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Showing posts from November, 2005
What am I reading? 1) The Art of computer Programming 2) How to think like Benjamin Graham and invest like Warren Buffet 3) Genomes 2
clawhmmer: blast: dynamic programming but relies on adhoc gap penalties, it still determines the type of guees HMMer:" probabilites model. Its robust, because it is a probabilisting it requires more flops new architectures: 1_ An order of magnitute more 2) Extremely parallel in nature 3) tiny processors 4) They share PC thousands of threads needed Brook of GPU: 1) Data is divided into streams 2) small function as KERNEL. fixed number of inputs and fix output 3) Encourages a data parallel type of programming challenges: 1) current software doesn't map well 2) large compute-> fetch ratio in the kernel 3)
Computational Grand Challenges in Assembling the tree of life: problems and solutions: Part I: - HPC in biology - Grappa for reconstructuring evolutionary histories from gene order Recompute or infer the tree of life: a) cipres: cyber infrastructure to attempt a reconstruction of the tree of life b) Its not sure whether its a network . But if its a network then the argument is whether can an individual have more than one ancestor. c)
developing a data warehouse solution for genomics and proteomics (Marshal Peterson-CTO- J craig venter institute) 1) Petabyte New challenges: 1) computational molecular biology 2) medicine 3) ecosystems 4) scale 5) locality Requirements: 1) data management: capture, storage, archival, distribution, analysis 2) data movement 3) scheduling computation - what living organisms are floating in the air - Microbial abundance - 4 to 6 x10^30 microbes - Sargasso sea. Decided to sample the sea water. Picked up because it is very low in nutrients. Didn't expect to see a lot there. - sargasso sea water - 100 million letters of genetic code very 24 hours - 1800 new species - 1.2 million new genes and 12 complete genomes. - before that we knew about 120k-180k genes. thus it increased by 1.2 million - Proteorhodopsin - take all the genes which might be efficient in producing ethanol.... - world sampling route: gollapogos. - birds are pink because they eat pink shrim. (remember: you ar ewhat you e