Wednesday, March 28, 2012

One-stop-shop for the life sciences

The ScalaLife is a recent European Commission FP7 project that provides services, to connect researchers in the computational Life Sciences with software developers and experts, to enable faster research using high-performance computing.

Computing has become an indispensable tool for Life Science research, from protein dynamics and structure predictions, to bioinformatics and neuroinformatics.

“But, some Life Science researchers coming from a biology background, for example, are not very familiar with using powerful software and hardware resources at their disposal optimally and efficiently,” said Rossen Apostolov, the Technical Director of ScalaLife, during a presentation at the EGI Community Forum in Munich, Germany.

If a biologist wants to study a certain protein, there are many online tutorials advising the necessary software applications for parallel computing that can help him. To gain maximum performance of the available high-performance computers advice by application experts can significantly reduce the time for running these computations.

For example, simple optimisations and runtime settings of a popular application for Molecular Dynamics simulations called GROMACS can increase the speed of the simulations two or three times.

This is where ScalaLife comes in. “General users can find some of the applications very hard to understand in order to gain maximum performance. The goal of our project is to connect software users with the software developers,” said Apostolov.

“To help accelerate research, ScalaLife provides a ‘one-stop-shop’ knowledge base and expert support centre for the Life Science software communities. We provide experts who give advice on how to optimally use these codes. So much is lost when there is a lack of communication between life scientists and computer scientists,” he said.

“ScalaLife also helps users to get access to EU e-infrastructures such as EGI and PRACE, and collaborate with other researchers on improving their code bases,” said Apostolov. He explained that by giving users just a little help their software can be accelerated five times faster.

“Right now, we’re focusing on direct interaction with users and sharing knowledge of how efficiently to use applications on high-performance computers. If the project is successful, then we could develop similar centres for other communities as well,” said Apostolov.

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