VMD
VMD is a visulaization program for the display and analysis of molecular systems.
Availability and Restrictions
Versions
The following versions of VMD are available on OSC clusters:
Cardinal
Abaqus
Abaqus is fully migrated from the Owens cluster to the Cardinal cluster on December 17, 2024.
ABAQUS is a finite element analysis program owned and supported by SIMULIA, the Dassault Systèmes brand for Realistic Simulation.
FastQC
FastQC provides quality control checks of high throughput sequence data that identify areas of the data that may cause problems during further analysis.
Perl
Perl is a family of programming languages.
Cufflinks
Cufflinks is a program that analyzes RNA -Seq samples. It assembles aligned RNA-Seq reads into a set of transcripts, then inspects the transcripts to estimate abundances and test for differential expression and regulation in the RNA-Seq reads.
Apptainer (formerly Singularity)
Apptainer (formerly Singularity) is a container system designed for use on High Performance Computing (HPC) systems. It allows users to run both Docker and Singularity containers.
HTSlib
HTSlib is a C library used for reading and writing high-throughput sequencing data.
FreeSurfer
FreeSurfer is a software package used to anaylze nueroimaging data.
Availability & Restrictions
Versions
The following versions of FreeSurfer are available on OSC clusters:
HOWTO: Use Docker and Apptainer/Singularity Containers at OSC
It is now possible to run Docker and Apptainer/Singularity containers on all clusters at OSC. Single-node jobs are currently supported, including GPU jobs; MPI jobs are planned for the future.
From the Docker website: "A container image is a lightweight, stand-alone, executable package of a piece of software that includes everything needed to run it: code, runtime, system tools, system libraries, settings."
FSL
FSL is a library of tools for analyzing FMRI, MRI and DTI brain imaging data.
Availability and Restrictions
Versions
The following versions of FSL are available on OSC clusters:
