HPC Software Availability

Software	Category	How to get?

Software	Category	How to get?
Alphafold	protein, structure prediction,	module load
ClinicaDL	biology, neural imaging	module load
d2go	AI training/deployment to mobile platforms	module load
fairseq	AI training	module load
fftw	Fourier transforms	module load
gromacs	molecular dynamics	module load
hdf5	data management	module load
prokka	genome annotation	module load

Here, ‘module’ or ‘module load’ refers to software that is accessible through modules created by ITS.

MATLAB

Users can use UAlbany’s MATLAB license to work in MATLAB themselves. Instructions can be found here (link)

RStudio

Users can use RStudio by following instructions at this link: link

Python (Jupyter Notebooks)

Users can spawn a Jupyter Notebook in two ways:

Through JupyterHub: link

or

by creating a custom job via our SLURM job scheduler: link

The former has predefined resource options, while the latter allows you to allocate the resources you know or anticipate you will need for your notebook.

SAS/STATA

Instructions for SAS: link

Instructions for STATA: link

Miniconda

Users can also install python packages for themselves in conda environments within a lab directory. Instructions on how to do this can be found here (link). Examples of software that can be installed via conda are shown in the table below:

Software	Category

Software	Category
Albumentations	imaging, image recognition
BERTopic	topic modelling
DeepMicrobes	biology, genomics, deep learning
DeepVariant	sequencing, genomics
dscribe	physics, chemistry, materials science
Fairseq	language modelling, translation, summary
Pytorch Forecasting	framework for deep learning/pandas
GalaxyML	biomedical classification
ReLeaSE	chemistry, drug design,
SampleDock	molecular docking, chemistry
StableDiffusion v1/v2	image generation, neural network