Computing Infrastructure and Industrial Partnerships

Coordinated by R. Cukier (Chemistry)

Phenotypic attributes versus genome positions within digital organisms (C. Ofria and R. Lenski)

Quantitative Biology and Modeling has a computing facility that is located in the MSU Computer Center and also hosts the MSU Compute Node of the Life Sciences Corridor (LSC) Michigan Center for Biological Information (MCBI). The QBM and LSC MCBI will help make the MCBI facilities available to the Life Sciences Corridor as a whole, as well as work with MSU LSC researchers in related fields, such as the Michigan Center for Structural Biology.

Particular emphases are the development of new biological software, the assessment of computing and graphics hardware, and software optimization for the manipulation of large data sets and for the large-scale modeling and analysis of complex biological systems.

The QBM Cluster consists of 17 compute nodes (dual 2800+ AMD Athlons, 1GB RAM each) and a head-node (dual 2.66 GHz Xeon, 1GB RAM). All nodes run the Redhat 9 Operating System. Currently installed software includes Gaussian 98, Amber 7.0, Mopac, Dock and CNS. The cluster is administered by Paul Reed (reedp@cem.msu.edu)

Useful Links:
How to use the CBM Cluster
Current Status of Cluster Nodes

MCBISGI is the Silicon Graphics Node of the MSU LSC MCBI. It is a 16-processor SGI Origin 2400 with 12GB RAM, 370 GB of Disk and 1 TB (2 TB compressed) tape backup located in the Chemistry Department, and is administered by Paul Reed Among the available programs are Gaussian 98, Amber 7.0, GAMESS, CNSsolve, NMRPipe, MOE, and SHARP.

The MCBILIN is the Linux cluster Node of the MSU LSC MCBI. It has 32 compute nodes (dual 2.66 GHz Xeons, 2GB RAM). The admin nodes consist of a head node (dual 2.66 GHz Xeon, 2GB RAM), an application server node (dual 2.66 GHz Xeon, 2GB RAM) and IO node (dual 2.66 Xeon, 2GB RAM, 2 TB storage). The nodes are connected via a gigabit backbone. The cluster runs ROCKS 3.1.0 and is located in the MSU Computer Center. The work of integrating MCBILIN with the MCBI cluster at the University of Michigan, to create a GRID using GLOBUS software is underway. The cluster is oriented toward computational-biology and bioinformatics tasks and is administered by Paul Reed (reedp@cem.msu.edu). Please contact R. Cukier (cukier@cem.msu.edu) for information on accessing MCBILIN.

R. Cukier coordinates personnel and interactions between the QBM and MCBI LSC groups.

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