How EPCC can help
with computationally
demanding code and
large data sets
MVM Research Symposium,
3rd November 2008
Eilidh Grant
Applications Consultant, EPCC
egrant1@epcc.ac.uk
+44 131 650 5115
Overview
• What is EPCC?
• Sample projects
– Modelling gene regulatory networks
– Storing large amounts of microscopy data
• How to get involved
How EPCC can help – 3rd November 2008
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What is EPCC?
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High performance computing
Develop software for all areas of science and technology
80 expert staff
2 national UK supercomputers - HECToR and HPCx
QuickTime™ and a
decompressor
are needed to see this picture.
QuickTime™ and a
decompressor
are needed to see this picture.
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Biology projects
Genetic markers of
Circadian rhythm of
colorectal cancer
Gene regulatory
Arabidopsis thaliana
EPCC
networks
Parallel R for the
statistical analysis of
microarray data
A data grid for
cell biology
Evolution of virulence
in bird flu
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Gene regulatory networks
• Aim is to statistically analyse various biological data
(microarrays, proteomics) to produce a bayesian network
model of the underlying gene regulatory network.
• Can only handle small networks of genes on a desktop
computer.
• EPCC are investigating how to get this code, originally
written in Matlab to run on HPCx.
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Gene regulatory networks
CSBE Research Fellow Marco Grzegorczyk said: The
implementation of the Metropolis-coupled Markov chain Monte
Carlo algorithms [on HPCx] will allow us to infer more
interesting networks with much more genes."
– Centre for Systems Biology at Edinburgh
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Data grid
• Aim is to help scientists to share their data:
– in simple, secure, and effective manner.
• Microscope image data from cell biology:
– though any (experimental) data could be relevant.
• Working with researchers in Oxford and Edinburgh:
– Davis and Finnegan groups studying early development of fruit fly
Drosophilia Melanogaster.
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Data grid
• EPCC have developed a technology called
DiGS (Distributed Grid Storage),
• Data grid software, provides:
– multi-Terabyte, distributed storage capability.
– automated data replication and backup function.
– periodic validation and consistency checking of data.
• Supports annotation of experiments, with scientific metadata:
– assisting with data provenance.
– allowing fast and efficient searches across large volumes of data.
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How to get involved
• Speak to us
• Collaborative research through a joint funding bid
• HECToR - dCSE grants available for 6-12 months of effort
and 10 000s CPU hours.
• MSc projects or co-supervision of a PhD
• HPCx - for the next year there will be time available on HPCx
with some developer support.
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Contact Details
• Please get in touch to discuss any projects that could benefit
from working with EPCC
• http://www.epcc.ed.ac.uk
• Contact EPCC at EPCC-Support@ed.ac.uk
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