Bioinformatics Applications on and APBioGrid ONG Guan SinTAN Chee Chiang Grid EvangelistManager, Computer Centre Singapore Computer Sys LtdNational University of Singapore APBioNet GridAsia06

Tera-scale Campus 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 ) 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 Genome DB Sequences m n m x n UD-Blast m x n result

Details of UD-Blast Jobs  Target database: nt v –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  is collaborating with APBioNet on a number of projects at the regional level  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.

Thank You Contacts ONG Guan Sin TAN Chee Chiang