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Community-driven data analysis training for biology

View ORCID ProfileBérénice Batut, View ORCID ProfileSaskia Hiltemann, View ORCID ProfileAndrea Bagnacani, View ORCID ProfileDannon Baker, Vivek Bhardwaj, View ORCID ProfileClemens Blank, View ORCID ProfileAnthony Bretaudeau, View ORCID ProfileLoraine Brillet-Guéguen, View ORCID ProfileMartin Čech, View ORCID ProfileJohn Chilton, View ORCID ProfileDave Clements, View ORCID ProfileOlivia Doppelt-Azeroual, View ORCID ProfileAnika Erxleben, View ORCID ProfileMallory Ann Freeberg, View ORCID ProfileSimon Gladman, Youri Hoogstrate, View ORCID ProfileHans-Rudolf Hotz, View ORCID ProfileTorsten Houwaart, View ORCID ProfilePratik Jagtap, View ORCID ProfileDelphine Larivière, View ORCID ProfileGildas Le Corguillé, View ORCID ProfileThomas Manke, View ORCID ProfileFabien Mareuil, View ORCID ProfileFidel Ramírez, View ORCID ProfileDevon Ryan, View ORCID ProfileFlorian Christoph Sigloch, View ORCID ProfileNicola Soranzo, Joachim Wolff, View ORCID ProfilePavankumar Videm, View ORCID ProfileMarkus Wolfien, View ORCID ProfileAisanjiang Wubuli, View ORCID ProfileDilmurat Yusuf, Galaxy Training Network, View ORCID ProfileRolf Backofen, View ORCID ProfileAnton Nekrutenko, View ORCID ProfileBjürn Gröning
doi: https://doi.org/10.1101/225680
Bérénice Batut
1Albert-Ludwigs-University, Freiburg Germany.
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Saskia Hiltemann
2Erasmus Medical Centre, Rotterdam, The Netherlands.
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Andrea Bagnacani
3Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany.
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Dannon Baker
4Johns Hopkins University, Baltimore MD USA.
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Vivek Bhardwaj
5Department of Biology, Albert-Ludwigs-University, Schänzlestraße 1, 79104 Freiburg, Germany.
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Clemens Blank
6Albert-Ludwigs-University, Freiburg, Germany.
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Anthony Bretaudeau
7INRA, UMR IGEPP, BIPAA/GenOuest, Campus Beaulieu, Rennes, France
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Loraine Brillet-Guéguen
8CNRS, UMPC, FR2424, ABiMS, Station Biologique, Roscoff, France.
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Martin Čech
9The Pennsylvania State University, University Park, PA, USA.
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John Chilton
10The Pennsylvania State University, University Park, PA, USA.
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Dave Clements
11Johns Hopkins University, Baltimore MD USA.
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Olivia Doppelt-Azeroual
12Bioinformatics and Biostatistics HUB, Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI, USR 3756 Institut Pasteur et CNRS) – Paris, France.
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Anika Erxleben
13Albert-Ludwigs-University, Freiburg, Germany.
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Mallory Ann Freeberg
14European Bioinformatics Institute, Hinxton, Cambridge, UK.
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Simon Gladman
15Melbourne Bioinformatics, The University of Melbourne, Australia.
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Youri Hoogstrate
16Erasmus Medical Centre, Rotterdam, The Netherlands.
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Hans-Rudolf Hotz
17Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
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Torsten Houwaart
18Albert-Ludwigs-University, Freiburg Germany.
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Pratik Jagtap
19Biochemistry, Molecular Biology and Biophysics, University of Minnesota Medical School, Minneapolis, USA.
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Delphine Larivière
20The Pennsylvania State University, University Park, PA, USA.
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Gildas Le Corguillé
21UPMC, CNRS, FR2424, ABiMS, Station Biologique, Roscoff, France.
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Thomas Manke
22Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
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Fabien Mareuil
23Bioinformatics and Biostatistics HUB, Centre de Bioinformatique, Biostatistique et Biologie Integrative (C3BI, USR 3756 Institut Pasteur et CNRS) – Paris, France.
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Fidel Ramírez
24Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
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Devon Ryan
25Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
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Florian Christoph Sigloch
26Albert-Ludwigs-University, Freiburg, Germany.
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Nicola Soranzo
27Earlham Institute, Norwich, UK.
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Joachim Wolff
28Albert-Ludwigs-University, Freiburg, Germany
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Pavankumar Videm
29Albert-Ludwigs-University, Freiburg, Germany.
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Markus Wolfien
30Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany.
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Aisanjiang Wubuli
31Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany.
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Dilmurat Yusuf
32Albert-Ludwigs-University, Freiburg, Germany.
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33
Rolf Backofen
34Albert-Ludwigs-University, Freiburg Germany.
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Anton Nekrutenko
35The Pennsylvania State University, University Park, PA, USA.
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Bjürn Gröning
36Albert-Ludwigs-University, Freiburg Germany.
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  • Abstract
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Abstract

The primary problem with the explosion of biomedical datasets is not the data itself, 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.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted November 29, 2017.
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Community-driven data analysis training for biology
Bérénice Batut, Saskia Hiltemann, Andrea Bagnacani, Dannon Baker, Vivek Bhardwaj, Clemens Blank, Anthony Bretaudeau, Loraine Brillet-Guéguen, Martin Čech, John Chilton, Dave Clements, Olivia Doppelt-Azeroual, Anika Erxleben, Mallory Ann Freeberg, Simon Gladman, Youri Hoogstrate, Hans-Rudolf Hotz, Torsten Houwaart, Pratik Jagtap, Delphine Larivière, Gildas Le Corguillé, Thomas Manke, Fabien Mareuil, Fidel Ramírez, Devon Ryan, Florian Christoph Sigloch, Nicola Soranzo, Joachim Wolff, Pavankumar Videm, Markus Wolfien, Aisanjiang Wubuli, Dilmurat Yusuf, Galaxy Training Network, Rolf Backofen, Anton Nekrutenko, Bjürn Gröning
bioRxiv 225680; doi: https://doi.org/10.1101/225680
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Community-driven data analysis training for biology
Bérénice Batut, Saskia Hiltemann, Andrea Bagnacani, Dannon Baker, Vivek Bhardwaj, Clemens Blank, Anthony Bretaudeau, Loraine Brillet-Guéguen, Martin Čech, John Chilton, Dave Clements, Olivia Doppelt-Azeroual, Anika Erxleben, Mallory Ann Freeberg, Simon Gladman, Youri Hoogstrate, Hans-Rudolf Hotz, Torsten Houwaart, Pratik Jagtap, Delphine Larivière, Gildas Le Corguillé, Thomas Manke, Fabien Mareuil, Fidel Ramírez, Devon Ryan, Florian Christoph Sigloch, Nicola Soranzo, Joachim Wolff, Pavankumar Videm, Markus Wolfien, Aisanjiang Wubuli, Dilmurat Yusuf, Galaxy Training Network, Rolf Backofen, Anton Nekrutenko, Bjürn Gröning
bioRxiv 225680; doi: https://doi.org/10.1101/225680

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