proks-salehin-et-al

Deep Learning Based Models for Preimplantation Mouse and Human Development

• Datasets:
• Portal: https://brickman-preimplantation.streamlit.app
• Portal codebase: https://github.com/brickmanlab/preimplantation-portal

1 Installation

mamba env create -p /home/fdb589/projects/data/Brickman/conda/envs/scvi-1.0.0 -f environment.yml

Package f2 has to be installed manually, follow these steps.

Note: If you have issues with cuda make sure the loaded modules are on the same version as the pip jaxlib and nvidia-cudnn-cu11.

2 Running

module load cuda/11.8-dangpu cudnn/8.6.0-dangpu miniconda/latest && source activate brickman
jupyter-lab --no-browser