{"id":"https://openalex.org/W2555194672","doi":"https://doi.org/10.1186/s13321-016-0179-6","title":"Towards agile large-scale predictive modelling in drug discovery with flow-based programming design principles","display_name":"Towards agile large-scale predictive modelling in drug discovery with flow-based programming design principles","publication_year":2016,"publication_date":"2016-11-24","ids":{"openalex":"https://openalex.org/W2555194672","doi":"https://doi.org/10.1186/s13321-016-0179-6","mag":"2555194672"},"language":"en","primary_location":{"id":"doi:10.1186/s13321-016-0179-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-016-0179-6","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-016-0179-6","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","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":"Journal of Cheminformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-016-0179-6","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5076964957","display_name":"Samuel Lampa","orcid":"https://orcid.org/0000-0001-6740-9212"},"institutions":[{"id":"https://openalex.org/I123387679","display_name":"Uppsala University","ror":"https://ror.org/048a87296","country_code":"SE","type":"education","lineage":["https://openalex.org/I123387679"]}],"countries":["SE"],"is_corresponding":true,"raw_author_name":"Samuel Lampa","raw_affiliation_strings":["Department of Pharmaceutical Biosciences, Uppsala University, Box 591, 751 24, Uppsala, Sweden"],"affiliations":[{"raw_affiliation_string":"Department of Pharmaceutical Biosciences, Uppsala University, Box 591, 751 24, Uppsala, Sweden","institution_ids":["https://openalex.org/I123387679"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027509528","display_name":"Jonathan Alvarsson","orcid":"https://orcid.org/0000-0002-8682-7206"},"institutions":[{"id":"https://openalex.org/I123387679","display_name":"Uppsala University","ror":"https://ror.org/048a87296","country_code":"SE","type":"education","lineage":["https://openalex.org/I123387679"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Jonathan Alvarsson","raw_affiliation_strings":["Department of Pharmaceutical Biosciences, Uppsala University, Box 591, 751 24, Uppsala, Sweden"],"affiliations":[{"raw_affiliation_string":"Department of Pharmaceutical Biosciences, Uppsala University, Box 591, 751 24, Uppsala, Sweden","institution_ids":["https://openalex.org/I123387679"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5046663348","display_name":"Ola Spjuth","orcid":"https://orcid.org/0000-0002-8083-2864"},"institutions":[{"id":"https://openalex.org/I2800139495","display_name":"Science for Life Laboratory","ror":"https://ror.org/04ev03g22","country_code":"SE","type":"facility","lineage":["https://openalex.org/I2800139495"]},{"id":"https://openalex.org/I123387679","display_name":"Uppsala University","ror":"https://ror.org/048a87296","country_code":"SE","type":"education","lineage":["https://openalex.org/I123387679"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Ola Spjuth","raw_affiliation_strings":["Department of Pharmaceutical Biosciences, Uppsala University, Box 591, 751 24, Uppsala, Sweden","Science for Life Laboratory, Uppsala University, Box 3037, 750 03, Uppsala, Sweden"],"affiliations":[{"raw_affiliation_string":"Department of Pharmaceutical Biosciences, Uppsala University, Box 591, 751 24, Uppsala, Sweden","institution_ids":["https://openalex.org/I123387679"]},{"raw_affiliation_string":"Science for Life Laboratory, Uppsala University, Box 3037, 750 03, Uppsala, Sweden","institution_ids":["https://openalex.org/I2800139495"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5076964957"],"corresponding_institution_ids":["https://openalex.org/I123387679"],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1290,"currency":"GBP","value_usd":1582},"fwci":16.0026,"has_fulltext":true,"cited_by_count":36,"citation_normalized_percentile":{"value":0.98653363,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":91,"max":99},"biblio":{"volume":"8","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.9998999834060669,"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":0.9998999834060669,"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/T10715","display_name":"Distributed and Parallel Computing Systems","score":0.9983999729156494,"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/T10101","display_name":"Cloud Computing and Resource Management","score":0.9822999835014343,"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":0.8248902559280396},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.7283282279968262},{"id":"https://openalex.org/keywords/agile-software-development","display_name":"Agile software development","score":0.6072954535484314},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.5183704495429993},{"id":"https://openalex.org/keywords/automation","display_name":"Automation","score":0.4834045469760895},{"id":"https://openalex.org/keywords/cloud-computing","display_name":"Cloud computing","score":0.45772653818130493},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.43638113141059875},{"id":"https://openalex.org/keywords/distributed-computing","display_name":"Distributed computing","score":0.40828344225883484},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.38554951548576355},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.371318519115448},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.16695377230644226},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.14069825410842896}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8248902559280396},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.7283282279968262},{"id":"https://openalex.org/C14185376","wikidata":"https://www.wikidata.org/wiki/Q30232","display_name":"Agile software development","level":2,"score":0.6072954535484314},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.5183704495429993},{"id":"https://openalex.org/C115901376","wikidata":"https://www.wikidata.org/wiki/Q184199","display_name":"Automation","level":2,"score":0.4834045469760895},{"id":"https://openalex.org/C79974875","wikidata":"https://www.wikidata.org/wiki/Q483639","display_name":"Cloud computing","level":2,"score":0.45772653818130493},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.43638113141059875},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.40828344225883484},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.38554951548576355},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.371318519115448},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.16695377230644226},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.14069825410842896},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0},{"id":"https://openalex.org/C78519656","wikidata":"https://www.wikidata.org/wiki/Q101333","display_name":"Mechanical engineering","level":1,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1186/s13321-016-0179-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-016-0179-6","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-016-0179-6","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","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":"Journal of Cheminformatics","raw_type":"journal-article"},{"id":"pmh:oai:DiVA.org:uu-315089","is_oa":true,"landing_page_url":"http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-315089","pdf_url":null,"source":{"id":"https://openalex.org/S4306401559","display_name":"KTH Publication Database DiVA (KTH Royal Institute of Technology)","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Article in journal"},{"id":"pmh:oai:europepmc.org:4085728","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5123367","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"}],"best_oa_location":{"id":"doi:10.1186/s13321-016-0179-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-016-0179-6","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-016-0179-6","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","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":"Journal of Cheminformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.6000000238418579,"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320317161","display_name":"Swedish e-Science Research Centre","ror":"https://ror.org/01e59yk92"},{"id":"https://openalex.org/F4320336376","display_name":"Uppsala Multidisciplinary Center for Advanced Computational Science","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2555194672.pdf","grobid_xml":"https://content.openalex.org/works/W2555194672.grobid-xml"},"referenced_works_count":37,"referenced_works":["https://openalex.org/W187096259","https://openalex.org/W1583240815","https://openalex.org/W1596936080","https://openalex.org/W1598064945","https://openalex.org/W1835740130","https://openalex.org/W2009942590","https://openalex.org/W2027702238","https://openalex.org/W2045673749","https://openalex.org/W2052008210","https://openalex.org/W2052822586","https://openalex.org/W2060062036","https://openalex.org/W2061939373","https://openalex.org/W2065656474","https://openalex.org/W2097438318","https://openalex.org/W2110417468","https://openalex.org/W2114739399","https://openalex.org/W2118585731","https://openalex.org/W2123100726","https://openalex.org/W2123179625","https://openalex.org/W2135653217","https://openalex.org/W2136482257","https://openalex.org/W2138193360","https://openalex.org/W2140493325","https://openalex.org/W2144610372","https://openalex.org/W2152521444","https://openalex.org/W2153166923","https://openalex.org/W2161645441","https://openalex.org/W2169594074","https://openalex.org/W2189465200","https://openalex.org/W2213735563","https://openalex.org/W2264449466","https://openalex.org/W2310259903","https://openalex.org/W2323034105","https://openalex.org/W2413944633","https://openalex.org/W2493157521","https://openalex.org/W2612073675","https://openalex.org/W4394430204"],"related_works":["https://openalex.org/W4244478748","https://openalex.org/W1981780420","https://openalex.org/W2182707996","https://openalex.org/W4223488648","https://openalex.org/W45233828","https://openalex.org/W2964988449","https://openalex.org/W2134969820","https://openalex.org/W2251605416","https://openalex.org/W4389340727","https://openalex.org/W4205786897"],"abstract_inverted_index":{"Predictive":[0],"modelling":[1,37,119],"in":[2,61,73],"drug":[3],"discovery":[4],"is":[5],"challenging":[6],"to":[7,49,77],"automate":[8],"as":[9,41,98],"it":[10],"often":[11],"contains":[12],"multiple":[13],"analysis":[14],"steps":[15],"and":[16,20,80],"might":[17],"involve":[18],"cross-validation":[19],"parameter":[21],"tuning":[22],"that":[23],"create":[24],"complex":[25],"dependencies":[26],"between":[27],"tasks.":[28],"With":[29],"large-scale":[30],"data":[31],"or":[32,43],"when":[33,118],"using":[34,115,126],"computationally":[35],"demanding":[36],"methods,":[38],"e-infrastructures":[39],"such":[40],"high-performance":[42],"cloud":[44],"computing":[45],"are":[46,71],"required,":[47],"adding":[48],"the":[50,67,74,93,102,112,116],"existing":[51],"challenges":[52],"of":[53,63,92,101,123],"fault-tolerant":[54],"automation.":[55],"Workflow":[56],"management":[57],"systems":[58,70],"can":[59],"aid":[60],"many":[62],"these":[64],"challenges,":[65],"but":[66],"currently":[68],"available":[69],"lacking":[72],"functionality":[75],"needed":[76],"enable":[78],"agile":[79],"flexible":[81],"predictive":[82],"modelling.":[83],"We":[84,109],"here":[85],"present":[86],"an":[87,99],"approach":[88,117],"inspired":[89],"by":[90],"elements":[91],"flow-based":[94],"programming":[95],"paradigm,":[96],"implemented":[97],"extension":[100],"Luigi":[103],"system":[104],"which":[105],"we":[106],"name":[107],"SciLuigi.":[108],"also":[110],"discuss":[111],"experiences":[113],"from":[114],"a":[120,127],"large":[121],"set":[122],"biochemical":[124],"interactions":[125],"shared":[128],"computer":[129],"cluster.":[130]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":9},{"year":2017,"cited_by_count":3}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2016-11-30T00:00:00"}
