CSC - CBS collaboration within ELIXIR


The purpose of ELIXIR is to construct and operate a sustainable infrastructure for biological information in Europe to support life science research and its translation to medicine and the environment, the bio-industries and society.

Due to new technologies such as next-generation DNA sequencing, data produced in biological experiments is doubling every few months, and this rate is increasing. In addition, new types of data are constantly emerging that need to be integrated meaningfully.

The collection, curation, storage, archiving, integration and deployment of biomolecular data is an immense challenge that cannot be handled by a single organisation or by one country alone, but requires international coordination.

ELIXIR and the Nordics

The Nordic countries have been very active in ELIXIR since the start of the project. The emerging ELIXIR nodes in Denmark, Finland, Norway and Sweden have been coordinating their efforts continuously. The collaboration described below is an example of such coordination.

CSC - CBS collaboration

CSC (IT Center for Science Ltd) is the coordinating institution of the Finnish ELIXIR Node. One of the focus areas of the Node is provision of cloud services customized for the needs of the life sciences community.

CBS (Center for Biological Sequence Analysis) is the coordinating institution of the Danish ELIXIR Node on bioinformatics tool interoperability and integration. The mission of the Node includes consultancy aiming at assisting tool providers in various ways, among them in solving the uptime and capacity problems involved in tool provision.

In this context tool cloudification is a natural area of collaboration between CSC and CBS. A pilot project is under way: a number of tools hosted by CBS have been cloudified already. For those tools the computations can be executed on the CSC cloud as well as locally, adding significantly to the stability and the processing capacity of the service. The entire setup is completely transparent to the user.

The development effort addresses in detail the common problems involved in cloudification of tools in life sciences e.g. stability, bandwidth, storage capacity and system software compatibility are being analyzed in detail. The resulting implementation guidelines should be of value to many tool providers facing uptime or capacity problems.

Examples of cloudified tools

The following CBS hosted tools have been cloudified so far (May 10, 2013):
  • ChloroP
    Technically simple service involving limited data traffic and no reference data on the cloud.

  • TargetP
    As above but involving calling several other auxiliary services.


At CSC:        At CBS: