Software

QGIS

QGIS is a user friendly Open Source Geographic Information System (GIS) licensed under the GNU General Public License. QGIS is an official project of the Open Source Geospatial Foundation (OSGeo). It runs on Linux, Unix, Mac OSX, Windows and Android and supports numerous vector, raster, and database formats and functionalities.

Availability and Restrictions

Versions

The following versions of QGIS are available on OSC clusters:

Gaussian

Gaussian is the most popular general purpose electronic structure program. Recent versions can perform density functional theory, Hartree-Fock, Möller-Plesset, coupled-cluster, and configuration interaction calculations among others. Geometry optimizations, vibrational frequencies, magnetic properties, and solution modeling are available. It performs well as black-box software on closed-shell ground state systems. 

Bismark

Bismark is a program to map bisulfite treated sequencing reads to a genome of interest and perform methylation calls in a single step.

Availability and Restrictions

Versions

The following versions of bedtools are available on OSC clusters:

Gurobi

Gurobi is a mathematical optimization solver that supports a variety of programming and modeling languages.

Availability and Restrictions

Versions

The following versions of bedtools are available on OSC clusters:

LS-OPT

LS-OPT is a package for design optimization, system identification, and probabilistic analysis with an interface to LS-DYNA.

Availability and Restrictions

Versions

The following versions of bedtools are available on OSC clusters:

Clustal W

Clustal W is a multiple sequence alignment program written in C++.

Availability and Restrictions

Versions

The following versions of bedtools are available on OSC clusters:

MUSCLE

MUSCLE is a program for creating multiple alignments of protein sequences.

Availability and Restrictions

Versions

The following versions of bedtools are available on OSC clusters:

Horovod

"Horovod is a distributed training framework for TensorFlow, Keras, PyTorch, and MXNet. The goal of Horovod is to make distributed Deep Learning fast and easy to use. The primary motivation for this project is to make it easy to take a single-GPU TensorFlow program and successfully train it on many GPUs faster."

Quote from Horovod Github documentation

metilene

metilene is a software tool to annotate differentally methylated regions and differentially methylated CpG sites.

Availability and Restrictions

Versions

The following versions of bedtools are available on OSC clusters:

CP2K

CP2K is a quantum chemistry and solid state physics software package that can perform atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems. CP2K provides a general framework for different modeling methods such as DFT using the mixed Gaussian and plane waves approaches GPW and GAPW. Supported theory levels include DFTB, LDA, GGA, MP2, RPA, semi-empirical methods and classical force fields.

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