Building a Centre of Excellence for computational biomolecular research

Author: Adam Carter
Posted: 15 Jun 2017 | 11:59

The BioExcel project, which is establishing a Centre of Excellence in Computational Biomolecular Research, is now well into its second year. Here is an update on our progress.

I’ll start with the part of the project that I’m most closely involved with, which is reaching out to possible users of the Centre and ensuring its work will reflect the needs and interests of the computational biomolecular research community. 

Interest groups 

The interest groups (IGs) – see my article in EPCC News 80 – are growing both in their membership and activity:

• The Integrative Modelling IG now has its own page at bioexcel.eu where it highlights news and upcoming events specifically for this community. 
• The Practical Applications for Industry IG has started regular phone meetings to discuss how best the Centre can support users from industry. 

• The Hybrid Methods IG has been launched with a meeting in Sardinia, in conjunction with the European Joint Doctorate Programme in HPC for Life Sciences, Engineering and Physics, where a mix of early-career and established academics in the field met to discuss state-of-the-art techniques in this area. 

In November, there will be an opportunity for all BioExcel interest group members to meet up in Amsterdam for the BioExcel community forum. Registration opens soon, but you can sign up to our Interest Groups now to be kept informed.

Code development

The Sardinia meeting also offered the opportunity for BioExcel to introduce to the community new technical work that we have undertaken as part of the project to develop a new QM/MM interface for the code CPMD. This will make it easier to conduct simulations which take into account quantum effects to accurately represent how particles are interacting at atomic scale, but which also scale up to systems that are big enough to be of interest in real biological applications. As part of one of BioExcel’s use cases, this new interface is being evaluated using a real problem in collaboration with the Human Brain Project.

As well as CPMD, the project is also supporting the development of Gromacs and HADDOCK. These codes continue to be independently developed but BioExcel is helping to coordinate the code development, to share best practice between the code developers and to coordinate a number of BioExcel releases of the codes, the first of which has just been published.

Find out more

On our website you can watch webinars, join interest groups, sign up for training courses, download our software, ask questions, and have your say: www.bioexcel.eu

Author

Adam Carter, Project Manager, EPCC

Stem cells. Image: iStock.com/luismmolina