Research Platforms
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Funding Success Case Studies

Awards made through the Research Platforms Initiative have facilitated the purchase of many cutting-edge pieces of equipment. Below are case studies detailing some of these awards, and the impact that the new equipment has made on research at UCL.

2011: Prospective Motion Compensation Systems

Dr Nikolaus Weiskopf and colleagues received funding through the 2011-2012 SLMS capital equipment award program, an internal funding scheme which enables SLMS researchers to bid for new research equipment.

Their award enabled the purchase of three cutting-edge systems which improve the quality of brain scan images obtained through magnetic resonance imaging (MRI). Conventionally, individuals must remain completely still during the MRI scanning process, as motion blurs images, complicating interpretation. Eliminating head movement however can be challenging, especially when subjects are children or have movement disorders, and scans often need to be repeated or conducted under general anaesthetic or sedation, with associated risk.

The new systems, manufactured by KinetiCor, are fitted to existing MRI scanners. Employing a technology called 'prospective motion compensation', they accurately track focus on the brain to a small fraction of a millimetre, compensating for any head motion in real time. By reducing movement artefacts, the systems can produce clearer images and allow more subtle signal changes to be discerned (see image).

Prospective Motion Compensation

At UCL, one of the systems resides with the Weiskopf group at the Wellcome Trust Centre for Neuroimaging (WTCN), one in Dr David Carmichael's lab at the Institute of Child Health (ICH), and one with Prof Marty Sereno's group at the Birkbeck-UCL Centre for Neuroimaging. These researchers, and their collaborators intend to apply the technology to different scientific questions, ranging from basic neurobiology in health and disease, to functional studies investigating cognition, emotion and memory.

As early adopters of the system, the award recipients have been working closely with one another, with KinetiCor, and with other groups - notably the Physics department at the University of Freiburg - to optimise their setups and implement MRI pulse sequences, the computational instructions which specify scanning parameters, and are tailored according to the type of experiment being conducted.

Preliminary data confirm that the system generates high-quality images, and work is underway to develop and maximally exploit the technology. Having the equipment in place has already helped leverage further funding. At WTCN, a PhD student jointly funded by Siemens and the UCL Impact Award benefits from it for the development of robust clinical quantitative imaging, whilst a new research project at ICH, funded by Action Medical Research, will use it to study focal cortical dysplasia in children, an epilepsy-causing condition which is treatable by surgery if the affected brain region can be clearly identified. Dr Weiskopf's application for an ERC Consolidator Grant, which was selected for funding, included some pilot data generated with the system. This project aims at in-vivo histology using MRI with unprecedented resolution and specificity and will benefit from the robust motion correction. 

This SLMS equipment award has already brought great benefits, keeping UCL at the cutting-edge of neuroimaging, fostering and developing collaborations within the university and beyond, and helping to attract additional funding. Dr Weiskopf commented, 'It's hard to think of a more efficient funding project.'

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The annual SLMS capital equipment call goes out each autumn. For more information, visit www.ucl.ac.uk/platforms.

2011: PAMELA Accessibility Research Group double-deck bus

  •  2011 award to the UCL PAMELA group, for the purchase of a double-deck bus, to be used in accessibility research and fuel cell development.
Accessibility Research Bus

In 2011, the UCL Department of Civil, Environmental and Geomatic Engineering funded the purchase of a double decker bus, for the UCL Pedestrian Accessibility Movement Environment Laboratory (PAMELA) to use in experiments. A major stream of work at PAMELA is accessibility research; examining how the design and implementation of transport systems influence the safety and comfort of users.  

Since the bus arrived in January 2013, it has been used in two lines of work. The first examines how passengers are affected by bus acceleration and deceleration, when walking through the upper or lower decks, or when using the stairs. Experimental subjects wear special shoes and gloves with pressure sensors, allowing the researchers to measure changes in posture, balance and gait as the bus manoeuvres. Computer equipment stored behind the driver’s cabin collects data on the move allowing for subsequent analysis. The aim of this work is to identify driving practices most compatible with passenger well-being, and thereby inform bus driver training.

The second strand of work involves the development of new hydrogen fuel cells as a means of powering the bus. Existing hydrogen cell technology cannot effectively power large, double deck vehicles. To reduce power consumption and carbon emissions, new fuel cells with improved power cycles need to be created. Researchers from across UCL are collaborating to develop a super-capacitor to capture and store the kinetic energy normally released during braking, and prevent its dissipation as heat. The Department of Mechanical Engineering is working on the power pack itself, Chemical Engineering and Chemistry are investigating methods for purifying hydrogen (necessary for it to perform optimally as a fuel), and PAMELA scientists will integrate the elements into a working system.

The bus was an important strategic investment: experiments can now be performed in a real vehicle, with the desired road conditions. This will allow more meaningful data to be generated than would have been possible before. 

In the future, PAMELA hopes to undertake additional work for London Transport and other transport system providers.  

Links:

UCL PAMELA

2012: nCounter Analysis System

  •  2012 award to Dr Paola Oliveri for the purchase of an nCounter analysis system, for the quantification of genetic material.

In 2011, Paola Oliveri’s group in the UCL Department of Genetics, Evolution and Environment received a SLMS capital infrastructure award to purchase an nCounter Analysis system (Nanostring). This cutting-edge equipment quantifies the abundance of RNA and other nucleic acids with sensitivity and precision surpassing current standard protocols, and can be used in a variety of genetic studies. At the time of purchase it was the first such machine in the UK.

To detect genetic material, the system uses colour-coded probes which are designed to bind specific genetic sequences. The coloured probes bind their targets and, acting as barcodes, they are digitally imaged, allowing abundance to be determined by the system’s software. The technology can be used in diverse scientific areas, ranging from the elucidation of gene expression levels in health and disease, and throughout the process of development. The Oliveri group is using the equipment to investigate mechanisms of cell specification during early development in the sea urchin model.

Initial data from UCL and other institutions show that the technology quantifies genetic material more accurately than microarrays, and has similar sensitivity to polymerase chain reaction (the current gold standard). Importantly, the nCounter can analyse the abundance of several hundred genes simultaneously, with minute amounts of starting material, and without the need for prior amplification. Using small samples of patient DNA or RNA, the equipment can thus be used to support molecular diagnosis – the identification of disease on the basis of specific genetic changes. Cancer research is one area for which the nCounter has great potential to confirm the genetic changes associated with disease progression. The machine is fully-automated and with a user-friendly interface, experiments can be set up rapidly and require minimal hands-on time, increasing the efficiency of data acquisition.

Moreover, the system facilitates the analysis of archived tissue. The formalin-fixing and paraffin-embedding procedures used for long-term tissue preservation typically damage genetic material, limiting expression analysis by conventional methods. However, the high sensitivity of the nCounter system overcomes this issue, allowing preserved biopsy tissue to be more accurately investigated.

UCL was an early adopter of the system. The technology has since gained momentum, with researchers from more institutions using it to answer a range of scientific questions. UCL is keen to make its nCounter system available for users within the college and beyond to access – contact research-equipment@ucl.ac.uk with details of your project if interested.

Emerald High Performance Computing Case Study

Summary:

The focus of this case study is a UK High Performance Computing (HPC) facility called Emerald. Funded by the EPSRC, and launched in spring 2012, Emerald is a large Graphics Processing Unit (GPU)-based supercomputer which facilitates computationally-intensive experiments. As a collaborative venture between the Universities of Bristol, Oxford, Southampton and UCL – together forming the Centre for Innovation (CfI), the cluster is of a significantly higher specification than any of the institutions would have been able to invest in individually. Emerald has driven cross-disciplinary academic, SME and industry engagement, and the partner institutions are actively working to train researchers and maximise utilisation of the resource. Continued investment will be necessary to sustain and develop Emerald in the future. 

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Introduction:

In March 2012, an EPSRC-funded High Performance Computing (HPC) facility called Emerald was launched. Emerald is a supercomputer built with Graphics Processing Unit (GPU) architecture, which at the time of launch was amongst the largest GPU-based systems in Europe, and remains the largest such system in the UK. It was launched jointly by the Universities of Bristol, Oxford, Southampton and UCL, which together form a consortium called the Centre for Innovation (CfI) and the system is hosted and operated by the Science & Technology Facilities Council (STFC) in a strategic partnership with CfI. The major aim of the CfI is to support the co-development and sharing of e-infrastructure capabilities (including hardware, software, people and skills) between the partners, and to develop links with other academic and industrial organisations. 

Emerald supports all of these objectives and has greatly benefited research output, industry collaboration and the training and development of users.

Research highlights:

High Performance Computing

By providing access to significant computational power, the Emerald cluster has

enabled researchers to perform theoretical experiments in much shorter timescales. The outputs of these model investigations can be used to guide physical experiments.

Important research highlights include:

  • UCL researchers are using the resource to simulate and predict the chemical processes that take place at the surfaces of metal and other materials.
  • Scientists at Bristol are investigating how mutations of a key enzyme in H1N1 (the ‘Swine influenza’ virus) lead to the development of resistance to current antiviral flu treatments.
  • Researchers at UCL are working with GPU specialists at Oxford to optimise the performance of a tsunami simulation code.
  • UCL scientists are simulating the effect of gene mutations linked to the spread of cancer. This can aid the development of more robust and effective cancer treatments.
  • Scientists at Imperial College London have been able to achieve unprecedented levels of accuracy in computational fluid dynamics, specifically relating to Unmanned Aerial Vehicles, allowing engineers to understand complex flow patterns and thus perform aerodynamic design, without flying an aircraft or even starting up a wind tunnel.

Industrial collaborations:

The CfI has actively engaged with industry through workshops at STFC and UCL, to publicise and promote the potential of GPU-based computing technology to industrial research applications. CfI has directly engaged with SMEs including NAG Ltd., Zenotech and Cresset Biomolecular Discovery Ltd. When allocating computing resource for Emerald, priority is given to collaborative work, especially between academic partners and industry.

Improved awareness, training and skills:

The CfI institutions are working hard to drive user engagement and facilitate training. NVIDIA, who manufactured Emerald’s processors, offer training in CUDA, a programming model they developed to harnesses the power of GPU cores. This training is available across CfI partner institutions and a summer school is run every year at Oxford. Researchers are increasingly learning to code and are collaborating with internal and external software development teams to create and optimise algorithms that emulate real-life behaviours in a virtual world. Developing code that operates efficiently on multi-core systems is a challenge, and researchers frequently request Emerald resource to ‘pressure test’ their code at scale.

Oxford also holds regular lunchtime events to promote Emerald to its academic community. Total utilisation of the resource peaked in February 2014 at 85%, with individual institutions making greater use of their allocated portions: UCL’s usage, for instance, grew from around 12% in mid-2013 to approximately 22% in Q1 2014.

Efficiency outcomes:

The Emerald facility is a tier 2 (regional) scaled machine, and is of a significantly higher specification than any of the partner institutions would have been able to invest in individually. Operational costs are shared amongst the CfI members, and the resource has been administered by a single team. This pooling avoids the need for each institution to invest separately in duplicate resource, and facilitates cross-fertilisation of ideas, knowledge and experience between the partners. Monthly usage metrics are circulated to all CfI members, encouraging institutions to fully utilise their allocated resources. Moreover, key case studies are shared among the group, highlighting areas where benefits are being realised. Had this facility been implemented on a smaller scale or been more inward-looking, some institutions would not have developed the expertise required to leverage the technology fully and knowledge would have remained within institutional silos.

The future of Emerald:

Capital funding from RCUK allowed the Emerald facility to be set up. Without this major investment in GPU architecture, the technology would have remained small-scale and unproven in a large, industrial environment.

On-going RCUK funding is critical to sustain and develop Emerald. One future challenge is the development of a set of common tools to assist the partner institutions in managing the resource. Currently, there is no funding in place beyond summer 2015, when the current system will reach end-of-life and be decommissioned.



Page last modified on 19 feb 14 13:00