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 |
|---|---|
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 |