Computational Research in the

Battelle Center for Mathmatical

medicine

Statistical Genetics Research

• Develop statistical methodologies• Localize and characterize human disease

genes– Autism, CLP, AITD, Schizophrenia

• Our approach involves millions of likelihood calculations at each genomic position

• Each multi-parameter likelihood could be slow

Polynomial approach

• Represent likelihoods as algebraic polynomials

• Built once/family/position

• Evaluated millions of times

• Challenges – High memory demand– Time consuming

Computing Infrastructure

• 65 node Cluster w/ 4TB storage– Head Node (AMD Opteron 2xDuo Core 2.4

GHz, 16GB RAM) – 16 Compute Nodes (AMD Opteron 2xDuo

2.4GHz, 8GB RAM)– 16 Compute Nodes (AMD Opteron 2xDuo 2.4

GHz, 16GB RAM)– 32 Compute Nodes (AMD Opteron 2xDuo 2.8

GHz, 16GB RAM)

Database Servers

• Master server– 2 x 3.0 GHz Intel Xeon Quad Core– 16GB RAM– 300GB RAID 1 for OS– 900GB RAID 5 for data

• Slave server– 2 x 2.0 GHz Intel Xeon Dual Core– 16GB RAM– 300GB RAID 1 for OS– 900GB RAID 5 for data

Data Management

MySQL master/slave setup

Client

Master Slave

replicate

inputinput

Webserver

output

output

Data Management

• Manage/store genetic data– Million SNPs per individual

• Data upload to OSC– ~ 1TB a week– ~ 30 TB total

• Current live disk is full• Move data to tape library

– View content (just file and folder names)– start retrieve jobs on our own

Desire Summary

• Access to nodes with sufficient memory

• Access to massive storage

• Great collaborations