Topaz
Topaz is a software package for particle detection and image denoising in cryo-electron microscopy (cryo-EM) that uses convolutional neural networks.
Software
IQmol
IQmol is a molecular visualization tool used to view, analyze, and create high-quality 3D images of chemical systems, including small molecules and quantum chemistry results.
Availability and Restrictions
Versions
The following versions of IQmol are available on OSC clusters:
Code Server
Code Server provides a browser-based instance of Visual Studio Code, enabling users to write, edit, and run code directly on OSC cluster resources without local installation.
PyMOL
PyMOL is a molecular visualization tool used to view, analyze, and create high-quality 3D images of biological molecules like proteins and DNA.
Availability and Restrictions
Versions
The following versions of PyMOL are available on OSC clusters:
OpenAI Python
OpenAI Python is the package used by python to access OpenAI's Ai models. OpenAI python provides support for OpenAI's REST API, It also provides synchronous and asynchronous sessions clients.
Availability and Restrictions
OpenAI python is currently available on the following clusters.
HOWTO: Use Docker and 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."
Podman
Podman is an Open Containers Initiative (OCI)‑compliant, daemonless and rootless container tool developed by Red Hat. Unlike Docker, Podman operates without a central daemon and supports secure rootless execution, making it well‑suited for HPC environments and schedulers such as Slurm.
Availability and Restrictions
Versions
Podman is available on all OSC clusters. Only one version is available at any given time. To find out the current version:
Intel MPI
Intel's implementation of the Message Passing Interface (MPI) library. See Intel Compilers for available compiler versions at OSC.
Ruby
Ruby is a dynamic, open source programming language with a focus on simplicity and productivity.
Availability and Restrictions
Versions
The following versions of ruby are available on OSC clusters:
AlphaFold 3
AlphaFold 3 developed by DeepMind and Isomorphic Labs, is an advanced artificial intelligence system that predicts the 3D structures of proteins and their interactions with other molecules, including DNA, RNA, ligands, and ions.
