title	date	author
proks-salehin-et-al	16-02-2024	Martin Proks, Nazmus Salehin

Deep Learning Based Models for Preimplantation Mouse and Human Development

• Tutorial:
• Datasets:
• Trained models: https://huggingface.co/brickmanlab
• Portal: https://brickman-preimplantation.streamlit.app
• Portal codebase: https://github.com/brickmanlab/preimplantation-portal
• bioRxiv paper: https://www.biorxiv.org/content/10.1101/2024.02.16.580649v1

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.

Running

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