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Promoting collaboration in the life sciences

CSC provides IT support and resources for the academic community, research institutes, and companies, with Finland’s widest range of scientific software and databases and the country’s most powerful supercomputing environment, all available through the Funet network.
CSC - It Center for Science Ltd.

Much of cutting-edge research today relies on collaboration between different disciplines, whether in medicine, mathematics, statistics, or computer science. Researchers need access to increasingly sophisticated data analysis tools for both their day-to-day activities and specialist explorative work.

CSC is one of those that has been particularly active in developing bioinformatics software and standardised interfaces to help make this happen, working through initiatives coordinated by the European Bioinformatics Institute (EMBL-EBI) and the European Network of Excellence EMBRACE. Many of the tools that have been created employ an open source licensing model, allowing software to be extended as new requirements arise.

Chipster users can easily track the progress of their analysis using the application’s graphical workflow view. Analysis workflows can also be saved for re-use and shared with collaborators. Automating analysis through workflows in this way not only saves time, but also promotes consistency.

One such software package is Chipster (chipster.csc.fi), which focuses on microarray data analysis. Particular priority has been given to usability with this package, and the generic Chipster platform can be easily applied to other areas of data analysis.

Written entirely in Java, Chipster allows users to carry out data analysis using R/Bioconductor and other tools through an intuitive graphical user interface, and the program can be installed locally or accessed via CSC’s servers.

Helping build tomorrow’s infrastructure

CSC is also collaborating with the EBI on the ELIXIR project to support life science research in Europe and promote the use of research data in medicine, environmental technology, bio-based industries, and society generally. CSC’s specific role here is to demonstrate how access to an advanced supercomputing environment can contribute to life science research and leverage the opportunities for making novel discoveries.

In addition to, and often as part of, projects like this, CSC organises a number of training events every year in a wide variety of disciplines. Training is becoming an increasingly important part of CSC’s services, especially internationally. CSC is involved in organising global training for people using Chipster and ELIXIR, for example, ranging from basic users getting to grips with the software’s potential all the way to powers users.

> Juha Haataja
(Published in HighTech Finland 2009)