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Software | Category | How to get? |
|---|---|---|
Albumentations | imaging, image recognition | conda |
Alphafold | protein, structure prediction, | module load |
BERTopic | topic modelling, | conda install |
ClinicaDL | biology, neural imaging | module load |
d2go | AI training/deployment to mobile platforms | module load |
DeepMicrobes | biology, genomics, deep learning | conda |
DeepVariant | sequencing, genomics | conda |
dscribe | physics, chemistry, materials science | conda |
Fairseq | language modelling, translation, summary | conda |
Pytorch Forecasting | framework for deep learning/pandas | conda |
GalaxyML | biomedical classification | conda |
ReLeaSE | chemistry, drug design, | conda |
SampleDock | molecular docking, chemistry | conda |
StableDiffusion v1/v2 | image generation, neural network | conda/DGX |
Here, conda refers to the ability of PIs or other lab members with permission to create conda environments with the software they need
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.
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Instructions for STATA: link
Cadence
Instructions for Cadence: 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 |