Bioinformatics & Biology

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:

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:

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:

Rosetta

Rosetta is a software suite that includes algorithms for computational modeling and analysis of protein structures. It has enabled notable scientific advances in computational biology, including de novo protein design, enzyme design, ligand docking, and structure prediction of biological macromolecules and macromolecular complexes.

 

Desmond

Desmond is a software package that perform high-speed molecular dynamics simulations of biological systems on conventional commodity clusters, general-purpose supercomputers, and GPUs. The code uses novel parallel algorithms and numerical techniques to achieve high performance and accuracy on platforms containing a large number of processors, but may also be executed on a single computer. Desmond includes code optimized for machines with an NVIDIA GPU.

Software Refresh - August/September 2018

OSC is refreshing the software stack for Owens and Ruby on September 4, 2018. This will be done by a rolling reboot. During the software refresh, some default versions are updated to be more up-to-date. Information about the old and new default versions, as well as all available versions of each software package will be included on the corresponding OSC software webpage. See https://www.osc.edu/supercomputing/software-list.

BLAST Database

 

OSC periodically updates The NCBI BLAST database. 

Versions

BLAST database is available on the Owens and Oakley clusters. The versions currently available at OSC are:

VERSION OWENS PITZER

2017-03

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