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Report

Teaser, summary, work performed and final results

Periodic Reporting for period 1 - CompBioMed (A Centre of Excellence in Computational Biomedicine)

Teaser

Summary

Computational methods, based on human biology, are now 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.
Our Centre of Excellence has innovation at the forefront of its aims, promoting interdisciplinary entrepreneurial opportunities driven by our usersâ€™ needs. Our industrial and clinical partners participate fully in the Centreâ€™s activities, with the number of associate partners growing continuously over the lifetime of the Centre. We target research scientists from physical, computer and biomedical sciences, software and infrastructure developers and clinicians from industry, academia and medicine. We also invest in community building to spread knowledge, tools and best practice to students, researchers and decision makers across the domain. HPC has the potential to enhance industries in the healthcare sector including pharmaceuticals and medical device manufacturers, and underpinning a range of emerging sectors, such as those concerned with e-health and personalised medicine. The innovative modelling and simulation techniques we develop and promote within this Centre have therefore proven to be of great interest and relevance to industrial researchers, HPC manufacturers and independent software vendors.

Work performed

We have deployed several application codes across HPC centres. Current codes have been improved, with some on track for the exascale, and new functionalities have been determined, often involving further collaborations within and without the Core Partnership. As part of the Cardiovascular Exemplar our partners have developed a 1D model of the full arterial system, simulated problems within small vessels (red blood cells, aneurisms, particle transport etc) and simulated part and full heart geometries. In the Molecularly-based Medicine Exemplar, collaborations are investigating drug interactions with potential targets in the body, especially highly complex targets. Drug discovery tools based on state-of-the-art 3D-convolutional neural networks, are being developed, concentrating on overcoming sampling and accuracy limitations in the simulations by applying machine learning algorithms. The Neuro-musculoskeletal Exemplar has been using bone modelling software developed within the project and coupling this to other software packages to expand the simulations.

Our most high-profile dissemination activity has been the production and screening of an IMAX film called â€œThe Virtual Humanâ€ (https://youtu.be/1FvRSJ9W734) which created over 1 million Twitter impressions. The film was constructed from simulations from our Core and Associate Partners, with animations rendered on the MareNostrum Supercomputer at Barcelona Supercomputer Centre (BSC). We have published 27 scientific papers, and participated in over 60 major conferences and workshops, organising 10 workshops and sessions, attended by approx. 1,200 people. We have established two courses for UCLâ€™s medical degree programme and biomedical students that have been attended by 123 students in total. We intend to extend these courses in subsequent years as they were very well received. These events, when recorded, are then made available on our YouTube channel, receiving over 400 views to date.

We have established an Innovation Advisory Board, increasing and diversifying its initial membership by including clinicians. We have held two face-to-face meetings during which recommendations for the future direction of CompBioMed were proposed. These recommendations have, where appropriate and possible, been implemented in our Centre. Our Innovation Exchange Programme has enabled twenty visits across our Core and Associate Partners. This has been aided through a memorandum of understanding between CompBioMed and HPC-Europa3, with their Transnational Access programme.

The current mechanisms for accessing services offered by HPC centres and cloud providers were analysed, together with the requirements of CompBioMed users for non-conventional access (such as advanced reservations, on-demand access etc), resulting in a feasibility study of implementing such mechanisms from the HPC providers. We have enabled CompBioMed partners to deploy their applications on cloud and HPC architectures for real biomedical applications and are pushing the boundaries of several of the largest supercomputers in the world with some of our applications en route to the exascale. CompBioMed is working to promote the use of application container solutions in order to facilitate more efficient, reliable and portable application deployment, opening the possibility of using them in a clinical setting. We have updated and enhanced our software hub, detailing software applications from our Core Partners; we are currently extending this to include applications available through our Associate Partners.

We have undertaken an extensive analysis and identification of solutions available within the consortium and analysed in detail the taxonomy of end-users that can benefit from the services offered by the CoE. Data storage and transfer technologies have been investigated, resulting in a deployment of the EUDAT B2SHARE service for data archive. Work has been conducted with two synchrotron facilities (European Synchrotro

Final results

Through engagement with HPC resources and our partners, we will systematically identify the applications that would benefit from a higher quality of service and on-demand access, opening the possibility of bringing our applications and solutions into a clinical setting. To enhance the likelihood of such developments, we are working with cloud providers adapting our core applications to run on cloud resources.

We have made numerous advances in our research and published over 25 papers. We will continue to work on applications where a combination of capabilities and community plus market demand makes most sense. This is helped by the recommendations of the IAB and the diverse partners within the project, including Associate Partners.

In our training we are focussing on the core principles of biomedical research, and we are reaching out not only to computational scientists, but targeting a new generation of clinicians who will soon be working in hospitals. We have integrated a course into the medical training at UCL, which teaches medical students how to work with supercomputers to solve specific problems.

We are working directly on our Sustainability Plan by analysing our potential stakeholders and determining the communities that could sustain the project in the long term. This first stage of analysis will sit alongside the detailed and more rigorous work on developing trials with users. Two start-up/spin-out companies have been established from developments within the project.