BarraCUDA – a Fast Sequence Mapping Software using Graphics Processing Units

High-throughput DNA sequencing (HTS) instruments today are capable of generating millions of sequencing reads in a short period of time, and this represents a serious challenge to current bioinformatics pipeline in processing such an enormous amount of data in a fast and economical fashion. Modern graphics cards are powerful processing units that consist of hundreds of scalar processors in parallel in order to handle the rendering of high-definition graphics in real-time. It is this computational capability that we propose to harness in order to accelerate some of the time-consuming steps in analyzing data generated by the HTS instruments. We have developed BarraCUDA, a novel sequence mapping software that utilizes the parallelism of NVIDIA CUDA graphics cards to map sequencing reads to a particular location on a reference genome. While delivering a similar mapping fidelity as other mainstream programs , BarraCUDA is a magnitude faster in mapping throughput compared to its CPU counterparts. The software is also capable of supporting multiple CUDA devices in parallel to further accelerate the mapping throughput. BarraCUDA is designed to take advantage of the parallelism of GPU to accelerate the mapping of millions of sequencing reads generated by HTS instruments. By doing this, we could, at least in part streamline the current bioinformatics pipeline such that the wider scientific community could benefit from the sequencing technology. BarraCUDA is currently available at http://seqbarracuda.sf.net

Designing inclusive systems

The Cambridge Workshops on Universal Access and Assistive Technology (CWUAAT) are a series of workshops held at a Cambridge University College every two years.

Tomorrow's cities - a framework for building resilience

Urbanisation is the great driving force of the twenty-first century. Cities are associated with both productivity and creativity, and the benefits offered by closely connected and high density living and working contribute to sustainability. At the same time, cities need extensive infrastructure – like water, power, sanitation and transportation systems – to operate effectively. Cities therefore comprise multiple components, forming both static and dynamic systems that are interconnected directly and indirectly on a number of levels, all forming the backdrop for the interaction of people and processes. Bringing together large numbers of people and complex products in rich interactions can lead to vulnerability from hazards, threats and even trends, whether natural hazards, epidemics, political upheaval, demographic changes, economic instability and/or mechanical failures; The key to countering vulnerability is the identification of critical systems and clear understanding of their interactions and dependencies. Critical systems can be assessed methodically to determine the implications of their failure and their interconnectivities with other systems to identify options. The overriding need is to support resilience – defined here as the degree to which a system or systems can continue to function effectively in a changing environment. Cities need to recognise the significance of devising adaptation strategies and processes to address a multitude of uncertainties relating to climate, economy, growth and demography. In this paper we put forward a framework to support cities in understanding the hazards, threats and trends that can make them vulnerable to unexpected changes and unpredictable shocks. The framework draws on an asset model of the city, in which components that contribute to resilience include social capital, economic assets, manufactured assets, and governance. The paper reviews the field, and draws together an overarching framework intended to help cities plan a robust trajectory towards increased resilience through flexibility, resourcefulness and responsiveness. It presents some brief case studies demonstrating the applicability of the proposed framework to a wide variety of circumstances.

Designing Inclusive Systems

The Cambridge Workshops on Universal Access and Assistive Technology (CWUAAT) are a series of workshops held at a Cambridge University College every two years.

Advances in nanodevices and nanofabrication: Selected publications from symposium of nanodevices and nanofabrication in ICMAT2011

A variety of devices at nanometer scale / molecular scale for electronic, photonics, optoelectronics, biological and mechanical applications have been created through a rapid development of materials and fabrication technology. Further development of nanodevices strongly depends on the state-of-the-art knowledge of science and technology at the sub-100nm length scale. This symposium proceedings serves as a nice platform on which scientists and engineers can present and highlight some of the key advances in the following topics: Electronic and optoelectronic devices of nanometer scale / molecular scale. Nanomechanics and NEMS. Electromechanical coupled devices. Manipulation and aligning processes at nanometer scale / molecular scale. Quantum phenomena. Modeling of nanodevices and nanostructures. Fabrication and property characterization of nanodevices. Nanofabrication with focused beam technology, e.g., focused ion beam, laser and proton beam. © 2012 by Pan Stanford Publishing Pte. Ltd. All rights reserved.

Functional magnetic resonance imaging of impaired sensory prediction in schizophrenia.

IMPORTANCE: Forward models predict the sensory consequences of planned actions and permit discrimination of self- and non-self-elicited sensation; their impairment in schizophrenia is implied by an abnormality in behavioral force-matching and the flawed agency judgments characteristic of positive symptoms, including auditory hallucinations and delusions of control. OBJECTIVE: To assess attenuation of sensory processing by self-action in individuals with schizophrenia and its relation to current symptom severity. DESIGN, SETTING, AND PARTICIPANTS: Functional magnetic resonance imaging data were acquired while medicated individuals with schizophrenia (n = 19) and matched controls (n = 19) performed a factorially designed sensorimotor task in which the occurrence and relative timing of action and sensation were manipulated. The study took place at the neuroimaging research unit at the Institute of Cognitive Neuroscience, University College London, and the Maudsley Hospital. RESULTS: In controls, a region of secondary somatosensory cortex exhibited attenuated activation when sensation and action were synchronous compared with when the former occurred after an unexpected delay or alone. By contrast, reduced attenuation was observed in the schizophrenia group, suggesting that these individuals were unable to predict the sensory consequences of their own actions. Furthermore, failure to attenuate secondary somatosensory cortex processing was predicted by current hallucinatory severity. CONCLUSIONS AND RELEVANCE: Although comparably reduced attenuation has been reported in the verbal domain, this work implies that a more general physiologic deficit underlies positive symptoms of schizophrenia.

AI in the 21st century - With historical reflections

The discipline of Artificial Intelligence (AI) was born in the summer of 1956 at Dartmouth College in Hanover, New Hampshire. Half of a century has passed, and AI has turned into an important field whose influence on our daily lives can hardly be overestimated. The original view of intelligence as a computer program - a set of algorithms to process symbols - has led to many useful applications now found in internet search engines, voice recognition software, cars, home appliances, and consumer electronics, but it has not yet contributed significantly to our understanding of natural forms of intelligence. Since the 1980s, AI has expanded into a broader study of the interaction between the body, brain, and environment, and how intelligence emerges from such interaction. This advent of embodiment has provided an entirely new way of thinking that goes well beyond artificial intelligence proper, to include the study of intelligent action in agents other than organisms or robots. For example, it supplies powerful metaphors for viewing corporations, groups of agents, and networked embedded devices as intelligent and adaptive systems acting in highly uncertain and unpredictable environments. In addition to giving us a novel outlook on information technology in general, this broader view of AI also offers unexpected perspectives into how to think about ourselves and the world around us. In this chapter, we briefly review the turbulent history of AI research, point to some of its current trends, and to challenges that the AI of the 21st century will have to face. © Springer-Verlag Berlin Heidelberg 2007.

Report on the British Society of Rheology mid-winter meeting on The Rheology of Foams and Emulsions, Royal School of Mines, Imperial College, London 10th - 11th December 2007

S.J. Cox, S. Neethling and H. Wilson (2008) British Society of Rheology mid-winter meeting on The Rheology of Foams and Emulsions. Applied Rheology 18:93-95

The Celtic Inscriptions of Britain: Phonology and Chronology, c. 400-1200, Publications of the Philological Society, 37

Sims-Williams, P. (2002). The Celtic Inscriptions of Britain: Phonology and Chronology, c. 400-1200. Publications of the Philological Society, 37. Oxford: Blackwell Publishing. RAE2008

Ancient Celtic Place-Names in Europe and Asia Minor: Publications of the Philological Society, 39

Sims-Williams, P. (2006). Ancient Celtic Place-Names in Europe and Asia Minor: Publications of the Philological Society, 39. Oxford: Blackwell Publishing. RAE2008

Femina (Trinity College, Cambridge MS B.14.40) : edited with an Introduction and Notes

Rothwell, W., Femina (Trinity College, Cambridge MS B.14.40); edited with an Introduction and Notes (The Anglo-Norman On-Line Hub, 2005) RAE2008