IGER research
ƒ Not directly part of IGF, but doing
genomics-based work
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grasses, legumes, oats, maize
ƒ Research includes
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plant molecular genetics, plant breeding
microbial ecology
rumen function
soils, manures, olfactometry
modelling of land use systems
ƒ Common issues: gathering, analysis,
dissemination of large volumes of data
Genomics issues
ƒ Genetic mapping, especially in support
of marker-assisted selection
ƒ DNA sequence analysis, including
phylogeny; SNP detection
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comparative analysis is of increasing importance
speed becoming a limiting factor
ƒ Molecular characterisation of genetic
resources (biodiversity studies)
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AFLPs: special software & throughput problems
ƒ Transcriptomics
DNA sequence analysis issues
ƒ Slow processing
ƒ Need to submit jobs individually rather
than as batch
ƒ Users often restrict searches to subsets
of databases to increase throughput
ƒ Would like access to more
powerful/sensitive search software
Metabolomics and other "omics"
ƒ Metabolomics techniques including FTIR, Raman spectroscopy generate very
large multivariate datasets
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need machine learning approaches
ranging from PCA/PLS to artificial neural
networks, genetic programming
Other approaches resulting in similar
datasets (acoustic grazing data, cattle
intake data, hyperspectral imaging)
ƒ Processing power, appropriate
software, data collection/dissemination
IGER participation in BBSRC grid
pilot project
ƒ First aim: access to remote compute
farms
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to increase throughput & efficiency of
sequence analysis
ƒ Subsequent aims
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access to high-performance computing for
machine-learning approaches to very large
multivariate datasets
faster phylogeny analysis for large gene
families