"Rewriting protein alphabets with language models"

Source code for Code Like a Pro in Rust

View the folder directory tree structure, similar to the output of the tree command

Genome modeling and design across all domains of life

A JupyterLab plugin to facilitate invocation of code formatters.

Zenith - sort of like top or htop but with zoom-able charts, CPU, GPU, network, and disk usage

This is the offical codebase to reproduce and use EVOLVEpro, a model for in silico directed evolution of protein activities using few-shot active learning.

The central location for code in the NewAtlantis fellowship program

🌊 Robust workflows for gathering data about your local ocean.

Nextflow plugin to render provenance reports for pipeline runs. Supports standard formats such as BioCompute Object and Workflow Run RO-Crate.

Scripts to benchmark and train foldseek

Regression test for foldseek

A Google Apps Script for syncing ICS/ICAL files faster than the current Google Calendar speed

Efficient evolution from protein language models

Facebook AI Research Sequence-to-Sequence Toolkit written in Python.

Evolutionary Scale Modeling (esm): Pretrained language models for proteins

Orpheum (Previously called and published under sencha) is a Python package for directly translating RNA-seq reads into coding protein sequence.

Computational analysis of single-cell alternative splicing: A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Bioinformatics and Systems Bi…

Simulation study of recoding effectiveness

A modern LaTeX Beamer theme

Converting genomic sequence data to tensor-valued orthogonal polynomials and projecting phenotypes onto sequence space.

MyGene.info: A BioThings API for gene annotations

A R Bioconductor package for accessing MyGene.info services

mygene is an easy-to-use Python wrapper to access MyGene.Info services.

Community Discovery Library

A Python interface to the Ensembl REST APIs, biological data at your fingertips.

Run tools on FASTA files with gnu parallel, and then parse the results.

OpenConnect wrapper which logs into a GlobalProtect gateway, authenticating with Okta

A tool for fast and accurate summarizing of variant calling format (VCF) files