Available Software

Title Version Systems Summary
Galaxy 1.1.0 HPC Galaxy is an open, web-based platform for data intensive biomedical research.
FASTQC 0.10.1 Spear A quality control tool for high throughput sequence data.
RNA-STAR 2.3.0 HPC, Spear Ultrafast universal RNA sequencing aligner
TopHat 2.0.10 HPC, Spear A spliced read mapper for RNA Sequencing
Cufflinks 2.1.1 HPC Transcript assembly, differential expression, and differential regulation for RNA Sequencing
LAST 4.11 HPC, Spear Finds similar regions between sequences, and aligns them.
SAMtools 0.1.19 HPC, Spear Flexible generic format for storing nucleotide sequence alignment
BWA 0.7.5a HPC, Spear Software package for mapping low-divergent sequences
Biopython 1.58 HPC Python library for computational molecular biology.
Bowtie2 2.1.0 HPC, Spear Bowtie2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences
Bowtie 1.0.0 HPC, Spear Bowtie is an ultrafast, memory-efficient short read aligner
ABySS 1.3.6 HPC Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler
Title Version Systems Summary
ARPACK 1.0 HPC, Condor, Spear A collection of Fortran77 subroutines designed to solve large scale eigenvalue problems
SuperLU 3.3 HPC Library for the direct solution of large, sparse, nonsymmetric systems of linear equations.
Deal.II 8.1.0 HPC C++ software library supporting the creation of finite element codes.
Model Coupling Toolkit (MCT) 2.8.3 HPC Set of open-source software tools for creating coupled models
ALPS 2.1 HPC Algorithms and Libraries for Physics Simulations
NAMD 2.8 HPC, Spear A parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.
Applications and Tools
Title Version Systems Summary
NWChem 6.5 HPC Application for high performance computational chemistry
freefem++ 3.31-2 HPC, Spear Partial differential equation solver based on the finite element method
GROMACS 4.5.7 HPC, Spear GROMACS is a versatile package to perform molecular dynamics
TotalView 8.13.0 HPC TotalView is a GUI-based parallel and serial debugging tool
Desmond HPC Simulation Software for Molecular Dynamics
TAU 2.23 HPC TAU (Tuning and Analysis Utilities) is a software performance analysis tool
Gerris 1.3.2 HPC Solver of partial differential equations used in fluid flow.
Blender 2.69 HPC Blender is a free and open source 3D animation suite
Chimera 1.8.1 Spear Molecular modeling system
IBM ILOG CPLEX Optimization Studio 12.5 HPC, Spear Mathematical optimization software package
Stata 10.1 HPC, Spear Stata is fully featured data analysis and statistical software
PyMOL 1.6 Spear A molecular visualization system on an open-source Python foundation
R (statistical computing) 2.15.1 HPC, Spear A popular, full featured, statistical computing package
Grace 5.1.22 HPC, Spear A WYSIWYG 2D plotting tool for scientific graphing
Gaussian v09 HPC, Condor, Spear An application that provides state-of-the-art capabilities for electronic structure modeling
ORCA 3.0.0 HPC ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties
VisIt 2.6.3 HPC, Spear A software package for visualizing scientific results
MATLAB 2014b HPC, Condor, Spear A high-level language and interactive environment for numerical computation, visualization, and programming
Programming Languages and Compilers
Title Version Systems Summary
Anaconda 2.7.7 HPC Python 2.7.7 with 195 popular packages
Python 2.6.6, 2.7.7 HPC, Spear Interactive, object-oriented, extensible programming language
GNU Octave 3.4.2 HPC, Spear A high-level language, primarily intended for numerical computations
Intel Compilers 13.0.1 HPC, Spear Intel C, C++, and Fortran Compilers
Portland Group Compilers 12.9.0 64-bit HPC, Spear PGI Compilers for C, C++, and Fortran
GNU Compilers 4.4.6 HPC, Condor, Spear GNU C, C++, and Fortran Compilers