Repository Index

Python framework for creating, editing, and running Noisy Intermediate-Scale Quantum (NISQ) circuits.

• nisq
• quantum-algorithms
• quantum-computing
• cirq

Biological foundation modeling from molecular to genome scale

Python+Numpy+OpenGL: fast, scalable and beautiful scientific visualization

• python
• numpy
• opengl
• engine

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis

Interactive network visualization in Python and Dash, powered by Cytoscape.js

• plotly-dash
• plotly
• dash
• cytoscape

Pathology Language and Image Pre-Training (PLIP) is the first vision and language foundation model for Pathology AI (Nature Medicine). PLIP is a large-scale pre-trained model that can be used to extract visual and language features from pathology images and text description. The model is a fine-tuned version of the original CLIP model.

• artificial-intelligence
• clip
• pathology
• vision-and-language

An extension for Inkscape that makes it easier to draw optical diagrams.

• inkscape-extension
• optics-simulation
• python
• optics

Autonomous multi-agent framework to optimize scientific software

• acceleration
• agentic-ai
• ai-agents
• bioinformatics

MCP server for spatial transcriptomics analysis through natural language interfaces.

• bioinformatics
• cell-communication
• deconvolution
• machine-learning

Fast, deterministic cell-type deconvolution for million-bin spatial transcriptomics

• bioinformatics
• cell-type-deconvolution
• computational-biology
• deconvolution