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Community-Driven Data Analysis Training for Biology
Bérénice Batut
1
Saskia Hiltemann
2
Andrea Bagnacani
3
Dannon Baker
4
Vivek Bhardwaj
5
Clemens Blank
1
Anthony Bretaudeau
6, 7
Loraine Brillet-Guéguen
8
John Chilton
9
Dave Clements
4
Olivia Doppelt-Azeroual
10
Anika Erxleben
1
Mallory Ann Freeberg
11
Simon Gladman
12
Youri Hoogstrate
2
Hans-Rudolf Hotz
13
Torsten Houwaart
1
Pratik Jagtap
14
Delphine Larivière
9
Gildas Le Corguillé
8
Thomas Manke
15
Fabien Mareuil
10
Fidel Ramírez
15
Devon Ryan
15
Florian Christoph Sigloch
1
Nicola Soranzo
16
Joachim Wolff
1
Pavankumar Videm
1
Markus Wolfien
3
Aisanjiang Wubuli
17
Dilmurat Yusuf
1
James Taylor
4
Rolf Backofen
1, *
Anton Nekrutenko
9, *
Bjorn Grüning
1
*
Corresponding author
6
Plateforme bioinformatique GenOuest [Rennes]
UR1 - Université de Rennes 1, Plateforme Génomique Santé Biogenouest®, Inria Rennes – Bretagne Atlantique , IRISA-D7 - GESTION DES DONNÉES ET DE LA CONNAISSANCE
Vivek Bhardwaj 5
Author
Clemens Blank 1
Author
Anthony Bretaudeau 6, 7
Author Employer institution : Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement IdHAL : anthony-bretaudeau
Loraine Brillet-Guéguen 8
Author
John K. Chilton 9
Author
Dave Clements 4
Author
Olivia Doppelt-Azeroual 10
Author
Anika Erxleben 1
Author
Mallory Ann Freeberg 11
Author
Simon Gladman 12
Author
Youri Hoogstrate 2
Author
Hans-Rudolf Hotz 13
Author
Torsten Houwaart 1
Author
Pratik Jagtap 14
Author
Delphine Larivière 9
Author
Gildas Le Corguillé 8
Author
Thomas Manke 15
Author
Fabien Mareuil 10
Author IdHAL : fabien-mareuil ORCID : https://orcid.org/0000-0002-3832-9157
Fidel Ramírez 15
Author
Devon Ryan 15
Author
Florian Christoph Sigloch 1
Author
Nicola Soranzo 16
Author
Joachim Wolff 1
Author
Pavankumar Videm 1
Author
1
Bioinformatics Group [Freiburg] (Department of Computer Science
Albert-Ludwigs-University Freiburg
Georges-Köhler-Allee 106
79110 Freiburg
Germany
- Germany)
- Department of Computer Science [Freiburg] (University of Freiburg
Georges-Köhler-Allee 106
79110 Freiburg
Germany - Germany)
- Albert-Ludwigs-Universität Freiburg (Georges-Köhler Allee 51 79110 Freiburg im Breisgau (Germany) - Germany)
2
Erasmus MC - Erasmus University Medical Center [Rotterdam] (Rotterdam - Netherlands)
3
Department of Systems Biology and Bioinformatics (Germany)
- University of Rostock (Albert-Einstein-Straße 22 18059 Rostock Germany - Germany)
4
JHU - Johns Hopkins University (Baltimore, Maryland 410-516-8000 - United States)
5
Department of Biology [Fribourg] (Chemin du musée 10 - 1700 Fribourg - Switzerland)
- University of Freiburg [Freiburg] (Friedrichstr. 39 79098 Freiburg - Germany)
6
Plateforme bioinformatique GenOuest [Rennes] (France)
- UR1 - Université de Rennes 1 (2 rue du Thabor - CS 46510 - 35065 Rennes cedex - France)
- UNIV-RENNES - Université de Rennes (France)
- Plateforme Génomique Santé Biogenouest® (France)
- Inria Rennes – Bretagne Atlantique (Campus de beaulieu
35042 Rennes cedex - France)
- Inria - Institut National de Recherche en Informatique et en Automatique (Domaine de Voluceau Rocquencourt - BP 105 78153 Le Chesnay Cedex - France)
- IRISA-D7 - GESTION DES DONNÉES ET DE LA CONNAISSANCE (France)
- IRISA - Institut de Recherche en Informatique et Systèmes Aléatoires (Avenue du général Leclerc
Campus de Beaulieu
35042 RENNES CEDEX - France)
- UR1 - Université de Rennes 1 (2 rue du Thabor - CS 46510 - 35065 Rennes cedex - France)
- UNIV-RENNES - Université de Rennes (France)
- INSA Rennes - Institut National des Sciences Appliquées - Rennes (20, avenue des Buttes de Coësmes - CS 70839 - 35708 Rennes cedex 7 - France)
- UBS - Université de Bretagne Sud (BP 92116 - 56321 Lorient cedex - France)
- ENS Rennes - École normale supérieure - Rennes (Campus de Ker Lann - avenue Robert Schuman - 35170 Bruz - France)
- Inria - Institut National de Recherche en Informatique et en Automatique (Domaine de Voluceau Rocquencourt - BP 105 78153 Le Chesnay Cedex - France)
- CentraleSupélec (3, rue Joliot Curie, Plateau de Moulon, 91192 GIF-SUR-YVETTE Cedex - France)
- CNRS - Centre National de la Recherche Scientifique : UMR6074 (France)
- IMT Atlantique - IMT Atlantique Bretagne-Pays de la Loire (Campus Brest : Technopôle Brest-Iroise CS 8381829238 BREST Cedex 3 -
Campus Nantes : 4, rue Alfred Kastler- La chantrerie 44300 NANTES -
Campus Rennes : 2 Rue de la Châtaigneraie, 35510 CESSON SEVIGNE - France)
- IMT - Institut Mines-Télécom [Paris] (37-39 Rue Dareau, 75014 Paris - France)
- UR1 - Université de Rennes 1 (2 rue du Thabor - CS 46510 - 35065 Rennes cedex - France)
- IRISA - Institut de Recherche en Informatique et Systèmes Aléatoires (Avenue du général Leclerc
Campus de Beaulieu
35042 RENNES CEDEX - France)
7
IGEPP - Institut de Génétique, Environnement et Protection des Plantes (Domaine de la Motte au Vicomte BP 35327
35653 Le Rheu - France)
- INRA - Institut National de la Recherche Agronomique : UMR1349 (France)
- UR1 - Université de Rennes 1 : UMR1349 (2 rue du Thabor - CS 46510 - 35065 Rennes cedex - France)
- UNIV-RENNES - Université de Rennes (France)
- AGROCAMPUS OUEST : UMR1349 (Institut Supérieur des Sciences Agronomiques, Agroalimentaires, Horticoles et du Paysage - 65, rue de St Brieuc - CS 84215 - 35042 Rennes cedex - France)
8
FR2424 - ABiMS - Informatique et bioinformatique = Analysis and Bioinformatics for Marine Science (Station Biologique de Roscoff
Place Georges Teissier
29680 Roscoff
+33 0 2 98 29 23 23 - France)
- SBR - Station biologique de Roscoff (Place Georges Teissier - BP 74 29682 ROSCOFF CEDEX - France)
- SU - Sorbonne Université (21 rue de l’École de médecine - 75006 Paris - France)
- CNRS - Centre National de la Recherche Scientifique : FR2424 (France)
9
Penn State - Pennsylvania State University (201 Old Main, University Park, Pennsylvania 16802 - United States)
- Penn State System (Pennsylvania, PA, USA, Etats-Unis - United States)
10
Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB (Département de biologie computationnelle (ex C3BI), 25-28 rue du Docteur Roux, 75724 Paris cedex 15 - France)
- Institut Pasteur [Paris] (25-28, rue du docteur Roux, 75724 Paris cedex 15 - France)
- CNRS - Centre National de la Recherche Scientifique : USR3756 (France)
11
EMBL-EBI - European Bioinformatics Institute [Hinxton] (EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK - United Kingdom)
- EMBL Heidelberg (Meyerhofstraße 1 69117 Heidelberg - Germany)
12
Melbourne Bioinformatics [Australia] (187 Grattan Street
University of Melbourne 3010
Victoria, Australia - Australia)
- University of Melbourne (Parkville VIC 3010 - Australia)
13
FMI - Friedrich Miescher Institute for Biomedical Research (Basel - Switzerland)
- Novartis Research Foundation (Switzerland)
14
University of Minnesota Medical School (420 Delaware Street SE | Minneapolis, MN 55455 - United States)
- University of Minnesota System (United States)
15
MPI-IE - Max Planck Institute of Immunobiology and Epigenetics (Stübeweg 51 , D-79108 Freiburg - Germany)
- Max-Planck-Gesellschaft (Jägerstrasse, 10-11, D-10117 Berlin - Germany)
16
Earlham Institute [Norwich] (Norwich Research Park Innovation Centre, Colney Ln, Norwich NR4 7UH - United Kingdom)
17
FBN - Leibniz Institute for Farm Animal Biology (Leibniz-Institut für Nutztierbiologie
Wilhelm-Stahl-Allee 2
18196 Dummerstorf - Germany)
Abstract : The primary problem with the explosion of biomedical datasets is not the data, not computational resources, and not the required storage space, but the general lack of trained and skilled researchers to manipulate and analyze these data. Eliminating this problem requires development of comprehensive educational resources. Here we present a community-driven framework that enables modern, interactive teaching of data analytics in life sciences and facilitates the development of training materials. The key feature of our system is that it is not a static but a continuously improved collection of tutorials. By coupling tutorials with a web-based analysis framework, biomedical researchers can learn by performing computation themselves through a web browser without the need to install software or search for example datasets. Our ultimate goal is to expand the breadth of training materials to include fundamental statistical and data science topics and to precipitate a complete re-engineering of undergraduate and graduate curricula in life sciences. This project is accessible at https://training.galaxyproject.org.
Document type :
Preprints, Working Papers, ...
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https://hal-pasteur.archives-ouvertes.fr/pasteur-02613129
Contributor : Fabien Mareuil Connect in order to contact the contributor
Submitted on : Tuesday, September 8, 2020 - 10:31:07 AM
Last modification on : Tuesday, April 12, 2022 - 4:28:03 PM
Long-term archiving on: : Wednesday, December 2, 2020 - 10:27:20 PM
Contributor : Fabien Mareuil Connect in order to contact the contributor
Submitted on : Tuesday, September 8, 2020 - 10:31:07 AM
Last modification on : Tuesday, April 12, 2022 - 4:28:03 PM
Long-term archiving on: : Wednesday, December 2, 2020 - 10:27:20 PM
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225680v2.full.pdf
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Identifiers
- HAL Id : pasteur-02613129, version 1
- BIORXIV : 225680
- DOI : 10.1016/j.cels.2018.05.012
- PRODINRA : 457551
- PUBMED : 29953864
- PUBMEDCENTRAL : PMC6296361
- WOS : 000436877800011
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PASTEUR | FR2424 | SORBONNE-UNIVERSITE | IRISA | CNRS | SU-SCIENCES | UR1-MATH-STIC | UR1-UFR-ISTIC | INSA-RENNES | INRIA | CENTRALESUPELEC | UNIV-RENNES | UNIV-RENNES1 | SU-TI | UR1-MATH-NUM | INRA | UNAM | INRAE | UR1-ENV | UR1-UFR-SVE | INRIA2
Citation
Bérénice Batut, Saskia Hiltemann, Andrea Bagnacani, Dannon Baker, Vivek Bhardwaj, et al.. Community-Driven Data Analysis Training for Biology. 2020. ⟨pasteur-02613129⟩
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