Tensors and Dynamic neural networks in Python with strong GPU acceleration

Must-read papers and resources related to causal inference and machine (deep) learning

Vina-GPU 2.0 accelerates AutoDock Vina and its related commonly derived docking methods, such as QuickVina 2 and QuickVina-W with GPUs.

NeuralPLexer: State-specific protein-ligand complex structure prediction with a multi-scale deep generative model

Interaction Fingerprints for protein-ligand complexes and more

Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Adasme et al. (2021), https://doi.org/10.1093/nar/gkab294

Solving differential equations in Python using DifferentialEquations.jl and the SciML Scientific Machine Learning organization

Connect Zotero and Dendron. No idea falls from the sky 🌦️, this tool is meant to allow for reproducible documentation of 💡 around the publishing process 📃.

Biological foundation modeling from molecular to genome scale

Inference Llama 2 in one file of pure 🔥

Selects tests affected by changed files. Executes the right tests first. Continuous test runner when used with pytest-watch.

CORNETO: A Unified Omics-Driven Framework for Network Inference

A unifying framework for biomedical research knowledge graphs

Advanced evolutionary computation library built directly on top of PyTorch, created at NNAISENSE.

Bootstrap an OBO Library ontology

The high-performance database for modern applications

Graphs for Everyone

GEARS is a geometric deep learning model that predicts outcomes of novel multi-gene perturbations

ProtTrans is providing state of the art pretrained language models for proteins. ProtTrans was trained on thousands of GPUs from Summit and hundreds of Google TPUs using Transformers Models.

Python Sorted Container Types: Sorted List, Sorted Dict, and Sorted Set

The OpenTF Manifesto expresses concern over HashiCorp's switch of the Terraform license from open-source to the Business Source License (BSL) and calls for the tool's return to a truly open-source …

Pretrain, finetune and deploy AI models on multiple GPUs, TPUs with zero code changes.

Species-aware DNA language modeling

A hyper-fast local vector database for use with LLM Agents. Now accepting SAFEs at $135M cap.

NetworkX-based Python library for representing ontologies

A Python frontend to (Open Biomedical) Ontologies.

Simple yet effective command line client for chatting with ChatGPT using the official API

Python Classes Without Boilerplate