├── .gitignore ├── Dockerfile ├── LICENSE ├── README.md ├── data ├── Test_seed1.fasta ├── Test_seed1_aligned.aln └── per_protein_embeddings.h5.zip ├── docker-compose.yml ├── img ├── fine-tuning.png ├── gpu.png ├── logo_small.gif ├── nb_logo.png └── protgpt2.png ├── notebooks ├── embeddings.ipynb ├── model_training.ipynb ├── prediction.ipynb ├── prot_design.ipynb └── seq_analysis.ipynb ├── poetry.lock ├── pyproject.toml ├── ran ├── embeddings.html ├── model_training.html ├── prediction.html ├── prot_design.html └── seq_analysis.html ├── requirements.txt ├── slides ├── intro_pLM.key └── intro_pLM.pdf └── topics.md /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Multiomics-Analytics-Group/course_protein_language_modeling/HEAD/.gitignore -------------------------------------------------------------------------------- /Dockerfile: -------------------------------------------------------------------------------- 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