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| More information about the group, including regular news on projects, publications and presentations, can be found at http://research.nesc.ac.uk/ |
More information about the group, including regular news on projects, publications and presentations, can be found at http://research.nesc.ac.uk/. Dr van Hemert's slides attachment:edikt2010-vanHemert.pdf (PDF) |
edikt2010 Symposium - Using computing in your research
Wednesday April 28th, 2010
e-Science Institute, 15 South College Street, Edinburgh
Agenda
09:30 Opening Address - Professor Arthur Trew, edikt2 Principal Investigator
Session 1 - Scientific Impact of access to computational resources
Chair: Dr Orlando Richards - Information Services, University of Edinburgh
09:45 Dr Carole Morrison - School of Chemistry, University of Edinburgh
10:10 Mr Tony Weir - Information Services, University of Edinburgh
10:35 Dr Jano van Hemert - NeSC/Informatics, University of Edinburgh
11:00 Coffee and posters
Session 2 - Imaging
Chair: Dr Paul Armitage - SFC Brain Imaging Research Centre, University of Edinburgh
11:45 Prof Joanna Wardlaw - SINAPSE and SBIRC, University of Edinburgh
12:10 Mr George Cameron - Aberdeen Biomedical Imaging Centre, University of Aberdeen
12:35 Dr Susana Munoz Maniega - SBIRC, University of Edinburgh
13:00 Lunch
Session 3 - Computational Engineering
Chair: Dr George Beckett - EPCC, University of Edinburgh
15:05 Coffee and posters
Session 4 - Biology and Bioinformatics
Chair: Mr Jan Wildenhain, - Wellcome Trust Centre for Cell Biology, University of Edinburgh
16:00 Prof Mike Tyers - Cell Biology, University of Edinburgh
16:25 Prof Peter Ghazal - Division of Pathway Medicine, University of Edinburgh
16:50 Wrap-up - Terry Sloan, edikt2 Project Manager
17:00 Wine Reception
18:15 Close
Abstracts and Slides
Professor Mark Ainsworth
Department of Mathematics and Statistics,University of Strathclyde
Towards Efficient and Practical High Order Adaptive Finite Element Methods
The finite element method has proved to be one of the most flexible and practical approaches for the numerical approximation of partial differential equations over the past fifty years or so. Nevertheless, the practical implementation and theory of the method is still an extremely active area of research with an increasing emphasis on the use of high order methods. We shall identify a number of issues relating to the realisation of a practical high order finite element code and discuss some of our recent progress in tackling these issues.
Professor Ainsworth's slides edikt2010-Ainsworth.pdf (PDF)
Mr George Cameron
Aberdeen Biomedical Imaging Centre, University of Aberdeen
Brain imaging applications and computational challenges
Aberdeen has long been associated with medical imaging technologies and techniques and was an early adopter of parallel and accelerated computing solutions for intensive computation tasks in medical imaging. This talk will present some examples from current brain imaging research projects being undertaken by ABIC and its collaborators, including the use of entropy, phase and correlation analyses in functional brain imaging and 'fuzzy' segmentation algorithms in structural brain imaging, highlighting some of the computational challenges arising and how they are being addressed.
Mr Cameron's slides edikt2010-Cameron.pdf (PDF)
Dr Tom Freeman
Division of Genetics and Genomics, The Roslin Institute
Visualisation and Analysis of Very Large Network Graphs Derived From High Dimensional Biological Data
Over the last four years we have been developing the network analysis tool BioLayout Express3D (http://www.biolayout.org/). The development of this tool has been driven by the need to analyse large datasets derived from biological systems and in particular gene expression data. I will describe something of the technology behind tool, the approach we use construct networks from primary data and display them in 3-dimensional space, and how we are now beginning to develop the tool further to model the dynamic behaviour of biological pathways.
Dr Freeman's slides edikt2010-Freeman.pdf (PDF)
Prof Peter Ghazal
Division of Pathway Medicine, University of Edinburgh
HPC for High Throughput Post-Genomic Data
The increasing amount of biological data produced by high throughput and highly parallel technology platforms is pushing Bioinformatics infrastructure to the limit. The shortcomings of the current standard IT setup are forcing biostatisticians to review the tools used to analyse this data. A high throughput problem requires a high throughput solution. Can High Performance Computing (HPC) provide some solutions?
Professor Ghazal's slides edikt2010-Ghazal.pdf (PDF)
Dr Susana Muñoz Maniega
SFC Brain Imaging Research Centre
From water random motion to brain’s white matter fibres and the study of cognition
The random or ‘Brownian’ motion of water molecules within tissues can be measured /in-vivo/ using magnetic resonance imaging (MRI). This technique, known as diffusion MRI, provides information regarding the directionality and anisotropic character of the diffusion, which reflect the microscopic architecture of the tissue. Computational techniques are used to model this information and to reconstruct ‘pathways’ of the brain. Diffusion data also provides bio-markers concerning the integrity of these pathways that can be related to age and brain cognitive functions.
Dr Maniega's slides edikt2010-Maniega.pdf (PDF)
Dr Carole A. Morrison
School of Chemistry, University of Edinburgh
The EaSTCHEM Research Compute Facility - 3½ years on, what have we done?
The EDIKT2 grant funded the start-up of the Research Compute Facility (RCF), which through EaSTCHEM was then mirrored at the University of St. Andrews. The primary objectives of the RCF are to promote the use of computational chemistry by providing training for non-expert users and access to software and hardware resources.
The impact that the RCF has had in this short time has been enormous. Computational chemistry is now recognised as being another mainstream characterisation technique alongside the more traditional crystallography, NMR and mass spectrometry facilities. To date more than 70 published papers in peer-reviewed journals cite support from the RCF.
This presentation will document some RCF case studies that represent the work from a number of research groups within the School of Chemistry.
Dr Morrison's slides edikt2010-Morrison.pdf (PDF)
Dr Mark Parsons
EPCC Commercial Director, University of Edinburgh
Advanced Engineering Simulation and its future at EPCC
Several recent industry research projects at EPCC have focussed on advanced engineering simulations. This talk will describe this work in the context of EPCC's Industry Hub and how the industrial simulation landscape is changing. Hardware developments such as multi-core microprocessors and very large-scale systems are challenging environments for many engineering applications. The talk will discuss some of the challenges facing engineering simulation over the next few years.
Dr Parsons' slides edikt2010-Parsons.pdf (PDF)
Professor Mike Tyers
SULSA Consortium Director & Wellcome Trust Centre for Cell Biology, University of Edinburgh
Systematic interrogation and manipulation of cellular networks: from the kinome to the chemome
Protein kinases and phosphatases regulate most if not all cellular processes through the reversible phosphorylation of myriad substrates. The systematic identification of the proteins that associate with kinases and phosphatases - termed the kinase interactome or kinome - is crucial for understanding the regulatory architecture of the cell. However, due to the often weak nature of these associations the kinome is only poorly charted. We applied sensitive gel-free mass spectrometric analysis and an advanced probability model-based statistical method to identify ~2,000 high confidence protein interactions in the budding yeast kinome. This dataset doubles the number of known kinome interactions and reveals many new kinase/phosphatase functions. Clustering analysis of bait proteins identified a number of super-hubs, notably the TOR kinases and the Cdc14 phosphatase. Many novel functional connections emanating from these super-hubs were validated by genetic, cell biological and biochemical criteria. Intriguingly, a kinase-kinase backbone appears to cross-connect much of the proteome, suggesting an overarching global signaling architecture.
The control of cellular responses in physiology and pathology is underpinned by a densely connected genetic landscape, which integrates the many diverse processes in the cell. To interrogate and manipulate this landscape, we have compiled a large set of chemical genetic interactions, a portion of the virtually infinite chemome, in order to identify combinations of small molecules that selectively target genotype and species-specific genetic networks. The potential therapeutic applications of combinatorial small molecule intervention - termed “the magic shotgun” - will be discussed.
Professor Tyers' slides edikt2010-Tyers.pdf (PDF)
Dr Jano van Hemert
National e-Science Centre, School of Informatics, University of Edinburgh
Edinburgh Data-Intensive Research
Data-intensive refers to huge volumes of data, complex patterns of data integration and analysis, and intricate interactions between data and users. Current methods and tools are failing to address data-intensive challenges effectively. They fail for several reasons, all of which are aspects of scalability. The deluge of computational methods and plethora of computational systems prevents effective and efficient use of resources, user interfaces are not adopted at a sufficient rate to satisfy demand for scientific computing and data and knowledge is created outside suitable contexts for collaborative research to be effective.
The Edinburgh Data-Intensive Research group addresses these scalability issues by providing mappings from abstract formulations to concrete and optimised executions of research challenges, by developing intuitive interfaces to enable access to steer these executions and by developing systems to aid in creating new research challenges. In this talk I will present several exemplars where we have dealt with scalability issues in scientific scenarios.
More information about the group, including regular news on projects, publications and presentations, can be found at http://research.nesc.ac.uk/.
Dr van Hemert's slides edikt2010-vanHemert.pdf (PDF)
Professor Joanna Wardlaw
Director of SFC Brain Imaging Research Centre & the SINAPSE Collaboration, Division of Clinical Neurosciences,Western General Hospital
Neuroimaging: Computational challenges and issues
Computing is essential in neuroimaging, both in research and daily clinical practice. Neuroimaging is a rapidly advancing field that is becoming increasingly dependent on computing for visualisation of images, analysis, management and storage of imaging data. However, despite ever closer interactions, the expectations of users as to what they require of the computing often differs substantially from the interests of providers. I will describe the common challenges in neuroimaging research and practice that we face now and in the near future to highlight areas where computer science could most effectively provide help.
Professor Wardlaw's slides edikt2010-Wardlaw.pdf (PDF)
Mr Tony Weir
Head of Unix Systems, University of Edinburgh Information Services
Building Central Research Services
The Edinburgh Compute and Data Facility (ECDF, link:www.ecdf.ed.ac.uk) was launched in August 2007 to provide the University with a central research compute service and associated data services. Three years on, the compute infrastructure is about to be refreshed and projects are underway to further develop data services.
This talk will provide an overview of current services and describe future developments. It will assess the impact of the current services and the challenges in providing centralised research services.
Mr Weir's slides edikt2010-Weir.pdf (PDF)