A solution designed and integrated by OCF has been shortlisted in the 2017 UK Cloud Awards in the ‘Best Public Sector Project’ category.
The MRC eMedLab consortium consists of University College London, Queen Mary University of London, London School of Hygiene & Tropical Medicine, the Francis Crick Institute, the Wellcome Trust Sanger Institute, the EMBL European Bioinformatics Institute and King’s College London and was funded by the Medical Research Council (£8.9M).
The vision of MRC eMedLab is to maximise the gains for patients and for medical research that will come from the explosion in human health data. To realise this potential, the consortium of seven prestigious biomedical research organisations need to accumulate medical and biological data on an unprecedented scale and complexity, to coordinate it, to store it safely and securely, and to make it readily available to interested researchers.
The partnership’s aim was to build a private cloud infrastructure for the delivery of significant computing capacity and storage to support the analysis of biomedical genomics, imaging and clinical data. Initially, its main focus was on a range of diseases such as cancer, cardiovascular and rare diseases, subsequently broadening it out to include neurodegenerative and infectious diseases.
The MRC eMedLab system is a private cloud with significant data storage capacity and very fast internal networking designed specifically for the types of computing jobs used in biomedical research. The new high-performance and big data environment consists of:
- Red Hat Enterprise Linux OpenStack Platform
- Red Hat Satellite
- Lenovo System x Flex system with 252 hypervisor nodes and Mellanox 10Gb network with a 40Gb/56Gb core
- Five tiers of storage, managed by IBM Spectrum Scale (formerly GPFS), for cost effective data storage – scratch, Frequently Accessed Research Data, virtual clusters image storage, medium-term storage and previous versions backup.
The project has become a key infrastructure resource for the Medical Research Council (MRC), which has funded six of these projects. The success has been attributed to MRC eMedLab’s concept of partnership working where everybody is using one shared resource. This means not just sharing the HPC resource and sharing it efficiently, but also sharing the learning, the technology and the science at MRC eMedLab. Jacky Pallas, Director of Research Platforms, UCL, comments, “From the beginning there was an excellent partnership between the MRC eMedLab operations team and the technical specialists at OCF, working together to solve the issues which inevitably arise when building and testing a novel compute and data storage system.”
In total, there are over 20 different projects running on the MRC eMedLab infrastructure which include:
- The London School of Hygiene & Tropical Medicine is working on a project looking at population levels and the prevalence of HIV and TB, how the pathogen/bacteria evolve and the genetics of human resistance. This research is done in collaboration with researchers in Africa and Vietnam
- Francis Crick Institute cancer based science – supporting a project run by Professor Charles Swanton investigating personalised immunotherapies against tumours
- Great Ormond Street Hospital – collaboration on research on rare diseases in children
- Linking genomics and brain imaging to better understand dementia
- Studying rare mitochondrial diseases and understanding how stem cells function
- Projects using the computing infrastructure use UK Biobank data to identify and improve treatments for cardiovascular diseases
- Deep mining of cancer genomics data to understand how cancer tumours evolve
- Analysing or looking at virus genome sequences to enable the modelling and monitoring of infectious flu type epidemic
The MRC eMedLab private cloud has shown that these new computing technologies can be used effectively to support research in the life sciences sector.
Professor Taane Clark, Professor of Genomics and Global Health, London School of Hygiene and Tropical Medicine comments, “The processing power of the MRC eMedLab computing resource has improved our ability to analyse human and pathogen genomic data, and is assisting us with providing insights into infectious disease genomics, especially in malaria host susceptibility, tuberculosis drug resistance and determining host-pathogen interactions.”