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Enhancing pre-defined workflows with ad hoc analytics using Galaxy, Docker and Jupyter

View ORCID ProfileBjörn A. Grüning, View ORCID ProfileEric Rasche, View ORCID ProfileBoris Rebolledo-Jaramillo, Carl Eberhard, View ORCID ProfileTorsten Houwaart, View ORCID ProfileJohn Chilton, View ORCID ProfileNate Coraor, Rolf Backofen, View ORCID ProfileJames Taylor, View ORCID ProfileAnton Nekrutenko
doi: https://doi.org/10.1101/075457
Björn A. Grüning
1Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University, Freiburg, Freiburg, Germany.
2Center for Biological Systems Analysis (ZBSA), University of Freiburg, Freiburg, Germany.
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  • For correspondence: bjoern.gruening@pharmazie.uni-freiburg.de james@taylorlab.org anton@nekrut.org
Eric Rasche
3Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA.
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Boris Rebolledo-Jaramillo
4Centro de Genética y Genómica, Universidad del Desarrollo, Santiago, Chile.
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Carl Eberhard
6Department of Biology, Johns Hopkins University, Baltimore, MD, USA.
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Torsten Houwaart
1Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University, Freiburg, Freiburg, Germany.
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John Chilton
5Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA.
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Nate Coraor
5Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA.
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Rolf Backofen
1Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University, Freiburg, Freiburg, Germany.
2Center for Biological Systems Analysis (ZBSA), University of Freiburg, Freiburg, Germany.
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James Taylor
6Department of Biology, Johns Hopkins University, Baltimore, MD, USA.
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  • For correspondence: bjoern.gruening@pharmazie.uni-freiburg.de james@taylorlab.org anton@nekrut.org
Anton Nekrutenko
5Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA.
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  • ORCID record for Anton Nekrutenko
  • For correspondence: bjoern.gruening@pharmazie.uni-freiburg.de james@taylorlab.org anton@nekrut.org
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Abstract

What does it take to convert a heap of sequencing data into a publishable result? First, common tools are employed to reduce primary data (sequencing reads) to a form suitable for further analyses (i.e., list of variable sites). The subsequent exploratory stage is much more ad hoc and requires development of custom scripts making it problematic for biomedical researchers. Here we describe a hybrid platform combining common analysis pathways with exploratory environments. It aims at fully encompassing and simplifying the “raw data-to-publication” pathway and making it reproducible.

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Posted September 22, 2016.
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Enhancing pre-defined workflows with ad hoc analytics using Galaxy, Docker and Jupyter
Björn A. Grüning, Eric Rasche, Boris Rebolledo-Jaramillo, Carl Eberhard, Torsten Houwaart, John Chilton, Nate Coraor, Rolf Backofen, James Taylor, Anton Nekrutenko
bioRxiv 075457; doi: https://doi.org/10.1101/075457
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Enhancing pre-defined workflows with ad hoc analytics using Galaxy, Docker and Jupyter
Björn A. Grüning, Eric Rasche, Boris Rebolledo-Jaramillo, Carl Eberhard, Torsten Houwaart, John Chilton, Nate Coraor, Rolf Backofen, James Taylor, Anton Nekrutenko
bioRxiv 075457; doi: https://doi.org/10.1101/075457

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