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biobert

BioBERT: a pre-trained biomedical language representation model

biobert-pretrained

BioBERT: a pre-trained biomedical language representation model for biomedical text mining

bioc

Data structures and code to read/write BioC XML and Json.

biotext

Get a nicely-chunked local copy of the biomedical literature (to use for other projects)!

capital

Contenxtual Annotations Pipeline with Tagging and Linking (CAPITAL)

datascientist_course

diamond_ml

Apps for identification of EP's optimal features for successful protein identification.

metrix-database

metrix_ml

metrix_reloaded

modelcraft

Automated model building pipeline for X-ray crystallography

openfold

Trainable PyTorch reproduction of AlphaFold 2

pdbe-api-training

Interactive Python notebooks for PDBe API training

pediip

Protein electron density map identification in Python

planets

plmpapers

Must-read Papers on pre-trained language models.

probe

Trainable representation analysis study repository

pyresid

pyresid West-Life Protein Residue Annotator

python_topaz3

scibert

A BERT model for scientific text.

scispacy

A full spaCy pipeline and models for scientific/biomedical documents.

spacy

💫 Industrial-strength Natural Language Processing (NLP) in Python

vartriage

wellcomeml

Repository for Machine Learning utils at the Wellcome Trust

xia2_processing

my bi-weekly automated run of xia2 through my test data