92,110,192,234],"sequence":[93],"repeated":[95],"simulations":[97],"or":[98,138,159,182],"parameter":[99,114,120,124,223],"estimations,":[100],"performs":[101],"from":[103,128,229],"this":[104,250],"generated":[105],"sequence,":[106],"finally":[108],"generates":[109],"LaTeX/PDF":[111],"report.":[112],"estimation":[115],"pipeline":[116],"offers":[117],"profile":[121],"likelihood":[122],"correlation":[125],"using":[126,189],"samples":[127],"computed":[130],"estimates.":[131],"Specific":[132],"pipelines":[133],"scanning":[135],"one":[137],"two":[139],"parameters":[141],"at":[142,255],"same":[144],"time":[145],"are":[146,252],"also":[147],"provided.":[148],"Pipelines":[149],"run":[151],"multicore":[153],"computers,":[154],"Sun":[155],"Grid":[156],"Engine":[157],"(SGE),":[158],"Load":[160],"Sharing":[161],"Facility":[162],"(LSF)":[163],"clusters,":[164],"speeding":[165],"up":[166],"processes":[168],"execute":[176],"implemented":[178],"COPASI,":[180],"Python":[181,190],"coded":[183],"any":[185],"other":[186,198],"programming":[187],"language":[188],"wrapper":[193],"module.":[194],"Future":[195],"support":[196],"simulators":[200],"dynamically":[203],"added":[204],"without":[205],"affecting":[206],"current":[208],"implementation.":[209],"CONCLUSIONS:":[210],"allows":[212],"users":[213],"automatically":[215],"simulation":[221],"estimation,":[224],"extract":[226],"robustness":[227],"information":[228],"sequences":[232],"solid":[235],"consistent":[237],"manner,":[238],"facilitating":[239],"analysis.":[243],"code":[246],"documentation":[248],"project":[251],"freely":[253],"available":[254],"web":[257],"site:":[258],"https://pdp10.github.io/sbpipe/":[259],".":[260]},"counts_by_year":[{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":2}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2019-06-27T00:00:00"}
