Software at OSC |
Software available on the Glenn ClusterABAQUS - a finite element analysis program ACML - The AMD Core Math Library (ACML) is a set of numerical routines tuned specifically for AMD64 platform processors Altair HyperWorks* - high-performance, comprehensive toolbox of CAE software for engineering design and simulation AMBER - a molecular simulation program ANSYS - an engineering package and support routines for general-purpose, finite-element analysis: statics, mode frequency, stability analysis, heat transfer, magnetostatics, coupled field analysis, and modeling bioperl - offers a set of perl modules which can be used for sequence manipulation BLAST - tools for searching DNA and protein databases for sequence similarity to identify homologs to a query sequence BLAT - a sequence analysis tool which performs rapid mRNA/DNA and cross-species protein alignments bowtie - an ultrafast, memory-efficient short read aligner geared toward quickly aligning large sets of short DNA sequences (reads) to large genomes. ClustalW - a general purpose multiple sequence alignment program for DNA or proteins COMSOL Multiphysics - (formerly FEMLAB) is a finite element analysis and solver software package for various physics and engineering applications EMBOSS - a sequence analysis package specially developed for the needs of the molecular biology user community ESPRESSO/PWscf - suite of computer codes for electronic-structure calculations FFTW - a C subroutine library for computing the discrete Fourier transform (DFT) fitmodel - a program that estimates the parameters of various codon-based models of substitution Fluent - a general-purpose program for modeling a wide range of fluid-flow and related transport problems Gambit - a software package designed to help analysts and designers build and mesh models for computational fluid dynamics (CFD) and other scientific applications GAMESS - is a flexible ab initio electronic structure program Gaussian 03 - a connected system of programs for performing semiempirical, ab initio, and density functional molecular orbital (MO) calculations Gnuplot - a portable command-line driven interactive data and function plotting utility GROMACS - a versatile package to perform molecular dynamics HDF5 - a general purpose library and file format for storing scientific data HMMER - used to do sensitive database searching using statistical descriptions of a sequence family's consensus Intel Compilers - an array of software development products from Intel, including C++, FORTRAN compilers and Math Kernel Library (MKL) LAMMPS - a classical molecular dynamics code designed for high-performance simulation of large molecular systems LSDYNA - an explicit three-dimensional, finite-element code for analyzing the large deformation dynamic response of inelastic solids and structures LS-PrePost - an advanced pre and post-processor that is delivered free with LS-DYNA MacroModel® - molecular modeling software package that allows the graphical construction of complex chemical structures and the application of molecular mechanics and dynamics techniques in vacuo or in solution MATLAB - a technical computing environment for high-performance numeric computation and visualization that integrates numerical analysis, matrix computation, signal processing, and graphics in an easy-to-use environment mpiexec - a replacement program for the script mpirun, which is part of the mpich package. It is used to initialize a parallel job from within a pbs batch or interactive environment. MrBayes - a program for the Bayesian estimation of phylogeny NAMD - a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems NetCDF (Network Common Data Form) - an interface for array-oriented data access Octave - a high-level language, primarily intended for numerical computations OpenFOAM - a suite of computational fluid dynamics applications PAML - a few programs for model fitting and phylogenetic tree reconstruction using nucleotide or amino-acid sequence data parallel-command-processor - a program for running a large number of serial processes on a number of allocated nodes/processors ParaView - an open-source, multi-platform application designed to visualize data sets PAUP -- a leading program for performing phylogenetic analysis for bioinformatics sequences PGI compilers - Parallel Fortran, C, C++ compilers for Intel platforms R - a language and environment for statistical computing and graphics RAxML - a fast implementation of maximum-likelihood phylogeny estimation that operates on both nucleotide and protein sequence alignments RECON - a package that performs de novo identification and classification of repeat sequence families from genomic sequences RepeatMasker - a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences ScaLAPACK - a library of high-performance linear algebra routines for distributed-memory message-passing MIMD computers and networks of workstations supporting PVM and/or MPI sprng & sprng2 - a scalable package for parallel pseudo random number generation Stata - a complete, integrated statistical package that provides everything needed for data analysis, data management, and graphics Torque - a networked subsystem for submitting, monitoring, and controlling a work load of batch jobs on one or more systems TotalView Technologies Totalview* - debugger for complex code treebest - an original tree builder for constrained neighbour-joining and tree merge Turbomole - a program package for ab initio electronic structure calculations VASP - the Vienna ab-initio simulation package VTK - an open source, freely available software system for 3D computer graphics, image processing, and visualization * Indicates software available through OSC's Statewide Software License Distribution
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