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High Performance Computing

Helix Systems at NIH

The Helix Systems supports high performance computing resources that are available for use by the NIH research community. These resources provide access to a wide range of software applications, installed on production computing platforms. To assist researchers in using and learning about these resources, Helix Systems provides training, documentation, and consulting on these resources. These applications are available to any NIH researcher who has a Helix account.

The NIH Biowulf cluster is a Linux parallel processing system designed and built at the National Institutes of Health. Managed by the Helix Systems Staff, Biowulf consists of a main login/administrative node and 2300 compute nodes (12000+ processors) running the GNU/Linux operating system. Accounts on the Biowulf cluster are available to all NIH scientists who have a need for large-scale computational resources.

The software applications available include the following:


Sequence Analysis: EMBOSS, Blast, ClustalW, HMMER, and others
Linkage Analysis: Fastlink, GeneHunter, SimWalk2, UnPhased, and others
Phylogenetic Analysis: Phylip, PAUP, PAML, Tree-Puzzle
Microarray Analysis: Bioconductor, R
Sequence and Molecular Databases: nucleotide, protein, transcription factor, and others

Structural Biology

Computational Chemistry: AMBER, CHARMm, GAMESS, Gaussian, NAMD, and others
Crystallography/NMR: CNS, HADDOCK, and others
Molecular Modeling: Rosetta, PROSPECT, ZDOCK, and others


Mascot, OMSSA, X!Tandem

Mathematical Analysis

Mathematica, Matlab, R, S-Plus, SAS, and others

Image Analysis

Huygens, IDL, AVS, and others

Molecular Graphics

Molscript, POVRay, ImageMagick, RasMol, and others

Program Development

C, C++, Fortran, awk, perl, tcl/tk, MPI, and others

In addition to command line applications, Helix Systems also supports many web-based applications, such as:


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This page last reviewed: January 13, 2012