# Software

This inventory includes major software packages available on our compute systems. If you would like us to install a package not listed here, please let us know.

## Available Software

### Applications and Tools

Package | Vers | Systems | Summary |
---|---|---|---|

ADF | 2016.101 | HPC | Amsterdam Density Functional |

atsas | 2.6.1 | HPC | A program suite for small-angle scattering data analysis from biological macromolecules |

Blender | 2.69 | HPC | Blender is a free and open source 3D animation suite |

Chimera | 1.8.1 | Spear | Molecular modeling system |

Crystal14 | 1.0.4 | HPC | Software computing electronic wave function and properties of periodic systems |

Desmond | 3.4.0.2 | HPC | Simulation Software for Molecular Dynamics |

freefem++ | 3.31-2 | HPC | Partial differential equation solver based on the finite element method |

Gaussian | v09 | HPC, Spear | An application that provides state-of-the-art capabilities for electronic structure modeling |

Gerris | 1.3.2 | HPC | Solver of partial differential equations used in fluid flow. |

Grace | 5.1.22 | HPC, Spear | A WYSIWYG 2D plotting tool for scientific graphing |

GROMACS | 4.5.7 | HPC, Spear | GROMACS is a versatile package to perform molecular dynamics |

GULP | 4.4.0 | HPC | Program for performing a variety of types of simulations on materials |

IBM ILOG CPLEX Optimization Studio | 12.5 | HPC, Spear | Mathematical optimization software package |

LAMMPS | 20150316 | HPC | Large-scale Atomic/Molecular Massively Parallel Simulator |

MATLAB | 2015b | HPC, Spear | A high-level language and interactive environment for numerical computation, visualization, and programming |

migrate-n | 3.6 | HPC | Estimates effective population sizes and past migration rates |

moltemplate | 1.34 | HPC | A general text-based molecule builder for LAMMPS. |

NWChem | 6.3.2 | HPC | Application for high performance computational chemistry |

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 |

ParaView | 4.4.0 | HPC, Spear | ParaView is an open-source, multi-platform data analysis and visualization application |

PyMOL | 1.6 | Spear | A molecular visualization system on an open-source Python foundation |

python-ase | 3.9.1.4567 | HPC | ASE is an Atomistic Simulation Environment written in the Python |

Quantum ESPRESSO | 5.3.0 | HPC | Nanoscale electronic-structure calculations and materials modeling |

R (statistical computing) | 3.1.3 / 3.2.0 | HPC, Spear | A popular, full featured, statistical computing package |

Stata | 10.1 | HPC, Spear | Stata is fully featured data analysis and statistical software |

TAU | 2.23 | HPC | TAU (Tuning and Analysis Utilities) is a software performance analysis tool |

TotalView | 8.13.0 | HPC | TotalView is a GUI-based parallel and serial debugging tool |

VisIt | 2.6.3 | HPC, Spear | A software package for visualizing scientific results |

### Programming Languages and Compilers

Package | Vers | Systems | Summary |
---|---|---|---|

Anaconda | 2.7 | HPC | Python 2.7 with 195 popular packages |

GNU Compilers | 4.4.6 | HPC, Spear | GNU C, C++, and Fortran Compilers |

GNU Octave | 3.4.2 | HPC, Spear | A high-level language, primarily intended for numerical computations |

HDF5 | 1.8.12 | HPC | unique technology suite that makes possible the management of large and complex data |

Hypre | 2.8.0b | HPC | Library for solving large, sparse linear systems of equations on massively parallel computers |

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 |

Python | 2.7.5, 3.5.1 | HPC, Spear | Interactive, object-oriented, extensible programming language |

### Libraries

Package | Vers | Systems | Summary |
---|---|---|---|

ALPS | 2.1 | HPC | Algorithms and Libraries for Physics Simulations |

ARPACK | 3.1.5 | HPC, Spear | A collection of Fortran77 subroutines designed to solve large scale eigenvalue problems |

BLAS | 3.2.1 | HPC | Linear Algebra Library |

Deal.II | 8.2.1 | HPC | C++ software library supporting the creation of finite element codes. |

FFTW | 3.3.4 | HPC | C library to compute the discrete Fourier transforms |

LAPACK | 3.8.4 | HPC | Standard software library for linear algebra |

Model Coupling Toolkit (MCT) | 2.8.3 | HPC | Set of open-source software tools for creating coupled models |

NAMD | 2.10 | HPC, Spear | A parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. |

netCDF | 4.3.3.1 | HPC | libraries for representing scientific data |

SuperLU | 4.3 | HPC | Library for the direct solution of large, sparse, nonsymmetric systems of linear equations. |

### Bioinformatics

Package | Vers | Systems | Summary |
---|---|---|---|

ABySS | 1.3.6 | HPC | Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler |

Biopython | 1.58 | HPC | Python library for computational molecular biology. |

Bowtie | 1.0.0 | HPC, Spear | Bowtie is an ultrafast, memory-efficient short read aligner |

Bowtie2 | 2.1.0 | HPC, Spear | Bowtie2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences |

BWA | 0.7.5a | HPC, Spear | Software package for mapping low-divergent sequences |

Cufflinks | 2.2.1 | HPC, Spear | Transcript assembly, differential expression, and differential regulation for RNA Sequencing |

FASTQC | 0.11.3 | Spear | A quality control tool for high throughput sequence data. |

LAST | 4.11 | HPC, Spear | Finds similar regions between sequences, and aligns them. |

RNA-STAR | 2.4.1d | HPC, Spear | Ultrafast universal RNA sequencing aligner |

SAMtools | 0.1.19 | HPC, Spear | Flexible generic format for storing nucleotide sequence alignment |

TopHat | 2.0.14 | HPC, Spear | A spliced read mapper for RNA Sequencing |

Trimmomatic | 0.33 | Spear | A flexible read trimming tool for Illumina NGS data |