Correction: An international consensus on effective, inclusive, and career-spanning short-format training in the life sciences and beyond.

Authors: Jason J Williams, Rochelle E Tractenberg, Bérénice Batut, Erin A Becker, Anne M Brown, Melissa L Burke, Ben Busby, Nisha K Cooch, Allissa A Dillman, Samuel S Donovan, Maria A Doyle, Celia W G van Gelder, Christina R Hall, Kate L Hertweck, Kari L Jordan, John R Jungck, Ainsley R Latour, Jessica M Lindvall, Marta Lloret-Llinares, Gary S McDowell, Rana Morris, Teresa Mourad, Amy Nisselle, Patricia Ordóñez, Lisanna Paladin, Patricia M Palagi, Mahadeo A Sukhai, Tracy K Teal, Louise Woodley

Source: PLoS ONE, Vol 20, Iss 2, p e0319613 (2025)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: https://doaj.org/toc/1932-6203

Access URL: https://doaj.org/article/22d6cf9b79ce465d861371cbc1061f3e

Integrative meta-omics in Galaxy and beyond

Authors: Valerie C. Schiml, Francesco Delogu, Praveen Kumar, Benoit Kunath, Bérénice Batut, Subina Mehta, James E. Johnson, Björn Grüning, Phillip B. Pope, Pratik D. Jagtap, Timothy J. Griffin, Magnus Ø. Arntzen

Source: Environmental Microbiome, Vol 18, Iss 1, Pp 1-13 (2023)

Subject Terms: Integrated meta-omics, Metagenomics, Metatrascriptomics, Metaproteomics, Galaxy, Bioinformatics, Environmental sciences, GE1-350, Microbiology, QR1-502

File Description: electronic resource

Relation: https://doaj.org/toc/2524-6372

Access URL: https://doaj.org/article/5bda6fda2ac74a489dfbe9e3e1b39257

Galaxy Training: A powerful framework for teaching!

Authors: Saskia Hiltemann, Helena Rasche, Simon Gladman, Hans-Rudolf Hotz, Delphine Larivière, Daniel Blankenberg, Pratik D Jagtap, Thomas Wollmann, Anthony Bretaudeau, Nadia Goué, Timothy J Griffin, Coline Royaux, Yvan Le Bras, Subina Mehta, Anna Syme, Frederik Coppens, Bert Droesbeke, Nicola Soranzo, Wendi Bacon, Fotis Psomopoulos, Cristóbal Gallardo-Alba, John Davis, Melanie Christine Föll, Matthias Fahrner, Maria A Doyle, Beatriz Serrano-Solano, Anne Claire Fouilloux, Peter van Heusden, Wolfgang Maier, Dave Clements, Florian Heyl, Galaxy Training Network, Björn Grüning, Bérénice Batut

Source: PLoS Computational Biology, Vol 19, Iss 1, p e1010752 (2023)

Subject Terms: Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://doaj.org/toc/1553-734X; https://doaj.org/toc/1553-7358

Access URL: https://doaj.org/article/418bd96910b049ef9a470281072747d4

An international consensus on effective, inclusive, and career-spanning short-format training in the life sciences and beyond.

Authors: Jason J Williams, Rochelle E Tractenberg, Bérénice Batut, Erin A Becker, Anne M Brown, Melissa L Burke, Ben Busby, Nisha K Cooch, Allissa A Dillman, Samuel S Donovan, Maria A Doyle, Celia W G van Gelder, Christina R Hall, Kate L Hertweck, Kari L Jordan, John R Jungck, Ainsley R Latour, Jessica M Lindvall, Marta Lloret-Llinares, Gary S McDowell, Rana Morris, Teresa Mourad, Amy Nisselle, Patricia Ordóñez, Lisanna Paladin, Patricia M Palagi, Mahadeo A Sukhai, Tracy K Teal, Louise Woodley

Source: PLoS ONE, Vol 18, Iss 11, p e0293879 (2023)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: https://doaj.org/toc/1932-6203

Access URL: https://doaj.org/article/a49dcc0dd897416796530319e570b6c8

Fostering accessible online education using Galaxy as an e-learning platform.

Authors: Beatriz Serrano-Solano, Melanie C Föll, Cristóbal Gallardo-Alba, Anika Erxleben, Helena Rasche, Saskia Hiltemann, Matthias Fahrner, Mark J Dunning, Marcel H Schulz, Beáta Scholtz, Dave Clements, Anton Nekrutenko, Bérénice Batut, Björn A Grüning

Source: PLoS Computational Biology, Vol 17, Iss 5, p e1008923 (2021)

Subject Terms: Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://doaj.org/toc/1553-734X; https://doaj.org/toc/1553-7358

Access URL: https://doaj.org/article/2203f8fac2ff4349a06b32591ebcd459

ASaiM-MT: a validated and optimized ASaiM workflow for metatranscriptomics analysis within Galaxy framework [version 2; peer review: 2 approved]

Authors: Subina Mehta, Marie Crane, Emma Leith, Bérénice Batut, Saskia Hiltemann, Magnus Ø Arntzen, Benoit J. Kunath, Phillip B. Pope, Francesco Delogu, Ray Sajulga, Praveen Kumar, James E. Johnson, Timothy J. Griffin, Pratik D. Jagtap

Source: F1000Research, Vol 10 (2021)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: https://f1000research.com/articles/10-103/v2; https://doaj.org/toc/2046-1402

Access URL: https://doaj.org/article/73e663f556a648a1931080c5ee40ac78

The de.NBI / ELIXIR-DE training platform - Bioinformatics training in Germany and across Europe within ELIXIR [version 2; peer review: 2 approved]

Authors: Daniel Wibberg, Bérénice Batut, Peter Belmann, Jochen Blom, Frank Oliver Glöckner, Björn Grüning, Nils Hoffmann, Nils Kleinbölting, René Rahn, Maja Rey, Uwe Scholz, Malvika Sharan, Andreas Tauch, Ulrike Trojahn, Björn Usadel, Oliver Kohlbacher

Source: F1000Research, Vol 8 (2020)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: https://f1000research.com/articles/8-1877/v2; https://doaj.org/toc/2046-1402

Access URL: https://doaj.org/article/f73043ea15c8452383683d0a7b21ba59

Ten simple rules for making training materials FAIR.

Authors: Leyla Garcia, Bérénice Batut, Melissa L Burke, Mateusz Kuzak, Fotis Psomopoulos, Ricardo Arcila, Teresa K Attwood, Niall Beard, Denise Carvalho-Silva, Alexandros C Dimopoulos, Victoria Dominguez Del Angel, Michel Dumontier, Kim T Gurwitz, Roland Krause, Peter McQuilton, Loredana Le Pera, Sarah L Morgan, Päivi Rauste, Allegra Via, Pascal Kahlem, Gabriella Rustici, Celia W G van Gelder, Patricia M Palagi

Source: PLoS Computational Biology, Vol 16, Iss 5, p e1007854 (2020)

Subject Terms: Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1007854&type=printable; https://doaj.org/toc/1553-734X; https://doaj.org/toc/1553-7358

Access URL: https://doaj.org/article/076c5999d13d41318e459708c1a9096b

Environmental Pollutant Benzo[a]Pyrene Impacts the Volatile Metabolome and Transcriptome of the Human Gut Microbiota

Authors: Clémence Defois, Jérémy Ratel, Sylvain Denis, Bérénice Batut, Réjane Beugnot, Eric Peyretaillade, Erwan Engel, Pierre Peyret

Source: Frontiers in Microbiology, Vol 8 (2017)

Subject Terms: human gut microbiota, polycyclic aromatic hydrocarbons, 16S amplicon sequencing, volatolomics, metatranscriptomics, Microbiology, QR1-502

File Description: electronic resource

Relation: http://journal.frontiersin.org/article/10.3389/fmicb.2017.01562/full; https://doaj.org/toc/1664-302X

Access URL: https://doaj.org/article/f423e5e12e484853b8065de0c70cbb01

Four simple recommendations to encourage best practices in research software [version 1; referees: 2 approved]

Authors: Rafael C. Jiménez, Mateusz Kuzak, Monther Alhamdoosh, Michelle Barker, Bérénice Batut, Mikael Borg, Salvador Capella-Gutierrez, Neil Chue Hong, Martin Cook, Manuel Corpas, Madison Flannery, Leyla Garcia, Josep Ll. Gelpí, Simon Gladman, Carole Goble, Montserrat González Ferreiro, Alejandra Gonzalez-Beltran, Philippa C. Griffin, Björn Grüning, Jonas Hagberg, Petr Holub, Rob Hooft, Jon Ison, Daniel S. Katz, Brane Leskošek, Federico López Gómez, Luis J. Oliveira, David Mellor, Rowland Mosbergen, Nicola Mulder, Yasset Perez-Riverol, Robert Pergl, Horst Pichler, Bernard Pope, Ferran Sanz, Maria V. Schneider, Victoria Stodden, Radosław Suchecki, Radka Svobodová Vařeková, Harry-Anton Talvik, Ilian Todorov, Andrew Treloar, Sonika Tyagi, Maarten van Gompel, Daniel Vaughan, Allegra Via, Xiaochuan Wang, Nathan S. Watson-Haigh, Steve Crouch

Source: F1000Research, Vol 6 (2017)

Subject Terms: Bioinformatics, Data Sharing, Medicine, Science

File Description: electronic resource

Relation: https://f1000research.com/articles/6-876/v1; https://doaj.org/toc/2046-1402

Access URL: https://doaj.org/article/ae593f223a074427850b1fb626642ba4

The RNA workbench 2.0: next generation RNA data analysis

Authors: Jörg Fallmann (Bioinformatics Group, Department of Computer Science, Leipzig University), Pavankumar Videm (Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg), Andrea Bagnacani (Department of Systems Biology and Bioinformatics, Institute of Computer Science, University of Rostock), Bérénice Batut (Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg), Maria A Doyle (Research Computing Facility, Peter MacCallum Cancer Centre), Tomas Klingstrom (SLU-Global Bioinformatics Centre, Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences), Florian Eggenhofer (Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg), Peter F Stadler (Department of Theoretical Chemistry, Faculty of Chemistry, University of Vienna), Rolf Backofen (Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg), Björn Grüning (Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg)

Availability: http://data.europeana.eu/aggregation/europeana/1300/https___phaidra_univie_ac_at_o_1169837

The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy

Authors: Björn A. Grüning (Bioinformatics Group, Department of Computer Science, University of Freiburg), Jörg Fallmann (Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig), Dilmurat Yusuf (Berlin Institute for Medical Systems Biology), Sebastian Will (Department of Theoretical Chemistry, Faculty of Chemistry, University of Vienna), Anika Erxleben (Bioinformatics Group, Department of Computer Science, University of Freiburg), Florian Eggenhofer (Bioinformatics Group, Department of Computer Science, University of Freiburg), Torsten Houwaart (Bioinformatics Group, Department of Computer Science, University of Freiburg), Bérénice Batut (Bioinformatics Group, Department of Computer Science, University of Freiburg), Pavankumar Videm (Bioinformatics Group, Department of Computer Science, University of Freiburg), Andrea Bagnacani (Department of Systems Biology and Bioinformatics, University of Rostock), Markus Wolfien (Department of Systems Biology and Bioinformatics, University of Rostock), Steffen C. Lott (Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg), Youri Hoogstrate (Department of Urology, Erasmus University Medical Center), Wolfgang R. Hess (Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg), Olaf Wolkenhauer (Department of Systems Biology and Bioinformatics, University of Rostock), Steve Hoffmann (Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig), Altuna Akalin (Berlin Institute for Medical Systems Biology), Uwe Ohler (Berlin Institute for Medical Systems Biology), Peter F. Stadler (Department of Theoretical Chemistry, Faculty of Chemistry, University of Vienna), Rolf Backofen (Bioinformatics Group, Department of Computer Science, University of Freiburg)

Availability: http://data.europeana.eu/aggregation/europeana/1300/https___phaidra_univie_ac_at_o_907611

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