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About the Authors:
Björn A. Grüning
* E-mail: [email protected] (BAG); [email protected] (JT); [email protected] (AN)
Affiliations Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University, Freiburg, Freiburg, Germany, Center for Biological Systems Analysis (ZBSA), University of Freiburg, Freiburg, Germany
ORCID http://orcid.org/0000-0002-3079-6586
Eric Rasche
Affiliation: Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
ORCID http://orcid.org/0000-0001-9760-8992
Boris Rebolledo-Jaramillo
Affiliation: Centro de Genética y Genómica, Universidad del Desarrollo, Santiago, Chile
ORCID http://orcid.org/0000-0001-8059-3202
Carl Eberhard
Affiliation: Department of Biology, Johns Hopkins University, Baltimore, Maryland, United States of America
Torsten Houwaart
Affiliation: Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University, Freiburg, Freiburg, Germany
John Chilton
Affiliation: Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
ORCID http://orcid.org/0000-0002-6794-0756
Nate Coraor
Affiliation: Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
Rolf Backofen
Affiliations Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University, Freiburg, Freiburg, Germany, Center for Biological Systems Analysis (ZBSA), University of Freiburg, Freiburg, Germany
James Taylor
* E-mail: [email protected] (BAG); [email protected] (JT); [email protected] (AN)
Affiliation: Department of Biology, Johns Hopkins University, Baltimore, Maryland, United States of America
ORCID http://orcid.org/0000-0001-5079-840X
Anton Nekrutenko
* E-mail: [email protected] (BAG); [email protected] (JT); [email protected] (AN)
Affiliation: Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
ORCID http://orcid.org/0000-0002-5987-8032Abstract
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., the list of variable sites). The subsequent exploratory stage is much more ad hoc and requires the development of custom scripts and pipelines, making it problematic for biomedical researchers. Here, we describe a hybrid platform combining common analysis pathways with the ability to explore data interactively. It aims to fully encompass and simplify the "raw data-to-publication" pathway and make it reproducible.
Author summary
Galaxy users can utilize a large number of tools and workflows. What they could not previously do is run ad hoc scripts and arbitrary tools within their Galaxy instance. This was very limiting, as initial analyses of data often involve interactive exploration with tools like Jupyter or RStudio-powerful platforms that are becoming increasingly popular in life...