Systems Biomedicine
Consortium leader: Professor Peter Coveney (p.v.coveney AT ucl.ac.uk)
Point of contact: Dr Rupert Nash (rupert.nash AT ucl.ac.uk)
Systems biomedicine holds the promise of providing tools to clinicians and researchers to study and understand the human body and its response the treatment of diseases. Not only limited to simulation based-studies, a natural outcome of systems biomedicine - patient-specific medical simulation, holds the promise of determining tailored medical treatment based on the characteristics of an individual patient, for example using a genotypic assay of a sequence of DNA, or a CT scan of a patient’s neurovasculature. Decision support systems based on patient-specific simulation can potentially revolutionise the way that clinicians plan courses of treatment for various conditions, ranging from viral infections to arterial abnormalities. Basing clinical decisions on simulation models generated from data derived from the patient in question means that the effectiveness of a range of potential treatments can be assessed before they are actually administered, preventing the patient experiencing unnecessary or ineffective treatments.
The consortium is currently involved in three exemplar projects which at their core employ patient-specific medical simulation: (1) The treatment of HIV/AIDS patients through the simulation of drug binding affinities to HIV protease, (2) Diagnosis of and surgical planning for the treatment of neuro-pathologies associated with the intracranial vasculature (in collaboration with clinicians at the National Hospital for Neurology and Neurosurgery and Great Ormond Street Children’s Hospital), and (3) the treatment of glioma cancers through the calculation of binding affinities of chemotherapeutic drugs with patient-specific mutations of tumour cell epidermal growth factor receptors (EGFR) (part of the EU-funded ContraCancrum project, of which UCL is a partner). The consortium also has involvement in various other ongoing projects where multi-scale simulation of human diseases and the treatment thereof is central.
Beyond the requirement of large-scale computing resources for these simulations, many other factors need to be considered for computer simulation to be successfully used within real-world clinical settings, where the timeliness of results is as important as their correctness. Such patient-specific medical simulations require access to both appropriate patient data and the computational resources on which to perform potentially very large simulations. To support patient-specific medical simulations, where life and death decisions are being made, computational resource providers must give urgent priority to such jobs, for example by allowing such jobs to pre-empt the queue on a machine and run straight away. As such, the consortium aims to enhance the way supercomputing resources are accessed and used in clinical scenarios, allowing access to resources to solve relevant real problems in computational biomedical research. In order to do this we employ: (1) large-scale parallel computing, (2) interactive simulation with computational steering and real-time visualisation, (3) improved HPC resource access and usability through the use of middleware tools such as the Application Hosting Environment (AHE), (4) workflows and problem integration, and (5) advance reservations and emergency computing.
