Set up your own bioinformatics server: Chipster in EGI Federated Cloud

Authors

  • Kimmo Mattila CSC - IT Center For Science, Espoo
  • Diego Scardaci EGI Foundation
  • Marica Antonacci INFN, Bari
  • Catalin Condurache Rutherford Appleton Laboratory, Oxfordshire

DOI:

https://doi.org/10.14806/ej.22.0.879

Keywords:

cloud computing, bioinformatics, chipster, data analysis

Abstract

Chipster is an easy to use data analysis platform for bioinformatics. It provides an uniform graphical interface for over 360 commonly used bioinformatics tools including several R/Bioconductor-based tools and standalone programs (i.e. BWA, TopHat). Chipster is based on a client-server system where the user runs locally a Chipster-client that submits analysis tasks to a Chipster server. Even though Chipster is an open source tool, there is no public Chipster server that would be open for everybody. Due to that, a researcher needs to have an access to some of the existing Chipster servers to be able to use this platform. Alternatively, a researcher can set up his own Chipster server.

In this paper, we describe how a Chipster server can be launched EGI Federated Could environment, that provides resources for all European researchers. With the instructions provided here, any European researcher can launch and manage his own Chipster server, suited for needs of a small research group or a bioinformatics course. The setup described here is based on a collaboration of several European instances. Chipster is developed by CSC – IT Center for Science Ltd. in Finland. European Grid Infrastructure (EGI) has fitted Chipster to cloud environment and provides the cloud computing resources. Finally, Rutherford Appleton Laboratory hosts the CVMFS server that provides the scientific tools and data sets for the Chipster servers running in EGI federated cloud.

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Published

2017-02-06

Issue

Vol. 22

Section

Technical Notes

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