biology

Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, Materials Science and Biology

Repository for the main Dockerfile with the OpenWorm software stack and project-wide issues

Hundreds of agent skills for medical research, including protocol design, data analysis, evidence insights, and academic writing.

Scripts to download genomes from the NCBI FTP servers

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

A PyTorch and TorchDrug based deep learning library for drug pair scoring. (KDD 2022)

Chainer Chemistry: A Library for Deep Learning in Biology and Chemistry

Software for writing protocols and running them on the Opentrons Flex and Opentrons OT-2

A general, evolvable, and distributed agent framework & harness for data science.

Library for Digital Pathology Image Processing

Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs

Terminal-based plasmid map viewer, sequence editor, and cloning/mutagenesis workbench in pure Python

A framework for state-of-the-art pre-trained bio foundation models on genomics and transcriptomics modalities.

Clone with Python! Data structures for double stranded DNA & simulation of homologous recombination, Gibson assembly, cut & paste cloning.

INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system interfacing with NLP systems and databases to collect knowledge, and through a process of assembly, produce causal graphs and dynamical models.

A Python Library for Conway's Game of Life

RiboNucleic Acid (RNA) Language Model

Lbster: Language models for Biological Sequence Transformation and Evolutionary Representation

Protein order and disorder data for Keras, Tensor Flow and Edward frameworks with automated update cycle made for continuous learning applications.

Hardware and software for accessible, extensible, and scalable bioreactors. Built on Raspberry Pi.