RELION
RELION (REgularised LIkelihood OptimisatioN) is a stand-alone computer program for the refinement of 3D reconstructions or 2D class averages in electron cryo-microscopy.
Ascend
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:
VirtualGL
VirtualGL allows OpenGL applications to run with 3D hardware accerlation.
Availability & Restrictions
Versions
The following versions of VirtualGL are available on OSC clusters:
Julia
From julialang.org:
"Julia is a high-level, high-performance dynamic programming language for numerical computing. It provides a sophisticated compiler, distributed parallel execution, numerical accuracy, and an extensive mathematical function library. Julia’s Base library, largely written in Julia itself, also integrates mature, best-of-breed open source C and Fortran libraries for linear algebra, random number generation, signal processing, and string processing. In addition, the Julia developer community is contributing a number of external packages through Julia’s built-in package manager at a rapid pace. IJulia, a collaboration between the Jupyter and Julia communities, provides a powerful browser-based graphical notebook interface to Julia."
OnDemand Desktop App: MATLAB
MATLAB allows matrix manipulations, plotting of functions and data, implementation of algorithms, creation of user interfaces, and interfacing with programs written in other languages, including C, C++, C#, Java, Fortran and Python.
Accessing through OnDemand
All the desktop apps can be found within the 'Interactive Apps' dropdown in our OnDemand web portal as shown in the image below:
OnDemand Desktop App: RStudio Server
RStudio is an integrated development environment (IDE) for R. It includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management.
Accessing through OnDemand
All the desktop apps can be found within the 'Desktop Apps' dropdown in our OnDemand web portal as shown in the image below:
GPU Computing
The OSC GPU Computing environment.
Desktop App Catalog
OSC OnDemand provides access to applications on compute nodes through the batch system, without the hassle or performance problems associated with X11 forwarding. To access one, please select an application under "Interactive HPC" from the "Desktop Apps" menu. For more information on each product, please go to its page provided below.
