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Software

Additional information about the following software may be found on the CRC wiki (http://crc.nd.edu/wiki)

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Abaqus

A finite element analysis for Engineering applications.

ACML (AMD Core Math Library)

Amber

Assisted model building energy refinement.

ARB

The ARB (from Latin arbor, tree) program package comprises a variety of directly interacting software tools for sequence database maintenance and analysis which are controlled by a common graphical user interface. Although it was initially designed for ribosomal RNA data, it can be used for any nucleic and amino acid sequence data as well. A central database contains processed (aligned) primary structure data. Any additional descriptive data can be stored in database fields assigned to the individual sequences or linked via local or worldwide networks. A phylogenetic tree visualized in the main window can be used for data access and visualization. The package comprises additional tools for data import and export, sequence alignment, primary and secondary structure editing, profile and filter calculation, phylogenetic analyses, specific hybridization probe design and evaluation and other components for data analysis. Currently, the package is used by numerous working groups worldwide.

Biosym

See InsightII

BLAS

Basic Linear Algebra Subprograms.

BLAST

BLAST is used to match DNA sequences.

Chemkin

Chemkin is used to model chemical reactions.

Femlab

FEMLAB is a complete environment for modelling any physical phenomenon that can be described using Partial Differential Equations.

FrameMaker (Sun Sparc)

Adobe FrameMaker is a word processor and document publishing package.

Gamess

General Atomic Molecular Electronic Structure Systems

Gaussian

Gaussian is an ab initio molecular modeling package.

Gaussview

Gaussview is a full-featured graphical user interface for Gaussian 98. With GaussView you can construct molecular systems of interest quickly and efficiently using its molecule building facility. You can also set up and run Gaussian calculations right from the interface, and monitor their progress as they run. When a calculation has completed, you can use GaussView to examine a variety of results graphically via its advanced visualization facilities.

GROMACS

hdf5

hdf5 is a general purpose library and file format for storing scientific data.

HPC Cluster Tools

MPI Tool Kit for Sun Sparc architecture

Intel Compilers

Documentation for Version 9.1 Tools

Intel Math Kernel Libraries (MKL)

Highly optimized, thread-safe math routines for HPC science, engineering and financial applications that require maximum performance on Intel processor.

Interactive Data Language (IDL)