Software

Open-source software and research tools I build and maintain.

Science

PantheonOS

The AgentOS that redefines data science

An evolvable, distributed multi-agent framework and harness for automatic scientific discovery.

Website ↗ GitHub ↗ ★ 473

Virtual Embryo

Developmental biology in the era of AI

An interactive AI atlas of mouse embryogenesis — 3D reconstructions, histology, and gene expression across 28 stages, with a spatiotemporal morphogenesis predictor and open REST / MCP endpoints.

Website ↗

CoolBox

Genomic data visualization in Jupyter

Jupyter-based genomic data visualization toolkit for Hi-C, ChIP-seq, and tracks.

GitHub ↗ ★ 260

U-FISH

Deep-learning spot detection for FISH images

Deep-learning based spot detection for FISH microscopy images.

Website ↗ GitHub ↗ ★ 34

U-Probe

Universal, agentic probe design for spatial omics

Universal and agentic probe design tool for imaging-based spatial omics.

Website ↗ GitHub ↗ ★ 4

Tool

bioView

Readability enhancement tool for bioinformatics file formats (FASTQ / FASTA / SAM).

Nim 29

executor-engine

Effortless, flexible, and powerful job execution engine for Python.

Python 10

web-python-console

A browser-based Python console powered by Pyodide and ImJoy.

HTML 9

funcdesc

Describe, validate, and introspect Python function inputs and outputs.

Python 3

executor-view

Web interface for the executor HTTP server.

TypeScript

oneFace

Generate CLI, Qt GUI, and Dash web-app interfaces from one Python function.

Python 41

Fun

AniNet

Interactive character-relationship network visualization for anime, manga, and games.

TypeScript 91

Rainbow-Fart-MBG

A Ma Baoguo voice pack for the Rainbow-Fart VSCode plugin — coding keywords trigger meme audio clips.

452