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:
Software
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 ls-opt 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:
PyTorch
PyTorch is an open source machine learning framework with GPU acceleration and deep neural networks that is based on the automatic differentiation in the Torch library of tensors.
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.
ORCA
ORCA is an ab initio quantum chemistry program package that contains modern electronic structure methods including density functional theory, many-body perturbation, coupled cluster, multireference methods, and semi-empirical quantum chemistry methods. Its main field of application is larger molecules, transition metal complexes, and their spectroscopic properties. ORCA is developed in the research group of Frank Neese. Visit ORCA Forum for additional information.
