{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,7]],"date-time":"2025-11-07T09:17:16Z","timestamp":1762507036709,"version":"3.37.3"},"reference-count":116,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2017,4,17]],"date-time":"2017-04-17T00:00:00Z","timestamp":1492387200000},"content-version":"vor","delay-in-days":1,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001602","name":"Science Foundation Ireland","doi-asserted-by":"publisher","award":["SFI\/12\/RC\/2289"],"award-info":[{"award-number":["SFI\/12\/RC\/2289"]}],"id":[{"id":"10.13039\/501100001602","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,9,28]]},"DOI":"10.1093\/bib\/bbx039","type":"journal-article","created":{"date-parts":[[2017,3,14]],"date-time":"2017-03-14T20:35:40Z","timestamp":1489523740000},"page":"1035-1050","source":"Crossref","is-referenced-by-count":16,"title":["Improving data workflow systems with cloud services and use of open data for bioinformatics research"],"prefix":"10.1093","volume":"19","author":[{"given":"Md Rezaul","family":"Karim","sequence":"first","affiliation":[{"name":"Semantics in eHealth and Life Sciences (SeLS), Insight Centre for Data Analytics, National University of Ireland, Galway, Ireland"}]},{"given":"Audrey","family":"Michel","sequence":"additional","affiliation":[{"name":"School of Biochemistry and Cell Biology, University College Cork, Ireland"}]},{"given":"Achille","family":"Zappa","sequence":"additional","affiliation":[{"name":"Insight Centre for Data Analytics, National University of Ireland Galway, Dangan, Galway, Ireland"}]},{"given":"Pavel","family":"Baranov","sequence":"additional","affiliation":[{"name":"School of Biochemistry and Cell Biology, University College Cork, Ireland"}]},{"given":"Ratnesh","family":"Sahay","sequence":"additional","affiliation":[{"name":"Semantics in eHealth and Life Sciences (SeLS), Insight Centre for Data Analytics, National University of Ireland, Galway, Ireland"}]},{"given":"Dietrich","family":"Rebholz-Schuhmann","sequence":"additional","affiliation":[{"name":"Insight Centre for Data Analytics, National University of Ireland Galway, Dangan, Galway, Ireland"}]}],"member":"286","published-online":{"date-parts":[[2017,4,16]]},"reference":[{"issue":"5","key":"key\n\t\t\t\t20180928113218_bbx039-B1","doi-asserted-by":"crossref","first-page":"541","DOI":"10.1016\/j.future.2008.06.013","article-title":"Scientific workflow design for mere mortals","volume":"25","author":"McPhillips","year":"2009","journal-title":"Future Gener Comput Syst"},{"issue":"12","key":"key\n\t\t\t\t20180928113218_bbx039-B2","doi-asserted-by":"crossref","first-page":"829","DOI":"10.1038\/nrg3337","article-title":"Text-mining solutions for biomedical research enabling integrative biology","volume":"13","author":"Rebholz-Schuhmann","year":"2012","journal-title":"Nat Rev Genet"},{"year":"2003","author":"Andrews","key":"key\n\t\t\t\t20180928113218_bbx039-B3"},{"volume-title":"Proceedings of the International Conference on Parallel Processing and Applied Mathematics (PPAM)","year":"2007","author":"Barker","key":"key\n\t\t\t\t20180928113218_bbx039-B4"},{"issue":"12","key":"key\n\t\t\t\t20180928113218_bbx039-B5","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1109\/MC.2007.421","article-title":"Examining the challenges of scientific workflows","volume":"40","author":"Gil","year":"2007","journal-title":"Computer"},{"key":"key\n\t\t\t\t20180928113218_bbx039-B6","doi-asserted-by":"crossref","first-page":"801","DOI":"10.1007\/s10822-012-9577-7","article-title":"Scientific workflow systems: Pipeline Pilot and KNIME","volume":"26","author":"Warr","year":"2012","journal-title":"J Comput Aided Mol Des"},{"volume-title":"Workflows for e-Science Scientific Workflows for Grids","year":"2014","author":"Taylor","key":"key\n\t\t\t\t20180928113218_bbx039-B7"},{"key":"key\n\t\t\t\t20180928113218_bbx039-B8","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1093\/bib\/bbv036","article-title":"Systematically evaluating interfaces for RNA-seq analysis from a life scientist perspective","volume":"17","author":"Poplawski","year":"2016","journal-title":"Brief Bioinform"},{"key":"key\n\t\t\t\t20180928113218_bbx039-B9","doi-asserted-by":"crossref","first-page":"e644.","DOI":"10.7717\/peerj.644","article-title":"Unipro UGENE NGS pipelines and components for variant calling, RNA-seq and ChIP-seq data analyses","volume":"2","author":"Golosova","year":"2014","journal-title":"PeerJ"},{"issue":"3","key":"key\n\t\t\t\t20180928113218_bbx039-B10","doi-asserted-by":"crossref","first-page":"545","DOI":"10.3390\/genes3030545","article-title":"Next-generation sequence analysis and computational genomics using graphical pipeline workflows","volume":"3","author":"Torri","year":"2012","journal-title":"Genes"},{"issue":"10","key":"key\n\t\t\t\t20180928113218_bbx039-B11","doi-asserted-by":"crossref","first-page":"726","DOI":"10.1038\/nrc3130","article-title":"A decade of exploring the cancer epigenome\u2014biological and translational implications","volume":"11","author":"Baylin","year":"2011","journal-title":"Nat Rev Cancer"},{"key":"key\n\t\t\t\t20180928113218_bbx039-B12","first-page":"6958","article-title":"Supporting genotype-to-phenotype association studies with grid-enabled knowledge discovery workflows","volume":"2009","author":"Koumakis","year":"2009","journal-title":"Conf Proc IEEE Eng Med Biol Soc"},{"issue":"1","key":"key\n\t\t\t\t20180928113218_bbx039-B13","doi-asserted-by":"crossref","first-page":"284.","DOI":"10.1186\/s12859-015-0714-x","article-title":"Scientific workflow optimization for improved peptide and protein identification","volume":"16","author":"Holl","year":"2015","journal-title":"BMC Bioinformatics"},{"volume-title":"International Conference on Data Integration in the Life Sciences (DILS 2013)","year":"2013","author":"Booth","key":"key\n\t\t\t\t20180928113218_bbx039-B14"},{"issue":"3","key":"key\n\t\t\t\t20180928113218_bbx039-B15","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1007\/s13206-011-5311-0","article-title":"Cnvas copy number variation analysis system\u2014the analysis tool for genomic alteration with a powerful visualization module","volume":"5","author":"Yoo","year":"2011","journal-title":"BioChip J"},{"issue":"1","key":"key\n\t\t\t\t20180928113218_bbx039-B16","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1016\/j.copbio.2011.11.013","article-title":"Next generation sequencing and bioinformatic bottlenecks the current state of metagenomic data analysis","volume":"23","author":"Scholz","year":"2012","journal-title":"Curr Opin Biotechnol"},{"volume-title":"Proceedings of the International Conference on E-Science (e-Science)","year":"2012","author":"Oca\u00f1a","key":"key\n\t\t\t\t20180928113218_bbx039-B17"},{"key":"key\n\t\t\t\t20180928113218_bbx039-B18","doi-asserted-by":"crossref","first-page":"e121","DOI":"10.4172\/2161-1459.1000e121","article-title":"On the exploitation of serendipity in drug discovery","volume":"3","author":"Baumeister","year":"2013","journal-title":"Clin Exp Pharmacol"},{"issue":"3","key":"key\n\t\t\t\t20180928113218_bbx039-B19","first-page":"381","article-title":"Scientific workflows as productivity tools for drug discovery","volume":"11","author":"Shon","year":"2008","journal-title":"Curr Opin Drug Discov Devel"},{"issue":"3","key":"key\n\t\t\t\t20180928113218_bbx039-B20","doi-asserted-by":"crossref","first-page":"345","DOI":"10.1021\/cc700187t","article-title":"Application of combinatorial chemistry science on modern drug discovery","volume":"10","author":"Kennedy","year":"2008","journal-title":"J Comb Chem"},{"key":"key\n\t\t\t\t20180928113218_bbx039-B21","article-title":"Scaling machine learning for target prediction in drug discovery using apache-spark","author":"Harnie","year":"2016","journal-title":"Future Gener Comput Syst"},{"year":"2015","author":"Arvidsson","key":"key\n\t\t\t\t20180928113218_bbx039-B22"},{"issue":"18","key":"key\n\t\t\t\t20180928113218_bbx039-B23","doi-asserted-by":"crossref","first-page":"2652","DOI":"10.1093\/bioinformatics\/btu343","article-title":"SparkSeq fast, scalable, cloud-ready tool for the interactive genomic data analysis with nucleotide precision","volume":"30","author":"Wiewi\u00f3rka","year":"2014","journal-title":"Bioinformatics"},{"issue":"3","key":"key\n\t\t\t\t20180928113218_bbx039-B24","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1007\/s11030-006-9041-5","article-title":"Cheminformatics analysis and learning in a data pipelining environment","volume":"10","author":"Hassan","year":"2006","journal-title":"Mol Divers"},{"issue":"1","key":"key\n\t\t\t\t20180928113218_bbx039-B25","doi-asserted-by":"crossref","first-page":"80","DOI":"10.1055\/s-0038-1633926","article-title":"AdaptFlow protocol-based medical treatment using adaptive workflows","volume":"44","author":"Greiner","year":"2005","journal-title":"Methods Inf Med"},{"volume-title":"Provenance and Annotation of Data and Processes, Second International Provenance and Annotation Workshop, IPAW 2008","year":"2008","author":"MacKenzie-Graham","key":"key\n\t\t\t\t20180928113218_bbx039-B26"},{"key":"key\n\t\t\t\t20180928113218_bbx039-B27","doi-asserted-by":"crossref","first-page":"22.","DOI":"10.3389\/neuro.11.022.2009","article-title":"Efficient, distributed and interactive neuroimaging data analysis using the LONI pipeline","volume":"3","author":"Dinov","year":"2009","journal-title":"Front Neuroinform"},{"issue":"5","key":"key\n\t\t\t\t20180928113218_bbx039-B28","doi-asserted-by":"crossref","first-page":"305","DOI":"10.1016\/j.compbiolchem.2007.08.009","article-title":"Workflow based framework for life science informatics","volume":"31","author":"Tiwari","year":"2007","journal-title":"Comput Biol Chem"},{"issue":"2","key":"key\n\t\t\t\t20180928113218_bbx039-B29","doi-asserted-by":"crossref","first-page":"570","DOI":"10.1147\/sj.402.0570","article-title":"An integration platform for heterogeneous bioinformatics software components","volume":"40","author":"Siepel","year":"2001","journal-title":"IBM Syst J"},{"volume-title":"IEEE International Conference on Big Data, 2013","year":"2013","author":"Vahi","key":"key\n\t\t\t\t20180928113218_bbx039-B30"},{"year":"2013","author":"Aloisioa","key":"key\n\t\t\t\t20180928113218_bbx039-B31"},{"issue":"2","key":"key\n\t\t\t\t20180928113218_bbx039-B32","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1093\/bib\/bbp015","article-title":"Semantic web for health care and life sciences a review of the state of the art","volume":"10","author":"Cheung","year":"2009","journal-title":"Brief Bioinform"},{"issue":"1","key":"key\n\t\t\t\t20180928113218_bbx039-B33","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1186\/s13062-015-0071-8","article-title":"Experiences with workflows for automating data-intensive bioinformatics","volume":"10","author":"Spjuth","year":"2015","journal-title":"Biol Direct"},{"issue":"10","key":"key\n\t\t\t\t20180928113218_bbx039-B34","doi-asserted-by":"crossref","first-page":"1039","DOI":"10.1002\/cpe.994","article-title":"Scientific workflow management and the Kepler system","volume":"18","author":"Lud\u00e4scher","year":"2006","journal-title":"Concurr Comput"},{"year":"2012","author":"Garijo","key":"key\n\t\t\t\t20180928113218_bbx039-B35"},{"volume-title":"IEEE International Workshop on Scientific Workflows, 2007","year":"2007","author":"Zhao","key":"key\n\t\t\t\t20180928113218_bbx039-B36"},{"key":"key\n\t\t\t\t20180928113218_bbx039-B37","first-page":"1","volume-title":"Parallel and Distributed Computing Applications and Technologies","author":"Chua","year":"2004"},{"volume-title":"Workflows for e-Science Scientific Workflows for Grids","year":"2007","author":"Von Laszewski","key":"key\n\t\t\t\t20180928113218_bbx039-B38"},{"issue":"3","key":"key\n\t\t\t\t20180928113218_bbx039-B39","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1145\/1084805.1084814","article-title":"A taxonomy of scientific workflow systems for grid computing","volume":"34","author":"Yu","year":"2005","journal-title":"ACM SIGMOD Rec"},{"year":"2006","author":"Lathers","key":"key\n\t\t\t\t20180928113218_bbx039-B40"},{"year":"2013","author":"Bux","key":"key\n\t\t\t\t20180928113218_bbx039-B41"},{"key":"key\n\t\t\t\t20180928113218_bbx039-B42","doi-asserted-by":"crossref","first-page":"18","DOI":"10.4018\/jwsr.2007100102","article-title":"An extensible architecture for high-performance, scalable, reliable publish-subscribe eventing and notification","volume":"4","author":"Ostrowski","year":"2007","journal-title":"Int J Web Serv Res"},{"volume-title":"IEEE International Symposium on Parallel & Distributed Processing, Workshops and PhD Forum (IPDPSW), 2010","year":"2010","author":"Wu","key":"key\n\t\t\t\t20180928113218_bbx039-B43"},{"volume-title":"Proceedings of the International Conference on Cloud and Green Computing (CGC), 2012","year":"2012","author":"Zhao","key":"key\n\t\t\t\t20180928113218_bbx039-B44"},{"issue":"6","key":"key\n\t\t\t\t20180928113218_bbx039-B45","doi-asserted-by":"crossref","first-page":"930","DOI":"10.1109\/TSC.2014.2341235","article-title":"A service framework for scientific workflow management in the cloud","volume":"8","author":"Zhao","year":"2015","journal-title":"IEEE Trans Serv Comput"},{"year":"2014","author":"Zhao","key":"key\n\t\t\t\t20180928113218_bbx039-B46"},{"volume-title":"Proceedings of IEEE International Conference on Services Computing, SCC 2012","year":"2012","author":"Luo","key":"key\n\t\t\t\t20180928113218_bbx039-B47"},{"volume-title":"Proceedings of the 2006 ACM SIGMOD International Conference on Management of Data","year":"2006","author":"Buneman","key":"key\n\t\t\t\t20180928113218_bbx039-B48"},{"volume-title":"Proceedings of the 2008 ACM SIGMOD International Conference on Management of Data","year":"2008","author":"Davidson","key":"key\n\t\t\t\t20180928113218_bbx039-B49"},{"author":"Ames","key":"key\n\t\t\t\t20180928113218_bbx039-B50"},{"volume-title":"Proceedings of International Conference on Database Theory","year":"2001","author":"Buneman","key":"key\n\t\t\t\t20180928113218_bbx039-B51"},{"key":"key\n\t\t\t\t20180928113218_bbx039-B52","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1186\/s13742-015-0092-3","article-title":"Enhanced reproducibility of SADI web service workflows with Galaxy and Docker","volume":"4","author":"Enga\u00f1a Aranguren","year":"2015","journal-title":"Gigascience"},{"volume-title":"Proceedings of the IEEE International Conference on E-Science Workshops, 2009","year":"2009","author":"Juve","key":"key\n\t\t\t\t20180928113218_bbx039-B53"},{"year":"2012","author":"Zhao","key":"key\n\t\t\t\t20180928113218_bbx039-B54"},{"issue":"1","key":"key\n\t\t\t\t20180928113218_bbx039-B55","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1186\/s12911-015-0130-1","article-title":"Pharmacogenomic knowledge representation, reasoning and genome-based clinical decision support based on OWL 2 DL ontologies","volume":"15","author":"Samwald","year":"2015","journal-title":"BMC Med Inform Decis Mak"},{"volume-title":"Proceedings of International Conference on Frontiers of Information Technology","year":"2009","author":"Rehman","key":"key\n\t\t\t\t20180928113218_bbx039-B56"},{"volume-title":"Proceedings of the OWLED*06 Workshop on OWL: Experiences and Directions, Athens, Georgia, USA","year":"2006","author":"Gil","key":"key\n\t\t\t\t20180928113218_bbx039-B57"},{"volume-title":"Conference on Innovative Applications of Artificial Intelligence (IAAI-07)","year":"2007","author":"Gil","key":"key\n\t\t\t\t20180928113218_bbx039-B58"},{"issue":"2","key":"key\n\t\t\t\t20180928113218_bbx039-B59","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1016\/j.websem.2011.06.003","article-title":"Robust and scalable linked data reasoning incorporating provenance and trust annotations","volume":"9","author":"Bonatti","year":"2011","journal-title":"J Web Semantics"},{"volume-title":"IEEE International Conference on Services Computing, 2008","year":"2008","author":"Lin","key":"key\n\t\t\t\t20180928113218_bbx039-B60"},{"volume-title":"Proceedings of International Semantic Web Conference (ISWC)","year":"2011","author":"Gil","key":"key\n\t\t\t\t20180928113218_bbx039-B61"},{"author":"Hasnain","key":"key\n\t\t\t\t20180928113218_bbx039-B62"},{"issue":"1","key":"key\n\t\t\t\t20180928113218_bbx039-B63","doi-asserted-by":"crossref","first-page":"136","DOI":"10.1186\/1471-2105-10-136","article-title":"Infrastructure for the life sciences design and implementation of the UniProt website","volume":"10","author":"Jain","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20180928113218_bbx039-B64","doi-asserted-by":"crossref","first-page":"D44","DOI":"10.1093\/nar\/gkt1066","article-title":"DDBJ progress reports a new submission system for leading to a correct annotation","volume":"42","author":"Kosuge","year":"2014","journal-title":"Nucleic Acids Res"},{"author":"Maloney","key":"key\n\t\t\t\t20180928113218_bbx039-B65"},{"issue":"1","key":"key\n\t\t\t\t20180928113218_bbx039-B66","doi-asserted-by":"crossref","first-page":"42.","DOI":"10.1186\/2041-1480-5-42","article-title":"Executing SADI services in Galaxy","volume":"5","author":"Aranguren","year":"2014","journal-title":"J Biomed Semantics"},{"issue":"1","key":"key\n\t\t\t\t20180928113218_bbx039-B67","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1186\/2041-1480-2-8","article-title":"The Semantic Automated Discovery and Integration (SADI) web service design-pattern, API and reference implementation","volume":"2","author":"Wilkinson","year":"2011","journal-title":"J Biomed Semantics"},{"issue":"3","key":"key\n\t\t\t\t20180928113218_bbx039-B68","doi-asserted-by":"crossref","first-page":"567","DOI":"10.1016\/j.jprot.2008.11.010","article-title":"The UniProtKB\/Swiss-Prot knowledgebase and its plant proteome annotation program","volume":"72","author":"Schneider","year":"2009","journal-title":"J Proteomics"},{"issue":"9","key":"key\n\t\t\t\t20180928113218_bbx039-B69","doi-asserted-by":"crossref","first-page":"1338","DOI":"10.1093\/bioinformatics\/btt765","article-title":"The EBI RDF platform linked open data for the life sciences","volume":"30","author":"Jupp","year":"2014","journal-title":"Bioinformatics"},{"issue":"1","key":"key\n\t\t\t\t20180928113218_bbx039-B70","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1093\/nar\/gkg088","article-title":"DNA data bank of Japan (DDBJ) in XML","volume":"31","author":"Miyazaki","year":"2003","journal-title":"Nucleic Acids Res"},{"issue":"5","key":"key\n\t\t\t\t20180928113218_bbx039-B71","doi-asserted-by":"crossref","first-page":"706","DOI":"10.1016\/j.jbi.2008.03.004","article-title":"Bio2RDF towards a mashup to build bioinformatics knowledge systems","volume":"41","author":"Belleau","year":"2008","journal-title":"J Biomed Inform"},{"year":"2008","author":"Nolin","key":"key\n\t\t\t\t20180928113218_bbx039-B72"},{"issue":"8","key":"key\n\t\t\t\t20180928113218_bbx039-B73","doi-asserted-by":"crossref","first-page":"677","DOI":"10.1101\/gr.9.8.677","article-title":"dbSNP\u2014database for single nucleotide polymorphisms and other classes of minor genetic variation","volume":"9","author":"Sherry","year":"1999","journal-title":"Genome Res"},{"issue":"1","key":"key\n\t\t\t\t20180928113218_bbx039-B74","doi-asserted-by":"crossref","first-page":"352","DOI":"10.1093\/nar\/28.1.352","article-title":"dbSNP a database of single nucleotide polymorphisms","volume":"28","author":"Smigielski","year":"2000","journal-title":"Nucleic Acids Res"},{"key":"key\n\t\t\t\t20180928113218_bbx039-B75","first-page":"D514","article-title":"Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders","volume":"33(Suppl 1)","author":"Hamosh","year":"2005","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"key\n\t\t\t\t20180928113218_bbx039-B76","doi-asserted-by":"crossref","first-page":"52","DOI":"10.1093\/nar\/30.1.52","article-title":"Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders","volume":"30","author":"Hamosh","year":"2002","journal-title":"Nucleic Acids Res"},{"key":"key\n\t\t\t\t20180928113218_bbx039-B77","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1002\/0470857897.ch8","volume-title":"\u2018In Silico\u2019 Simulation of Biological Processes 247","author":"Kanehisa","year":"2002"},{"issue":"6","key":"key\n\t\t\t\t20180928113218_bbx039-B78","doi-asserted-by":"crossref","first-page":"893","DOI":"10.1093\/bioinformatics\/btt612","article-title":"MetaboNetworks, an interactive Matlab-based toolbox for creating, customizing and exploring sub-networks from KEGG","volume":"30","author":"Posma","year":"2014","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20180928113218_bbx039-B79","first-page":"D428","article-title":"Reactome a knowledgebase of biological pathways","volume":"33(Suppl 1)","author":"Joshi-Tope","year":"2005","journal-title":"Nucleic Acids Res"},{"volume-title":"OTM Confederated International Conferences On the Move to Meaningful Internet Systems","year":"2006","author":"Schmidt","key":"key\n\t\t\t\t20180928113218_bbx039-B80"},{"key":"key\n\t\t\t\t20180928113218_bbx039-B81","doi-asserted-by":"crossref","first-page":"D674","DOI":"10.1093\/nar\/gkn653","article-title":"PID the pathway interaction database","volume":"37(Suppl 1)","author":"Schaefer","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"key\n\t\t\t\t20180928113218_bbx039-B82","first-page":"D8","article-title":"Database resources of the National Center for Biotechnology Information","volume":"41","author":"NCBI","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"key\n\t\t\t\t20180928113218_bbx039-B83","first-page":"243180","article-title":"Towards reproducibility in scientific workflows: an infrastructure-based approach","volume":"2015","author":"Santana-Perez","year":"2015","journal-title":"Sci Program"},{"issue":"3\u20134","key":"key\n\t\t\t\t20180928113218_bbx039-B84","first-page":"217","article-title":"Scheduling scientific workflow applications with a deadline and budget constraints using genetic algorithms","volume":"14","author":"Yu","year":"2006","journal-title":"Sci Program"},{"volume-title":"International Conference on Web-Age Information Management, 2008","year":"2008","author":"Chebotko","key":"key\n\t\t\t\t20180928113218_bbx039-B85"},{"issue":"5","key":"key\n\t\t\t\t20180928113218_bbx039-B86","doi-asserted-by":"crossref","first-page":"528","DOI":"10.1016\/j.future.2008.06.012","article-title":"Workflows and e-science: an overview of workflow system features and capabilities","volume":"25","author":"Deelman","year":"2009","journal-title":"Future Gener Comput Syst"},{"issue":"9","key":"key\n\t\t\t\t20180928113218_bbx039-B87","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1186\/gm186","article-title":"Large-scale data integration framework provides a comprehensive view on glioblastoma multiforme","volume":"2","author":"Ovaska","year":"2010","journal-title":"Genome Med"},{"issue":"Pt 2","key":"key\n\t\t\t\t20180928113218_bbx039-B88","first-page":"1304","article-title":"Scientific discovery workflows in bioinformatics: a scenario for the coupling of molecular regulatory pathways and gene expression profiles","volume":"160","author":"Kanterakis","year":"2009","journal-title":"Stud Health Technol Inform"},{"issue":"17","key":"key\n\t\t\t\t20180928113218_bbx039-B89","doi-asserted-by":"crossref","first-page":"3045","DOI":"10.1093\/bioinformatics\/bth361","article-title":"Taverna a tool for the composition and enactment of bioinformatics workflows","volume":"20","author":"Oinn","year":"2004","journal-title":"Bioinformatics"},{"issue":"2","key":"key\n\t\t\t\t20180928113218_bbx039-B90","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1109\/LLS.2015.2465870","article-title":"SNAPR a bioinformatics pipeline for efficient and accurate RNA-Seq alignment and analysis","volume":"1","author":"Magis","year":"2015","journal-title":"IEEE Life Sci Lett"},{"issue":"1","key":"key\n\t\t\t\t20180928113218_bbx039-B91","doi-asserted-by":"crossref","first-page":"304","DOI":"10.1186\/1471-2105-12-304","article-title":"Applications of the pipeline environment for visual informatics and genomics computations","volume":"12","author":"Dinov","year":"2011","journal-title":"BMC Bioinformatics"},{"issue":"8","key":"key\n\t\t\t\t20180928113218_bbx039-B92","doi-asserted-by":"crossref","first-page":"R86","DOI":"10.1186\/gb-2010-11-8-r86","article-title":"Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences","volume":"11","author":"Goecks","year":"2010","journal-title":"Genome Biol"},{"volume-title":"Cairo International Biomedical Engineering Conference","year":"2008","author":"Curcin","key":"key\n\t\t\t\t20180928113218_bbx039-B93"},{"issue":"1","key":"key\n\t\t\t\t20180928113218_bbx039-B94","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1186\/1471-2105-13-77","article-title":"Tavaxy integrating Taverna and Galaxy workflows with cloud computing support","volume":"13","author":"Abouelhoda","year":"2012","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20180928113218_bbx039-B95","doi-asserted-by":"crossref","first-page":"1745","DOI":"10.1016\/j.procs.2014.05.159","article-title":"Progress towards automated Kepler scientific workflows for computer-aided drug discovery and molecular simulations","volume":"29","author":"Ieong","year":"2014","journal-title":"Procedia Comput Sci"},{"key":"key\n\t\t\t\t20180928113218_bbx039-B96","doi-asserted-by":"crossref","first-page":"W677","DOI":"10.1093\/nar\/gkq429","article-title":"myExperiment a repository and social network for the sharing of bioinformatics workflows","volume":"38(Suppl 2)","author":"Goble","year":"2010","journal-title":"Nucleic Acids Res"},{"issue":"23","key":"key\n\t\t\t\t20180928113218_bbx039-B97","doi-asserted-by":"crossref","first-page":"1085","DOI":"10.1016\/j.drudis.2006.10.004","article-title":"Systems biology, metabolic modeling and metabolomics in drug discovery and development","volume":"11","author":"Kell","year":"2006","journal-title":"Drug Discov Today"},{"issue":"18","key":"key\n\t\t\t\t20180928113218_bbx039-B98","doi-asserted-by":"crossref","first-page":"1965","DOI":"10.2174\/156802612804910331","article-title":"Drug discovery applications for KNIME an open source data mining platform","volume":"12","author":"Mazanetz","year":"2012","journal-title":"Curr Top Med Chem"},{"issue":"4","key":"key\n\t\t\t\t20180928113218_bbx039-B99","doi-asserted-by":"crossref","first-page":"399","DOI":"10.1016\/j.drudis.2014.11.006","article-title":"Drug discovery FAQs workflows for answering multidomain drug discovery questions","volume":"20","author":"Chichester","year":"2015","journal-title":"Drug Discov Today"},{"volume-title":"IEEE International Conference on Bioinformatics and Bioengineering (BIBE), 2012","year":"2012","author":"Achilleos","key":"key\n\t\t\t\t20180928113218_bbx039-B100"},{"issue":"1","key":"key\n\t\t\t\t20180928113218_bbx039-B101","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/2043-9113-2-1","article-title":"A network flow approach to predict drug targets from microarray data, disease genes and interactome network case study on prostate cancer","volume":"2","author":"Yeh","year":"2012","journal-title":"J Clin Bioinforma"},{"volume-title":"IEEE\/ACM International Symposium on Cluster, Cloud and Grid Computing","year":"2015","author":"Zhao","key":"key\n\t\t\t\t20180928113218_bbx039-B102"},{"issue":"1","key":"key\n\t\t\t\t20180928113218_bbx039-B103","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1186\/2041-1480-6-3","article-title":"Implementation of linked data in the life sciences at BioHackathon 2011","volume":"6","author":"Aoki-Kinoshita","year":"2015","journal-title":"J Biomed Semantics"},{"year":"2005","author":"Brooks","key":"key\n\t\t\t\t20180928113218_bbx039-B104"},{"key":"key\n\t\t\t\t20180928113218_bbx039-B105","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1007\/978-0-85729-049-6_4","volume-title":"Grids, Clouds, and Virtualization","author":"Juve","year":"2011"},{"key":"key\n\t\t\t\t20180928113218_bbx039-B106","doi-asserted-by":"crossref","first-page":"W557","DOI":"10.1093\/nar\/gkt328","article-title":"The Taverna workflow suite designing and executing workflows of web services on the desktop, web or in the cloud","volume":"41","author":"Wolstencroft","year":"2013","journal-title":"Nucleic Acids Res"},{"issue":"20","key":"key\n\t\t\t\t20180928113218_bbx039-B107","doi-asserted-by":"crossref","first-page":"2907","DOI":"10.1093\/bioinformatics\/btr478","article-title":"Extending KNIME for next-generation sequencing data analysis","volume":"27","author":"Jagla","year":"2011","journal-title":"Bioinformatics"},{"year":"2009","author":"Fursov","key":"key\n\t\t\t\t20180928113218_bbx039-B108"},{"issue":"1","key":"key\n\t\t\t\t20180928113218_bbx039-B109","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1093\/bioinformatics\/btu595","article-title":"BigDataScript a scripting language for data pipelines","volume":"31","author":"Cingolani","year":"2015","journal-title":"Bioinformatics"},{"volume-title":"Proceedings of International Workshop on Petascal Data Analytics: Challenges and Opportunities","year":"2011","author":"Altintas","key":"key\n\t\t\t\t20180928113218_bbx039-B110"},{"issue":"10","key":"key\n\t\t\t\t20180928113218_bbx039-B111","doi-asserted-by":"crossref","first-page":"1067","DOI":"10.1002\/cpe.993","article-title":"Taverna lessons in creating a workflow environment for the life sciences","volume":"18","author":"Oinn","year":"2006","journal-title":"Concurr Comput"},{"issue":"3","key":"key\n\t\t\t\t20180928113218_bbx039-B112","first-page":"219","article-title":"Pegasus: a framework for mapping complex scientific workflows onto distributed systems","volume":"13","author":"Deelman","year":"2005","journal-title":"Sci Program"},{"key":"key\n\t\t\t\t20180928113218_bbx039-B113","doi-asserted-by":"crossref","first-page":"404525","DOI":"10.1155\/2013\/404525","article-title":"Workflow systems for science concepts and tools","volume":"2013","author":"Talia","year":"2013","journal-title":"ISRN Softw Eng"},{"volume-title":"Provenance and Annotation of Data International Provenance and Annotation Workshop, IPAW 2008","year":"2008","author":"MacKenzie-Graham","key":"key\n\t\t\t\t20180928113218_bbx039-B114"},{"volume-title":"Proceedings of the International Conference on Scientific and Statistical Database Management","year":"2004","author":"Altintas","key":"key\n\t\t\t\t20180928113218_bbx039-B115"},{"issue":"2","key":"key\n\t\t\t\t20180928113218_bbx039-B116","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1109\/LLS.2015.2483820","article-title":"Exact moment dynamics for feedforward nonlinear chemical reaction networks","volume":"1","author":"Sontag","year":"2015","journal-title":"IEEE Life Sci Lett"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bib\/article-pdf\/19\/5\/1035\/25861110\/bbx039.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,7,26]],"date-time":"2022-07-26T05:09:17Z","timestamp":1658812157000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article\/19\/5\/1035\/3737318"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,4,16]]},"references-count":116,"journal-issue":{"issue":"5","published-online":{"date-parts":[[2017,4,16]]},"published-print":{"date-parts":[[2018,9,28]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbx039","relation":{},"ISSN":["1467-5463","1477-4054"],"issn-type":[{"type":"print","value":"1467-5463"},{"type":"electronic","value":"1477-4054"}],"subject":[],"published-other":{"date-parts":[[2018,9]]},"published":{"date-parts":[[2017,4,16]]}}}