bioinformatics applications on and apbiogrid ong guan sintan chee chiang grid evangelistmanager,...
DESCRIPTION
Bioinformatics Applications UD-Blast UD-HMMER Modeller – protein structure prediction NestedMICA – finding over-represented short motifs AutoDock (in progress) Meta Driver – parametric studyTRANSCRIPT
Bioinformatics Applications on TCG@NUS and APBioGrid
ONG Guan Sin TAN Chee ChiangGrid Evangelist Manager, Computer CentreSingapore Computer Sys Ltd National University of Singapore
APBioNet Meeting @ GridAsia06
Tera-scale Campus Grid @ NUS
Two-year collaboration project between NUS and Singapore Computer Systems to develop applications and support community
Harnessing existing computation capacity campus-wide, creating large-scale supercomputing capability
Computers are aggregated through its gigabit network into a virtual supercomputing platform using United Devices Grid MP middleware
Great demonstration of community spirit and participation in NUS Current status:
* Accumulated average CPU speed of 2.456GHz as at Sep 20, 2005# Assuming 90% capacity effectively harnessed^ Assuming 50% capacity effectively harnessed
7.2 TFlops13 TFlops3,000 (Planned - 2007)
4.0 TFlops7.2 TFlops1,236 (May 11, 2006)
Practical^Theoretical#Number of Nodes
Bioinformatics Applications
UD-Blast
UD-HMMER
Modeller – protein structure prediction
NestedMICA – finding over-represented short motifs
AutoDock (in progress)
Meta Driver – parametric study
Deployable/Ready Applications
GOLD
LigandFit
FlexX
Glide
Nonmem
Archimedes
Flo
FRED
Structure Checker
Catalyst
Qu-Gene
Schematic View of UD-blast
GenomeDB
Sequencesm
n
m x n
UD-Blast
m x nm x nresult
Details of UD-Blast Jobs
Target database: nt v.2006-01-12– Chunkified into ~200mb units 82 chunks (n)– Actual size ranges between 52mb and 70mb after formatdb
Job 1: GIS-1– Input sequence: 22,484 seqs, 9,388,377 bytes
Chunkified into ~200kb units 46 chunks (m)
– Total workunits: 3,772 (m x n)– Total CPU time: 218 days 21 hours 46 minutes 14 seconds– Actual turn-around time: 22 hours
Job 2: JGI-1– Input sequence: 29,160 seqs, 27,408,996 bytes
Chunkified into ~200kb units 134 chunks (m)
– Total workunits: 10,988 (m x n)– Total CPU time: 248 days 12 hours 12 minutes 36 seconds– Actual turn-around time: 49 hours*
* Mainly due to system maintenance before completion
Contrast to a SMP server: SF01
Hardware specs – Sun Enterprise 6800– CPUs: 16 units of 900MHz UltraSPARC-III
– Memory: 16GB
Actual turn-around time for Job 1 (GIS-1): ~30 days (extrapolated)
APBioGrid Applications
TCG@NUS is collaborating with APBioNet on a number
of projects at the regional level
TCG@NUS hopes to be one of the anchor tenants of
APBioGrid, showcasing bioinformatics applications to
the Asia Pacific region.
We aim to support NUS researchers in their collaborative
research with APBioGrid participants from academia and
industry.
