The Computational Biology Facility provides researchers with access to high performance computing systems. In 2008 the facility acquired an SGI Altix 1300 cluster with a total of 304 2.8 GHz cores. This system supports parallel processing with a DDR Infininband interconects and 12 TB of shared storage via dual NFS servers. This a Linux cluster, called nagini.mssm.edu, which the facility plans to expand to 800 cores with QDR Infiniband interconnects before the end of 2009.
The facility also maintains faradis.mssm.edu, a 160-processor G5 Xserve cluster running the Mac OS X operating system. It has 3 head nodes and 77 compute nodes, of which, sixteen are equipped with 8 GB RAM and the remainder have 1 GB RAM. All the nodes are connected through a series of Asante GX5-2400W gigabit switches. There is also an attached Xsever RAID with 3.5 TB of storage.
Both clusters are ideal platforms for open source applications that can take advantage of a large numbers of processors, especially for parallel processing. It is also well suited for large scale batch processing. Both parallel and batch processing are supported through Sun Grid Engine.
Contacts:
Roman Osman, Ph.D., Scientific Director
Professor of Physiology and Biophysics
Tel: (212) 241-5609
Email: roman.osman@mssm.edu
Lynn Kasner Morgan, Director
Associate Dean for Information Resources and Systems/Library Director
Tel: (212) 241-7892
Email: Lynn.Morgan@mssm.edu
Kevin Kelliher, Systems Administrator
Email: kevin.kelliher@mssm.edu
Contact Kevin Kelliher for questions regarding establishing accounts, adding software, general usage or for information on including the facility in grant applications.
Please remember to cite The Computational Biology Facility on all publications and applications that make use of the facilities.
Location of Equipment: Data Center in tunnel between the Ichan Institute and Annenberg Building.
Bioperl, the Perl module for biology/bioinformatics processing
iNquiry, a unified web-based interface to over 200 open source bioinformatics packages.
NCBI Toolkit, which includes rpsblast, impala, blast, fastacmd, ncbisort and megablast.
Amber 10, molecular dynamics simulation package
ARIA, Ambiguous Restraints for Iterative Assignment, NOE analysis tool
CCP4, Macromolecular crystallography package
Charmm 3.2, molecular dynamics simulation package from Harvard
Gromacs 3.3, molecular dynamics simulation package
Autodock, molecular docking simulations
CNS, Crystallography and NMR System v. 1.1 A. Brunger et al.
Gamess, General Atomic and Molecular Electronic Structure System, quantum chemistry
Molden 4.2, a pre- and post processing program of molecular and electronic structure
NAMD 2.6, molecular dynamics simulation package
NEURON-6-2, empirically-based simulations of neurons and networks of neurons
Rasmol, Molecular graphics visualization Tool
FFTW, Library for computing the Discrete Fourier Transform
GMP, GNU multiple precision arithmetic library
GSL, Routines for numerical computing
Numeric, Multidimensional numerical arrays for Python, using Apple vecLib
Octave, Matlab-like language for computations
R, a language for statistical computing and graphics
To request additional software be added to the cluster, please contact: kevin.kelliher@mssm.edu.