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As a central player in key processes regulating gene expression, RNA is in the focus of many efforts to decipher the pathways that govern the transition of genetic information to a fully functional cell. As more and more researchers join this endeavour, there is a rapidly growing demand for comprehensive collections of tools that cover the diverse layers of RNA-related research. However, increasing amounts of data, from diverse types of experiments, addressing different aspects of biological questions need to be consolidated and integrated into a single framework. Only then is it possible to connect findings from e.g. RNA-Seq experiments and methods for e.g. target predictions. To address these needs, we present the RNA Workbench 2.0\u2009, an updated online resource for RNA related analysis. With the RNA Workbench we created a comprehensive set of analysis tools and workflows that enables researchers to analyze their data without the need for sophisticated command-line skills. This update takes the established framework to the next level, providing not only a containerized infrastructure for analysis, but also a ready-to-use platform for hands-on training, analysis, data exploration, and visualization. The new framework is available at https:\/\/rna.usegalaxy.eu\u2009, and login is free and open to all users. The containerized version can be found at https:\/\/github.com\/bgruening\/galaxy-rna-workbench.<\/jats:p>","DOI":"10.1093\/nar\/gkz353","type":"journal-article","created":{"date-parts":[[2019,4,30]],"date-time":"2019-04-30T15:23:21Z","timestamp":1556637801000},"page":"W511-W515","source":"Crossref","is-referenced-by-count":17,"title":["The RNA workbench 2.0: next generation RNA data analysis"],"prefix":"10.1093","volume":"47","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4573-9939","authenticated-orcid":false,"given":"J\u00f6rg","family":"Fallmann","sequence":"first","affiliation":[{"name":"Bioinformatics Group, Department of Computer Science; Leipzig University, H\u00e4rtelstra\u00dfe 16-18, D-04107 Leipzig"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5192-126X","authenticated-orcid":false,"given":"Pavankumar","family":"Videm","sequence":"additional","affiliation":[{"name":"Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Georges-K\u00f6hler-Allee 106, Freiburg 79110, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9675-8056","authenticated-orcid":false,"given":"Andrea","family":"Bagnacani","sequence":"additional","affiliation":[{"name":"Department of Systems Biology and Bioinformatics, Institute of Computer Science, University of Rostock, Ulmenstr. 69, 18057 Rostock, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9852-1987","authenticated-orcid":false,"given":"B\u00e9r\u00e9nice","family":"Batut","sequence":"additional","affiliation":[{"name":"Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Georges-K\u00f6hler-Allee 106, Freiburg 79110, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4847-8436","authenticated-orcid":false,"given":"Maria A","family":"Doyle","sequence":"additional","affiliation":[{"name":"Research Computing Facility, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia"},{"name":"Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria 3010, Australia"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9504-1352","authenticated-orcid":false,"given":"Tomas","family":"Klingstrom","sequence":"additional","affiliation":[{"name":"SLU-Global Bioinformatics Centre, Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9564-7525","authenticated-orcid":false,"given":"Florian","family":"Eggenhofer","sequence":"additional","affiliation":[{"name":"Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Georges-K\u00f6hler-Allee 106, Freiburg 79110, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5016-5191","authenticated-orcid":false,"given":"Peter F","family":"Stadler","sequence":"additional","affiliation":[{"name":"Bioinformatics Group, Department of Computer Science; Leipzig University, H\u00e4rtelstra\u00dfe 16-18, D-04107 Leipzig"},{"name":"Interdisciplinary Center of Bioinformatics; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig; Competence Center for Scalable Data Services and Solutions; and Leipzig Research Center for Civilization Diseases, Leipzig University, H\u00e4rtelstra\u00dfe 16-18, D-04107 Leipzig"},{"name":"Max-Planck-Institute for Mathematics in the Sciences, Inselstra\u00dfe 22, D-04103 Leipzig Inst. f. Theoretical Chemistry, University of Vienna, W\u00e4hringerstra\u00dfe 17, A-1090 Wien, Austria; Facultad de Ciencias, Universidad Nacional de Colombia, Sede Bogot\u00e1, Colombia Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8231-3323","authenticated-orcid":false,"given":"Rolf","family":"Backofen","sequence":"additional","affiliation":[{"name":"Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Georges-K\u00f6hler-Allee 106, Freiburg 79110, Germany"},{"name":"Signalling Research Centres BIOSS and CIBSS, Albert-Ludwigs-University Freiburg, Sch\u00e4nzlestr. 18, Freiburg 79104, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3079-6586","authenticated-orcid":false,"given":"Bj\u00f6rn","family":"Gr\u00fcning","sequence":"additional","affiliation":[{"name":"Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Georges-K\u00f6hler-Allee 106, Freiburg 79110, Germany"},{"name":"Center for Biological Systems Analysis (ZBSA), University of Freiburg, Habsburgerstr. 49, 79104 Freiburg, Germany"}]}],"member":"286","published-online":{"date-parts":[[2019,5,10]]},"reference":[{"key":"2019062808131072700_B1","doi-asserted-by":"crossref","first-page":"475","DOI":"10.1038\/s41592-018-0046-7","article-title":"Bioconda: sustainable and comprehensive software distribution for the life sciences","volume":"15","author":"Gr\u00fcning","year":"2018","journal-title":"Nat. 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