Investigating molecular machines with Alexandre Bonvin at ISGC2012

This morning at the ISGC2012 event in Taipei, Alexandre Bonvin of the University of Utrecht introduced us to how he is using the grid to investigate the molecular machines and the social life of proteins. In many diseases, for example, it is the breakdown in communication between proteins that leads to problems. “I’m coming at this as from the user perspective,” he told us. “A key part of my role is to hide the complexity of the grid from the users.”

Structural biology uses techniques such as NMR and synchrotron X-ray analysis to delve into the structure of complex molecules, such as proteins and peptides. The big machines acquire the data from samples, and this is processed to determine what the molecule contains and the constraints on its shape. The number crunching on its structure starts there – and this is where the grid comes in. The grid is just right for this process, which is CPU intensive, consists of lots of parallel jobs but needs limited data transfer and storage.

The WeNMR project leads the largest EGI Virtual Organisation in the life sciences. It has nearly 400 users across 41 countries, including 4 outside Europe - in Taiwan in collaboration with ASGC, Latin America through GISELA and in SAgrid’s South Africa. This represents around 30,000 cores and 1.6 million jobs in the last year. Just over half of the jobs run on the Dutch National Grid Infrastructure, BigGrid, which provides 75% of the CPU hours.

As Alexandre said, grid is a complex business, and WeNMR provides a web portal offering ‘protocolised’ access to the grid for protocols HADDOCK, CS-ROSETTA and GROMACS. This is both a user friendly gateway for the NRM and SAXS communities and a virtual research platform. Linked to the ESFRI-INSTRUCT project, WeNMR works to foster the adoption and use of e-infrastructure and to get over the entry barrier reported by many users, while at the same time offering the top of the line software and services that attract expert users. The secret to sustainability is of course to get scientists, and not just the computer experts but the average user as well.

There was also a brief word on scientific cloud computing. Alexandre’s team is using cloud computing, supported by the supercomputing centre SARA in Amsterdam, to process libraries of proteins. Because this needs several sets of software and libraries, it is much simpler to set up a virtual machine once with all the software installed, then you don’t have to deal with clashes with scientific linux on the grid. “For the other portals,” said Bonvin, “grid is the perfect solution- cloud will not gain us anything.”

You can hear more from Alexandre, his team at Utrecht University and the CONCO project on the newly released YouTube video “Stories from the Grid” by EGI (European Grid Infrastructure). The first episode shows how a component of the cone snail's toxic venom is being modified using the aid of computer models, to help produce new anaesthetics and alleviate the muscle spasms caused by the condition dystonia. Episodes 2 and 3 coming soon!