title: Integration of EGA secure data access into Galaxy.
abstract: High-throughput molecular profiling techniques are routinely generating vast amounts of data for translational medicine studies. Secure access controlled systems are needed to manage, store, transfer and distribute these data due to its personally identifiable nature. The European Genome-phenome Archive (EGA) was created to facilitate access and management to long-term archival of bio-molecular data. Each data provider is responsible for ensuring a Data Access Committee is in place to grant access to data stored in the EGA. Moreover, the transfer of data during upload and download is encrypted. ELIXIR, a European research infrastructure for life-science data, initiated a project (2016 Human Data Implementation Study) to understand and document the ELIXIR requirements for secure management of controlled-access data. As part of this project, a full ecosystem was designed to connect archived raw experimental molecular profiling data with interpreted data and the computational workflows, using the CTMM Translational Research IT (CTMM-TraIT) infrastructure http://www.ctmm-trait.nl as an example. Here we present the first outcomes of this project, a framework to enable the download of EGA data to a Galaxy server in a secure way. Galaxy provides an intuitive user interface for molecular biologists and bioinformaticians to run and design data analysis workflows. More specifically, we developed a tool -- ega_download_streamer - that can download data securely from EGA into a Galaxy server, which can subsequently be further processed. This tool will allow a user within the browser to run an entire analysis containing sensitive data from EGA, and to make this analysis available for other researchers in a reproducible manner, as shown with a proof of concept study.  The tool ega_download_streamer is available in the Galaxy tool shed: https://toolshed.g2.bx.psu.edu/view/yhoogstrate/ega_download_streamer.
authors.affiliation: Department of Bioinformatics, ErasmusMC Rotterdam, Rotterdam, Netherlands.
authors.forename: Youri
authors.initials: Y
authors.lastname: Hoogstrate
authors.affiliation: Department of Computer Science, Vrije Universiteit, Amsterdam, Netherlands.
authors.forename: Chao
authors.initials: C
authors.lastname: Zhang
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK.
authors.forename: Alexander
authors.initials: A
authors.lastname: Senf
authors.affiliation: The Hyve, Utrecht, Netherlands.
authors.forename: Jochem
authors.initials: J
authors.lastname: Bijlard
authors.affiliation: Department of Bioinformatics, ErasmusMC Rotterdam, Rotterdam, Netherlands.
authors.forename: Saskia
authors.initials: S
authors.lastname: Hiltemann
authors.affiliation: Genomics Coordination Centre, UMC Groningen, Groningen, Netherlands.
authors.forename: David
authors.initials: D
authors.lastname: van Enckevort
authors.affiliation: ELIXIR Hub, Wellcome Genome Campus, Hinxton, UK.
authors.forename: Susanna
authors.initials: S
authors.lastname: Repo
authors.affiliation: Department of Computer Science, Vrije Universiteit, Amsterdam, Netherlands.
authors.forename: Jaap
authors.initials: J
authors.lastname: Heringa
authors.affiliation: Department of Urology, ErasmusMC Rotterdam, Rotterdam, Netherlands.
authors.forename: Guido
authors.initials: G
authors.lastname: Jenster
authors.affiliation: Diagnostic Oncology, Netherlands Cancer Institute, Amsterdam, Netherlands.
authors.forename: Remond
authors.initials: R
authors.lastname: J A Fijneman
authors.affiliation: Lygature, Utrecht, Netherlands.
authors.forename: Jan-Willem
authors.initials: JW
authors.lastname: Boiten
authors.affiliation: Diagnostic Oncology, Netherlands Cancer Institute, Amsterdam, Netherlands.
authors.forename: Gerrit
authors.initials: G
authors.lastname: A Meijer
authors.affiliation: Department of Bioinformatics, ErasmusMC Rotterdam, Rotterdam, Netherlands.
authors.forename: Andrew
authors.initials: A
authors.lastname: Stubbs
authors.affiliation: Centre for Genomic Regulation, Parc de Recerca Biomédica de Barcelona, Barcelona, Spain.
authors.forename: Jordi
authors.initials: J
authors.lastname: Rambla
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK.
authors.forename: Dylan
authors.initials: D
authors.lastname: Spalding
authors.affiliation: Department of Computer Science, Vrije Universiteit, Amsterdam, Netherlands.
authors.forename: Sanne
authors.identifier: 0000-0002-2779-7174
authors.initials: S
authors.lastname: Abeln
keywords: EGA; Galaxy; bioinformatics; data management; translational research; workflows