CompBioMed Centre of Excellence in Computational Biomedicine

Author: Gavin Pringle
Posted: 15 Jun 2017 | 13:19

EPCC is one of 15 core partners in CompBioMed. This user-driven Centre of Excellence in Computational Biomedicine will nurture and promote the uptake and exploitation of high performance computing within the biomedical modelling community. Its users come from academia, industry and clinical practice.

Computational methods based on human biology are reaching maturity in the biomedical domain, rendering predictive models of health and disease increasingly relevant to clinical practice by providing a personalised aspect to treatment. Computer based modelling and simulation is well established in the physical sciences and engineering, where the use of high performance computing (HPC) is now routine.

The CompBioMed Centre of Excellence prioritises innovation, promoting interdisciplinary entrepreneurial opportunities driven by our users’ needs. Its industrial partners have participated fully in the Centre’s activities from the outset, with the number of Associate Partners, currently 21, expected to grow continuously over the lifetime of the Centre. 

CompBioMed will support and facilitate modelling and simulation activities, and provide education and training for a diverse set of user communities. The Centre will target research scientists from physical, computer and biomedical sciences, software and infrastructure developers, from industry, and medical end-users, including clinicians. It will therefore invest in community building to spread knowledge, tools and best practice to students and researchers across this domain.

The Centre will provide a focal point for the development and sustainability of software tools and services, which can deliver high fidelity three- and four-dimensional (including time) modelling and simulation of all aspects of the human body, from the genomic level to the whole human and beyond, in health and disease.

HPC has the potential to enhance industries in the healthcare sector including pharmaceuticals and medical device manufacturers, underpinning a range of emerging sectors such as those concerned with e-health and personalised medicine. The innovative modelling and simulation techniques developed and promoted by our Centre will be of great interest and relevance to industrial researchers, HPC manufacturers and independent software vendors.

EPCC and CompBioMed

As a Core Partner, EPCC is involved in many aspects of the CompBioMed Centre of Excellence. We enable CompBioMed members to access ARCHER, the UK’s National Tier-1 service. This includes access to the Research Data Facility (the UK-RDF service), which is ideal for the huge data files employed and the large pre- and post-processing demands of our users. Furthermore, CompBioMed users may employ Cirrus, EPCC’s new Tier-2 HPC service, which is ideally suited for high throughput computing (HTC). HTC includes task farming jobs for ensemble simulations that are often found in biomedical simulations. 

EPCC assists users to port their simulations to these platforms, and to enable the associated jobs to be managed remotely from a user’s own computer, ie HPC in the Cloud. This latter aspect is designed to enable medical practitioners to exploit the CompBioMed infrastructure without the need to be HPC-literate.

EPCC is also involved in this Centre’s management and its associated training programme. 

Further, we lead the Centre’s work package on “Innovation and Sustainability”. The purpose of this work package is to ensure the Centre of Excellence creates and implements both a strong sense of innovation and sustains its standing at the forefront of on-demand HPC for biomedical research. 

Innovation Advisory Board

Finally, Prof. Mark Parsons, Director of EPCC, is the Chair of the Centre’s Innovation Advisory Board, or IAB. The IAB will provide strategic guidance and support in Innovation Management within the project. The members of the IAB are drawn from stakeholder groups from within and external to the project to ensure a positive mix of perspectives and contributions: its composition will change to meet the specific needs of the emerging innovation activities as they evolve. The IAB will be called on for advice on both general and specific issues arising from Innovation Management activities, with specific focus on maximising impact within research, societal and commercial realms.

Modelling and simulation 

There are three key areas in which high-fidelity modelling and simulation will be employed in the CompBioMed Centre of Excellence:
• Drug design
• Cardiovascular and musculoskeletal medicine
• Personalised medicine and clinical decision support.

The Centre has access to, and will develop software for, petascale supercomputers through our Core and Associate Partners. We subsequently plan to develop our work towards the evolution of hardware to the exascale. 

Innovation Plan

The initial form of our Innovation Plan is publicly available from the CompBioMed website: www.compbiomed.eu/publications/deliverables

Image courtesy BSC.

Authors

Gavin J. Pringle, Applications Consultant, EPCC
Emily Lumley, Project Manager, UCL