A CCP to build capacity and capability in biomolecular simulation

As computers have got more powerful, it has become possible to use them for Biomolecular Simulation: simulations of how biologically important molecules like DNA and proteins work together inside the living cell. As molecular machines, these molecules work by moving, changing shape, performing chemical reactions, and by interacting with each other in very complex ways. At present, it is not possible to study most of these processes experimentally; techniques like X-ray crystallography and NMR spectroscopy can usually only give us static snapshots of small parts of the system when we need movies of bigger parts of the system to really understand how it works. There are many excellent research groups in the UK that use biomolecular simulation in their research, but up until now there has not been an organisation that can help them share their new ideas, learn about the latest advances from other groups, provide training to new students who are starting to work in this area, and offer advice on how the latest developments in computer technology could be used to help us improve our understanding of biological systems. The aim of this proposal is to set up an organisation that will act as a one stop shop to cover all these aspects, and help to make sure that the UK gets the best value and best science out of the money it invests in research that uses biomolecular simulation.

Our key mission is capacity building and strengthening the biomolecular simulation community in the UK. We propose to achieve this via: 1. Developing and sharing best practice. A. Biomolecular Simulation is a (relatively) young but rapidly developing field. By its nature, the field produced large quantities of complex data. Ensuring the quality of this (expensively acquired) data, and extracting the maximum value from it, is not straightforward since many of the tools that are required to do this have no clear parallels in other, more established fields. B. We therefore regard it as important that a well-supported Biomolecular simulation community is established to provide the forum for the exchange and development of simulation methodology, its implementation on HPC resources, and the training of new generations of researchers. 2. Influencing and informing HPC and HEC NGS development. A. To maintain international competitiveness in the field of Biomolecular Simulation, researchers in the UK need ready access to HPC resources well in excess of those that can be provided as part of responsive mode project grant applications. B. Though there is no one size fits all solution to this requirement, the needs of the Biomolecular Simulation community are well understood by that community, and are not necessarily the same as those required by other heavy users of HPC resources, eg. In the materials science field. Therefore it is imperative that the community has a recognised voice in the design and development of future HPC provision. We propose that this be established. To drive this forward we propose the establishment of a Collaborative Computational Project (CCP) in biomolecular Simulation, supported by BBSRC in regards of a part-time development officer and funding for training workshops and annual meeting.