CompBioMedEE: Computational Biomedicine Exascale Engagement
Lead Research Organisation:
UNIVERSITY COLLEGE LONDON
Department Name: Structural Molecular Biology
Abstract
Computational biomedicine offers many avenues for taking full advantage of emerging exascale computing resources and provides a wealth of benefits as one of the use-cases within the wider ExCALIBUR initiative. The CompBioMedEE project aims to promote and support the use of computational biomedical modelling and simulation at the exascale within the biomedical research community. We shall demonstrate to our community how to develop and deploy applications on emerging exascale machines to achieve increasingly high-fidelity descriptions of the proteins and small molecules of the human body in health and disease. Within the biomedical research domain, we will focus on the discipline of structural and molecular biology. This will enable us to provide the support needed to achieve a wide range of outcomes from determining how the functional and mechanistic understanding of how molecular components in a biological system interact to the use of drug discovery methods to the design of novel therapeutics for a diversity of inherited and acquired diseases. CompBioMedEE will use the IMPECCABLE drug discovery workflow from the UKRI-funded CompBioMedX project. The IMPECCABLE software has been taken through extreme scaling and is eminently suited to bringing computational biomedicine researchers, particularly those from experimental backgrounds who do molecular modelling, to the exascale. The molecular dynamics engine that is part of the IMPECCABLE code is suited to standalone use, enabling biomedical researchers new to HPC to perform molecular dynamics simulations and, through this, to develop the computational expertise required for peta- and exascale use of the IMPECCABLE code. The CompBioMedEE project will engage with biomedical researchers at all career stages, providing them with the compute resource needed to support computational research projects. Through proactive engagement with medical and undergraduate biosciences students, we will illustrate the benefits of using modelling and supercomputers and establish a culture and practice of using computational methods to inform the experimental and clinical work from bench to bedside.
Organisations
- UNIVERSITY COLLEGE LONDON (Lead Research Organisation)
- Evotec (UK) Ltd (Collaboration)
- CECAM (Euro Ctr Atomic & Molecular Comp) (Project Partner)
- Google Inc (Project Partner)
- DiRAC (Distributed Res utiliz Adv Comp) (Project Partner)
- Frederick National Lab for Cancer Res (Project Partner)
- Epistemic AI (EAI) (Project Partner)
- Evotec (UK) Ltd (Project Partner)
- KUANO LTD (Project Partner)
- nVIDIA (Project Partner)
- Alces Flight (Project Partner)
Publications
Martin RL
(2024)
High-Throughput Structure-Based Drug Design (HT-SBDD) Using Drug Docking, Fragment Molecular Orbital Calculations, and Molecular Dynamic Techniques.
in Methods in molecular biology (Clifton, N.J.)
Townsend-Nicholson A
(2024)
Teaching Medical Students to Use Supercomputers: A Personal Reflection.
in Methods in molecular biology (Clifton, N.J.)
| Description | Very few clinical or experimental researchers use supercomputers as part of their professional practice. This award aimed to engage biomedical researchers and students with supercomputing methods of relevance to them to increase their confidence and competence in the use of digital technologies. A significant factor in achieving this is to teach students how to use these resources as part of their taught programme of study. In the academic year 2024-2025, second year medical students at the University of Sheffield and first year Biochemistry students at UCL were using ARCHER2, one of the UK's national supercomputers, to study medical and biochemical questions of relevance to their degree programmes. This is the first time that undergraduates have ever used ARCHER2 and we are currently preparing a case study for EPSRC to showcase how we were able to engage practitioners at all career stages and levels of computational expertise with the level of compute that is a precursor to using exascale computers. |
| Exploitation Route | The award is still active and the outcomes have not been fully realised yet, however, they will be of use to academic and industrial researchers in the biomedical domain and to those in domains that are not yet engaging significantly with compute beyond the level of the desktop. |
| Sectors | Digital/Communication/Information Technologies (including Software) Education Healthcare Government Democracy and Justice Manufacturing including Industrial Biotechology Pharmaceuticals and Medical Biotechnology Other |
| Description | Evidence Week 2023 at UK Parliament |
| Geographic Reach | National |
| Policy Influence Type | Implementation circular/rapid advice/letter to e.g. Ministry of Health |
| URL | https://senseaboutscience.org/what-is-evidence-week/evidence-week |
| Description | Membership of the UK Exascale Project's Science and Industrial Advisory Board (SIAB) (UKRI) |
| Geographic Reach | National |
| Policy Influence Type | Participation in a guidance/advisory committee |
| Description | Benchmarking for Exascale Computing |
| Amount | £100,000 (GBP) |
| Funding ID | EP/Z53321X/1 |
| Organisation | Engineering and Physical Sciences Research Council (EPSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 03/2024 |
| End | 03/2025 |
| Description | UCL (Townsend-Nicholson) - Evotec (UK) Ltd. (Heifetz) academic-industrial collaboration |
| Organisation | Evotec (UK) Ltd |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | My contribution is to provide experimental expertise in cell surface receptors, specifically G protein-coupled receptors. The breadth of my expertise in this domain includes: 1) molecular biology (including cDNA cloning, mRNA quantification, characterisation of alternative splicing, protein expression and site-directed mutagenesis), 2) biochemical (including receptor-ligand binding assays, second messenger (cAMP and intracellular calcium) assays, high-throughput biochemical assays of protein quantification and characterisation, hTR-FRET assays) approaches to characterising receptor function. My research laboratory has started to use high-performance computing to perform ensemble-based analyses of GPCRs, comparing the output of these in silico studies with experimental data. |
| Collaborator Contribution | Dr Alexander Heifetz's contribution is to provide drug discovery methodologies including computational chemistry, computational modelling, virtual screening, Evotec's Hierarchical GPCR Modelling Protocol (HGMP), Fragment Molecular Orbital (FMO) and FMO-DTB quantum mechanical methods of analysing protein-ligand and protein-protein interactions in GPCRs, virtual screening and access to Evotec's extensive network of industrial collaborators and live drug discovery programmes. |
| Impact | Four publications have resulted from this collaboration, to date, and are listed in the publications section with PubmedIDs: 28675443, 29188563, 29188570, 29188574. Evotec (UK) Ltd. is a core partner in the UCL-led H2020-funded CompBioMed Centre of Excellence (www.compbiomed.eu) and Alexander Heifetz and I have extended our UCL-Evotec collaboration beyond our BBSRC-funded activities to include collaborative activities in CompBioMed, most recently by providing a training and dissemination activity at the CompBioMed Winter School Training (listed in the Other Outputs & Knowledge/Future Steps section). Our collaboration is multidisciplinary and all outputs/outcomes have involved integrating experimental and computational technologies to address key questions in GPCR structure and function. |
| Start Year | 2015 |
| Description | CBMC23 Hackathon |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Three of the EPSRC-funded ExCALIBUR grants (SEAVEA, CompBioMedX and CompBioMedEE) led a hackathon on VVUQ methods for HPC simulations using the SEAVEA tooling (SEAVEAtl), as an event associated with the CompBioMed Conference 2023. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.compbiomed-conference.org/compbiomed-seavea-hackathon/ |
| Description | CompBioMed Conference 2023 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | I was the chair of the organising committee for this international conference which was focused on computational biomedicine and gave biomedical researchers and clinicians the opportunity to engage with the state of the art in computational biomedicine. Numerous collaborations arose from the conference and additional activities (e.g. workshops and hackathons) have been planned as a result. We also ran a hackathon coordinated by three of the EPSRC-funded ExCALIBUR grants: SEAVEA, CompBioMedX and CompBioMedEE. this is reported separately. |
| Year(s) Of Engagement Activity | 2023 |
| URL | http://www.compbiomed-conference.org |
| Description | Departmental/Institute of Structural & Molecular Biology Seminar |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | The intended purpose of my seminar was to 1) demonstrate to colleagues the benefits of integrating computational methods into their experimental research, 2) find out what they would need to achieve this (e.g. specific software requirements, training, mentoring, access to resource) and 3) making HPC resource on ARCHER2 that is associated with the grant available to them. There was lively discussion and significant interest in adopting computational methods and at least one research group is now collaborating with me to learn how to apply these methods to their own research questions. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.ismb.lon.ac.uk/wp-content/uploads/2023/12/ISMB-Seminar-Series-Term-1-Autumn-2023-24.pdf |
| Description | Digital Health Rewired |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | ~100 participants attended a panel discussion and debate on Digital Twins in Healthcare, which sparked questions about digital technologies that can be used to democratise healthcare. Several connections were made as a result of networking at the event, which resulted in four invitations to speak at workshops and panels for industry and also for healthcare practitioners. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://digitalhealthrewired.com/class/inside-track-digital-twins-in-health/?wcs_timestamp=171033120... |
| Description | Digital Twins for Healthcare - Public Policy Briefing at Westminster as part of Evidence Week 2023 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Policymakers/politicians |
| Results and Impact | Evidence Week returned to Parliament in July to bring the public, MPs, Peers, national experts, and researchers together to discuss how evidence informs policy and what latest research findings Parliament should use to review current policies. The week including policy briefings, training sessions and lively discussions organised by Sense about Science and the Parliamentary Office of Science and Technology (POST) and in partnership with the House of Commons Library, the House of Lords Library, Ipsos, the UK Statistics Authority (UKSA) and universities and research institutions from across the UK, led this year by the University of Nottingham. I presented an Evidence Pod, engaging with Parliamentarians about how digital twins can be used for personalised medicine and health equity. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Digital Twins workshop at Supercomputing 23 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | I was one of the co-organisers and a panel member for this half-day workshop on digital twins, practices and principles for high performance computing. Pre-registration for the event showed it to be so popular that SC23 moved it to the largest room available and the workshop was sold out. Numerous outcomes and impacts have arisen from this event, including the establishment of new collaborations with colleagues working in Oak Ridge National Laboratory on Frontier, the US's first Exascale machine, engagement with Exascale use cases in addition to computational biomedicine and computational biology and requests for information on how the comptiomed education and training has been able to be delivered at such a large scale (>100 participants at a time). A proposal for a full day workshop has been submitted for SC24. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://sc23.supercomputing.org/proceedings/workshops/workshop_pages/wksp154.html |
| Description | Digital Twins workshop at Supercomputing 24 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | I was one of the co-organisers and a panel member for this full-day workshop on digital twins, practices and principles for high performance computing. Pre-registration for the event showed it to be so popular that SC24 moved it to the largest room available and the workshop was sold out. Numerous outcomes and impacts have arisen from this event, including the establishment of new collaborations with colleagues working in Oak Ridge National Laboratory on Frontier, the US's first Exascale machine, engagement with Exascale use cases in addition to computational biomedicine and computational biology and requests for information on how the CompBioMed education and training has been able to be delivered at such a large scale (>100 participants at a time). A proposal for a full day workshop has been submitted for SC25. Our unique workshop element "Bring Your Own Digital Twin" allowed digital twins from many different domains, including computational biomedicine, to be showcased. The organising committee for SC25 were very keen to help us expand this part of the workshop and we have submitted a proposal to SC25 for a full day workshop with hands-on sessions for people to engage with the digital twins being showcased. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://sc24.supercomputing.org/proceedings/workshops/workshop_sessions.html#sess735 |
| Description | Digital You - Public Policy Briefing at Westminster as part of Evidence Week 2024-2025 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Policymakers/politicians |
| Results and Impact | Evidence Week is a unique opportunity for the public, parliamentarians, and researchers to come together to share knowledge and insights. It empowers legislators and their staff to engage with evidence and equips them with the critical tools to unpack scenarios and understand cognitive bias. I presented an "Evidence Pod" to showcase the benefit of using Digital Twins for Healthcare and had the opportunity to network with Parliamentarians to spark questions and discussion. Lord Vallance attended my Pod and I was able to have a very good conversation with him about this area. |
| Year(s) Of Engagement Activity | 2025 |
| URL | https://senseaboutscience.org/evidence-week/institution/digital-you/ |
| Description | Invited speaker at Precision Medicine Networking Forum conference |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | An audience of approximately 200 was present in the session on AI/Big Data in Precision Medicine in which I spoke. There were numerous questions and discussions afterwards, and I was approached by the Latvian Science Minister for further discussion. I have had increased engagement with biomedical researchers in Latvia and a clinical researcher in Ireland, as a result. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://pmnetforum.com/programma-v-2/ |
| Description | Media Interviews at Supercomputing 23 |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | I was one of the participants interviewed at SC23 and a series of features showcasing the conference. So far, I am aware of two videos. Neither of these has been officially released yet, so I only have the provisional URLs (https://www.youtube.com/watch?v=U8s0IKs-Rpw, https://www.youtube.com/watch?v=4IqWA9H0Bec). Once released, as with other SC showcase features, each is likely to receive in excess of 2000 views. |
| Year(s) Of Engagement Activity | 2024 |
| Description | Royal Society of Medicine Digital Twins: Ethics and Clinical Uses (continuing professional development) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | This was an all-day workshop on Digital Twins and Ethics and Clinical Uses that was hosted by the Royal Society of Medicine. ~100 attendees were present and discussion on engaging experimental and clinical researchers with computational methods in healthcare took place, with particular emphasis on the ethical considerations. As a result of my presentation, I have been invited to speak at a private event at the Royal Society for Medicine on Living Well for Longer, where private equity investors, healthcare start-ups, innovators were present, providing an additional opportunity to engage biomedical researchers with computational biomedicine and Exascale computing. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://www.rsm.ac.uk/events/digital-health/2024-25/tet02/ |
| Description | Royal Society of Medicine Digital Twins: Tailoring Medicine in silico (continuing professional development) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | This was an all-day workshop on Digital Twins for Health that was hosted by the Royal Society of Medicine. ~100 attendees were present and discussion on how best to engage experimental and clinical researchers with computational methods in healthcare took place. As a result of my presentation, I have been invited to speak at Digital Health Rewired on 13 March 2024, the educational conference and networking event for the digital health community where professionals from the NHS and social care, private healthcare, suppliers, start-ups, innovators, policy makers and patients will be present, providing an additional opportunity to engage biomedical researchers with computational biomedicine and Exascale computing. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Royal Society of Medicine Living Well for Longer (Private event) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Supporters |
| Results and Impact | This was an unusual event at the RSM. It was focussed on 'Living Well for Longer' and covered lifestyle, physical and medical interventions that can help extend healthy lifespan particularly in relation to cancer, cardiovascular disease, diabetes and dementia. The conference was an opportunity for the RSM to invite successful technology entrepreneurs to engage in the wider health agenda. It washeld in conjunction with Tiger 21, a global community of ultra-high net worth entrepreneurs and investors. It wasn't an opportunity for anyone to pitch (!) but to share the latest evidence for compressing morbidity and increasing health-span in the hope of generating interest in health research more generally. |
| Year(s) Of Engagement Activity | 2024 |
| Description | Virtual Human Global Summit |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | This inaugural event held in New York City launched a global initiative in computational biomedicine and digital twins for healthcare. As one of the expert panel, I have been invited to join the organising committee to develop future events (e.g. conferences, workshops, topic specific meetings etc.) for a global community developing and deploying computational biomedicine methods to inform health and wellbeing. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.bnl.gov/virtual-human-global-summit/agenda.php |