QiStark

LLMs-from-scratch

Implementing a ChatGPT-like LLM in PyTorch from scratch, step by step

english-wordlists

常用英语词汇表

Scrapegraph-ai

Python scraper based on AI

IMPROVE_tool

TL-MHC

graphrag

A modular graph-based Retrieval-Augmented Generation (RAG) system

BAlaS

Source code for the BUDE Alanine Scan web application.

MHCfovea

mcmc-demo

Interactive Markov-chain Monte Carlo Javascript demos

cs228-notes

Course notes for CS228: Probabilistic Graphical Models.

RFdiffusion

Code for running RFdiffusion

pyrosetta-basic

CAGE-Prox

Computer aided proximal decaging as a universal strategy for temporal protein activation

PyRosetta.notebooks

Jupyter Notebooks for learning the PyRosetta platform for biomolecular structure prediction and design

protein-design-tutorials

Tutorials, cheat sheets, and other resources for computational methods for protein design.

adbias

AutoDock Bias

dl_binder_design

MHCXAI

Framework for generating SHAP and LIME explanations for MHC class I predictors

AIP_MDL

CapsNet-MHC

TripHLApan

Uni-Dock

Uni-Dock: a GPU-accelerated molecular docking program

whatshap

Read-based phasing of genomic variants, also called haplotype assembly

NVIDIA-Clara-Parabricks-Somatic-Variant-Calling-AWS-Blog

AWS Blog (Somatic Variant Calling )

ImmuBPI

gpu-acclerated-genomics

Scripts and documents related to gpu-accelerated-genomics benchmarking manuscript

AlphaFold3

Implementation of Alpha Fold 3 from the paper: "Accurate structure prediction of biomolecular interactions with AlphaFold3" in PyTorch

RFdiffusion

Code for running RFdiffusion

Sniffles

Structural variation caller using third generation sequencing

neoepiscope

predicts neoepitopes from phased somatic mutations detected using tumor/normal DNA-seq data