zenith-bot

Hierarchical Unified Graph Representation for quantum and classical programs

Dafny proofs for 16 selected computations in an 88-component research-workflow prototype, with generated Python and coverage maps. Not verification of the complete system.

Lean 4 skeleton of the Tate conjecture: statement only. Does not prove Tate. Does not prove Hodge. Author: Benjamin Stanley Frohman.

An MTBDD-based quantum circuit simulator

Evidence-grounded skills and software-tool records for scientific AI agents, distilled from method papers by the AgenticScienceBuilder pipeline. Metabolomics: 5,859 skills, 909 tools, 21 workflows.

Candidate executable language for formalizing physical structure and AI-assisted scientific reasoning

https://superstaq.readthedocs.io

Pure-Rust cheminformatics toolkit and RDKit-compatible alternative for SMILES/SMARTS, SDF, fingerprints, substructure search, ETKDG, UFF/MMFF, and Python workflows.

Trending open-source repository: SciML/FastBroadcast.jl

Whole genome sequencing analysis pipeline for consumer hardware. 100% local, Docker-powered, free and open source.

PDB2PQR - determining titration states, adding missing atoms, and assigning charges/radii to biomolecules.

verifyBamID2: A robust tool for DNA contamination estimation from sequence reads using ancestry-agnostic method.

Matrix-Free O(N^3) Plucker-Exterior THC Commutant & Polarized Bianchi SOS Certifier for Qualtran/OpenFermion (54.31 Ha FeMoCo T_K*, 196.88 Ha P-Cluster N=114, Lean 4.20.0 0 sorryAx).

MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. For documentation and downloading the program, please see the home page:

The fastest automatic differentiation library for C++, with Python bindings. Forward, adjoint and higher-order derivatives, checkpointing, Eigen support and JIT. Reproducible benchmarks against CppAD, Adept and autodiff.

Computer-checkable proofs and recorded checks for research on eight Erdős problems. Papers and current claims: wcook04/plectis-erdos.

Gut-metagenome multi-kingdom analysis platform: 183-script + Snakemake pipeline, agent-driven mining loop, MCP visualization — VibeCoding-ready

Modular, GPU-capable land surface model of the CliMA Earth System Model, designed for data-driven parameterizations

Clouds Coder is a local-first coding agent platform centered on separating the CLI execution plane from the Web user plane, with Web UI, Skills Studio, resilient streaming, and long-task recovery controls.

Collection of mostly novel math problems, along with their AI Lean/Rocq formalization