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Thoroughly Caffeinated
Thoroughly Caffeinated

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@GordonLab @ClinDesk @TheMITTech @BradnerLab @mit @Chaudhuri-Lab @mcwdsi

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Official Implementation of IgGM

Python 190 39 Updated Nov 30, 2025

Toward High-Accuracy Open-Source Biomolecular Structure Prediction.

Python 1,889 273 Updated May 6, 2026

Genie 3 is a fast, all-atom SE(3)-equivariant diffusion model for protein design. It achieves state-of-the-art performance on unconditional generation, motif scaffolding, and binder design while re…

Python 92 14 Updated May 10, 2026
C 4,516 704 Updated May 10, 2026

AI-powered biologics design campaign agent — multi-agent orchestration with BoltzGen, PXDesign, Protenix, and 200+ cloud tools. Antibodies, nanobodies, de novo binders, and beyond.

Python 63 6 Updated Mar 25, 2026

Advanced Claude Code usage dashboard for TRMNL e-ink displays

Python 7 Updated Apr 6, 2026

cfRNA QC + fragmentomics in a single BAM pass. Forked from seqeralabs/RustQC.

Rust 1 Updated May 13, 2026

Proof-of-concept code for beating Google's ZK proof of quantum cryptanalysis

Python 11 Updated Apr 17, 2026

🪨 why use many token when few token do trick — Claude Code skill that cuts 65% of tokens by talking like caveman

JavaScript 60,489 3,357 Updated May 12, 2026

Gene regulatory network containing signed transcription factor-target gene interactions

R 108 9 Updated May 27, 2025

A manifesto for AI-assisted modernisation of bioinformatics software.

Astro 44 1 Updated Apr 2, 2026

Repository to track versions of concrete strength data, models, and active learning proposals.

Jupyter Notebook 187 39 Updated May 14, 2026
Python 56 9 Updated Apr 10, 2026

A Python command line tool to query the Society of Thoracic Surgeons (STS) Adult Cardiac Risk Calculator API with bulk patient records.

Python 8 Updated Apr 17, 2026

Baochip 1x Silicon

SystemVerilog 357 32 Updated Apr 12, 2026

Autonomous experiment loop skill for Claude Code — port of pi-autoresearch

Python 300 29 Updated Mar 24, 2026

Autonomous experiment loop extension for pi

TypeScript 6,673 390 Updated May 6, 2026

A modernized rewrite of RSeQC (RNA-seq Quality Control)

Python 1 Updated Apr 14, 2026

Talk to your Mac, query your docs, no cloud required. On-device voice AI + RAG

C++ 1,507 81 Updated Mar 16, 2026

BullshitBench measures whether AI models challenge nonsensical prompts instead of confidently answering them, created by Peter Gostev.

Python 1,623 63 Updated May 15, 2026

"🐈 nanobot: The Ultra-Lightweight Personal AI Agent"

Python 42,513 7,469 Updated May 15, 2026

CLI proxy that reduces LLM token consumption by 60-90% on common dev commands. Single Rust binary, zero dependencies

Rust 48,275 2,927 Updated May 14, 2026

An ontology of cell types

Makefile 199 60 Updated May 15, 2026

Edit Banana: A framework for converting statistical formats into editable.

Python 5,181 346 Updated Apr 30, 2026

Your own personal AI assistant. Any OS. Any Platform. The lobster way. 🦞

TypeScript 372,042 77,022 Updated May 15, 2026

A symbiotic AI agent that remembers everything, challenges you, and extends your cognition.

Shell 711 75 Updated Apr 18, 2026
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