Sarah Hunter

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However… 17,159,442 proteins HMMs 44,117 HMMs Protein classified = 1.4 million CPU hrs 24 15.12.2008
Protein analysis problems and solutions • Problems: • For small-scale users this analysis is computationally very expensive • In the long-term, it will not scale • Short term solutions for this problem at EBI: • Purchase of specialised accelerated software (LDHmmer) • Investigation of Cell processor and GPU implementations • Increasing the size of compute farms • Longer term solutions for this problem : • Re-write of HMM searching software (HMMer3) • Using GRID or cloud computing resources to spread analysis load 25 15.12.2008
Page 1 and 2: Bioinformatics and the big data era
Page 3 and 4: Wired June 2008 Nature September 20
Page 5 and 6: Gene knock-outs Protein Assays Poin
Page 7 and 8: Big data in biology • The 1000 ge
Page 9 and 10: We are faced with is a deluge of da
Page 11 and 12: If you ever feel chilly… … just
Page 13 and 14: Data through the Hinxton Router Apr
Page 15 and 16: Challenge 2: Moving data around (se
Page 17 and 18: Sources of analysed data sets • S
Page 19 and 20: Bioinformatics analyses • Multipl
Page 21 and 22: Associate annotation describing the
Page 23: However… 10,000 average proteins
Page 27 and 28: Infrastructure for protein data acc
Page 29 and 30: Conclusions 29 15.12.2008
Page 31: Questions? 31 15.12.2008

Sarah Hunter

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