Repositories Owned by docxology
Production-grade scaffold for reproducible computational research — 10-stage DAG pipelines, ≥90% test coverage, cryptographic provenance, multi-project workspace, and agent-ready documentation · Zenodo software v3.3.0 · Zenodo · paper
Minecraft variant built on tetrahedral geometry — voxels replaced by Quadray-coordinate tetrahedra, exploring Buckminster Fuller's synergetics in an interactive 3D world
Meta-framework integrating computational entomology, Active Inference, and information theory for modeling ant colony cognition and beyond · paper
AI-native modular coding workspace — 100+ modules, 500+ MCP tools, 21K+ zero-mock tests, multi-agent orchestration (Claude/Gemini/GPT), PAI integration · Zenodo · paper
Networked Life Encoding — interactive D3 knowledge graph of human intellectual history; 24 relationship types, Perplexity AI enrichment; seeded around R. Buckminster Fuller's network
Hybrid neuro-symbolic AI combining fractal symbolic representations with probabilistic neural models for enhanced reasoning; includes Unipixel fractal building blocks and PEFF ethical reasoning
Comprehensive toolkit analyzing 250+ Palantir open-source repositories (6.2M+ lines of code) — automated discovery, multi-language analysis, dependency mapping, statistical profiling, and professional visualizations
Analysis and tooling around FORMIS, the world's largest ant-literature database; bibliometric mining and structured index generation
Active Inference for ants — multi-language implementations (Python) for modeling ant-colony cognition as Bayesian agents minimizing free energy · paper
End-to-end pipeline for ingesting, parsing, and querying the Crescent City, CA municipal code; TypeScript-based legal-text processing
Python library for 3D and 4D Quadray/IVM (Isotropic Vector Matrix) geometry — coordinate conversion, volume calculations, and polyhedral operations
Dynamic Markov Blanket Detection (DMBD) — PyTorch-accelerated framework for identifying causal relationships in complex systems; static and temporal modes with cognitive-structure labeling
Mathematical exposition of Quadray coordinate systems (4-vector tetrahedral coordinates); LaTeX documentation and computation library
Literature collection and analysis tools for structured ingestion, annotation, and exploration of scientific publications
Active Inference for, with, and by Generative AI — Python implementations of free-energy-minimizing agents integrated with modern AI tooling · paper
Active Inference & Agentic Mesh — modular Python infrastructure for building agentic systems using free-energy-minimizing Active Inference principles
Curriculum development framework for interdisciplinary education in Active Inference, biology, and computational science
Lean/minimal niche-construction modeling — formal computational representations of ecological niche dynamics
Automated Obsidian vault construction from unstructured text — NLP pipelines to generate bidirectionally-linked knowledge graphs
QR code-based live protocol system for real-time data exchange and interactive session management
Agentic Intelligence curriculum — modular educational scaffold for teaching bounded AI-agent support and synthetic analytic tradecraft · paper · Zenodo
UltraLink document format tooling — linking, rendering, and transformation utilities for rich hyperlinked documents
High-performance Rust tool for embedding BLAKE3+Ed25519 cryptographic signatures and visible watermarks into live video/audio via LSB steganography; four Rust crates, 132 tests, GStreamer integration
Algebraic NTQR evaluation study recovering LLM-persona accuracies from unlabeled votes · paper · Zenodo
Verification-first webcam eye-movement analysis toolkit for gaze, saccades, pupillometry, and diagnostic-quality exports · paper · Zenodo
Integration workspace aggregating and exercising the coasys (AD4M) agent-centric social-layer repositories
Multiharness cognitive-security and analytic-tradecraft skill library — 100 defensive SAT/cogsec skills runnable under Claude Code, Codex, and Hermes · paper · Zenodo
Deterministic token-injection exemplar for conditional IMRAD manuscripts — reproducible madlib-style variable substitution for scientific writing · paper · Zenodo
PyTorch-based Active Inference implementations — GPU-accelerated variational inference and free energy minimization
Computational simulation of ant pheromone trail dynamics and stigmergic communication
The Ant Stack — layered computational model of collective ant-colony intelligence · paper
Computational research on insect infrared sensing and olfaction modeling · paper · Zenodo · Zenodo
Ento-Linguistics corpus pipeline — term extraction, terminology networks, semantic entropy, CACE scoring · paper
Compositional linguistic case for cognitive modeling — categorical case systems, DisCoCat/DisCoCirc diagrams, tests and figures for the Active Inference Journal manuscript · paper
Active Inference-driven autonomous drone navigation in Microsoft AirSim simulation environment
BIOL-1: General Biology course materials — College of the Redwoods; lectures, labs, and interactive HTML content
BIOL-8: Human Biology course materials — College of the Redwoods; lectures, labs, and interactive HTML content
Open generative biology textbook — Markdown source, tested Python modules, programmatic figures; archived at Zenodo · paper
Cascadia bioregion modeling and data analysis tools
Course materials framework for structured interdisciplinary learning modules
Three-level hierarchical enactive inference model of mental action — focused-attention meditation with expert/novice profiles; reproducible simulations and figures · paper
Comprehensive Framework for Evolutionary Ontogenetic Analysis — modeling developmental trajectories and evolutionary dynamics · paper
Lightweight Python tooling for rapid data flicking and processing pipelines
Obsidian vault dedicated to R. Buckminster Fuller's ideas — synergetics, geodesics, and design science
Gödel numbering meets the IVM (Isotropic Vector Matrix) — formal encoding of geometric objects as prime products
Active Goference — production-ready Go framework for Active Inference autonomous agents; genuine variational inference, free energy minimization, POMDP policy planning via gonum
Analysis of HHS (Department of Health and Human Services) open data — policy analytics and public-health data pipelines
The Music Never Stopped citation-bound Grateful Dead data compendium · paper · Zenodo · Zenodo
Infrastructure calculator for estimating resource requirements and costs in multi-agent and AI systems
Framework for Probabilistic Document Analysis — Markov Decision Process over Markdown artifacts for structured document reasoning · paper
MKV-like key-value format and methods for Markdown — structured metadata embedding in plain-text documents · paper
Properties, Processes, and Perspectives Inter-Framework (P3IF) — multiplexing interdisciplinary requirements frameworks to manage information risk and foster cognitive security · paper
Service-layer infrastructure and API tooling for Python-based research applications
Classic snake game implemented in Python — used for testing multi-agent and reinforcement learning algorithms
Golden-ratio OBS Studio broadcast console and FractiSynth transducer — Python reference engine, native `libobs` plugin, and `obspython` bridge driven by fail-closed solar telemetry
William Blake, Professor Jiang, and the Architecture of Intelligence — AI-augmented scholarly response to Game Theory #24 with Blake, Jiang, and Active Inference framing · paper
Symbolic Synergetics — computer algebra and formal symbolic systems for Buckminster Fuller's synergetics mathematics
Transformer architecture explorations — attention mechanisms and architectural variants for Active Inference research
Cognitive Ecosystem Modeling Framework — Active Inference agents with Obsidian-compatible knowledge management, bidirectional graph validation, belief updating, and network visualization
Typed, deterministic multimodal illusion generator — visual, auditory, temporal, and audio-visual stimuli with scholarly evidence and publication outputs · Zenodo · paper
ENTO (ENcrypted, Typed, Omnitrack): a flat-ZIP authenticated container format for multimodal research data, with per-track AES-256-GCM, graded observability, and hash-chained proofs. Reference implementation. · Zenodo · paper
Source-faithful, fully reproducible software operationalizing the formalisms of There is no self-evidence: A physics of emptiness realisation (Sandved-Smith, Fields, Doctor, Laukkonen & Hohwy, 2026). · Zenodo · paper
Sortition Upstream of NTQR: how panel formation and size shape ground-truth-free evaluation (deterministic synthetic instrument + single-model Gemma postdoctoral-review companion) · Zenodo · paper
AlphaCOGANT: Recursive Corporate Self-Improvement as Active Inference — GNN-via-COGANT model of the AlphaFund Economic World Model · Zenodo · paper
DemoCreate: declarative, deterministic audio-visual demo generation for software packages and research papers. · Zenodo · paper
The Physics Engine for AI Coding Agents.
Active Inference Pocket Lab — portable simulation and learning environment for Active Inference experiments
Correlating Github activity with Solar activity
Reproducible, validated short/medium/long PDF+PPTX pitch-deck generation — a public exemplar extracted from docxology/template · Zenodo · paper
Autopoietic Project Generation: a combinatoric grammar for deterministic runnable project synthesis (DOI: 10.5281/zenodo.21227869) · Zenodo · paper
Data Descriptor Template: schema, file inventory, provenance, and release-readiness contract for dataset papers. Exemplar from the docxology/template research monorepo.
Exploratory Data Analysis: A Reproducible Notebook Template — public exemplar from docxology/template · Zenodo · paper
Illegal States, Mostly Unrepresentable: strongly typed multiagent colony exemplar (session-typed protocols, affine resource handles, Lean/TLA+ side-specs). From the docxology/template monorepo.
Public standalone template exemplar: template_gold_refinement
A Domain Language for Specifying Controlled Methods — public exemplar from docxology/template · Zenodo · paper
Pools, Rules, and Tools: a template-integrated resource architecture exemplar (fonds/rules/tools resource pools). From the docxology/template research monorepo.
Redacted Report Template: disclosure control and release-audit exemplar (classification ceiling, redaction ledger, mosaic-risk checks). From the docxology/template monorepo.
Registered Report Template: preregistration, deviations, and claim boundaries for confirmatory research. From the docxology/template research monorepo.
Private project mirror for archive/template_search_project in docxology/projects.
SIA self-improvement harness — deterministic Meta→Target→Feedback exemplar (template_sia) · Zenodo · paper
template_bioinformatics_project — Active Inference / research exemplar repository
Top-level wrapper manuscript and reproducible 33-package special-agent operations compendium, with generated chapters, unified bibliography, deterministic regeneration, and tested release artifacts · paper · Zenodo
A thin reader that declares the line set and checks that no two lines share a spelling — holding-instruments research practice · paper · Zenodo
A positive operating discipline for concise, inspectable, revisable work · paper · Zenodo
A typed ledger for the edge of a claim: absence, restraint, and the unknowable · paper · Zenodo
An aspirational thread and long-horizon direction for personal work · paper · Zenodo
A personal security boundary and explicit No document for dual-use development · paper · Zenodo
Co-registration without aggregation — the Witness Register holding instrument · paper · Zenodo
DigiPPPiP — Digital Partner Pen Play in Parallel: a composable, fully-tested computational companion for remote, semisynchronous, and asynchronous dyadic drawing · paper · Zenodo
Advanced multi-phase literature-review pipeline exemplar with iterative search refinement, multi-phrase querying, and deterministic synthesis
Comprehensive local intelligence platform for Crescent City, CA — municipal code, real-time alerts, RAG chat, and analytics
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Active Inference Institute Contributions
Content hub for the Active Inference Journal — 500+ video transcripts, stream archives, and multimedia publishing infrastructure for the Institute's primary educational output
Active Inference agents in cadCAD block-based simulation — formal agent-based modeling using complex-systems simulation framework
Active Inference models for/of ants across 32+ programming languages — multi-language reference implementation of stigmergic Active Inference
Unofficial repo for materials and code related to "Fundamentals of Active Inference" (Namjoshi 2026).
GNN — formal notation standard for specifying Active Inference generative models; JSON/YAML schema, validators, and transpilers to Python, Julia, and MATLAB · Zenodo software
Cognitive modeling and simulation tools — multi-agent Active Inference environments, benchmarks, and visualization
Formal OWL/RDF ontology for Active Inference — defines classes, properties, and axioms for free energy principle concepts
Case-Enabled Reasoning Engine with Bayesian Representations for Unified Modeling — grammatical case framework for compositional cognitive models · Zenodo · paper
Transcription, processing, and publishing pipelines for the Active Inference Journal — Whisper-based download, transcription, RAG/knowledge-graph, and export utilities · Zenodo release
Applied Active Inference Symposium materials — talks, workshops, proceedings, and collaborative session artifacts from annual Applied AIF symposia
Formal categorical foundations for Active Inference — string diagrams, functorial semantics, and compositional models using category theory
Geospatial Active Inference — applying free energy minimization to geographic systems, spatial planning, and bioregional intelligence
Active Entity Ontology for Science — OWL ontology for representing active entities, their actions, and causal relationships in scientific models
Structured Active Inference learning courses — cohort-based curriculum materials, exercises, and collaborative learning artifacts
AI-driven research synthesis and navigation — semantic search, citation graph analysis, and cross-domain connection discovery across the Active Inference literature
Active Inference Textbook Study Group — code, exercises, and reading notes accompanying Parr, Pezzulo & Friston (2022)
Bioregional Active Inference for organizational stewardship — applying free energy minimization to ecological and community governance systems
Institute onboarding hub — getting-started guides, contributor pathways, project index, and orientation materials for new participants
A computational meta-analysis of the Active Inference literature. An automated LLM pipeline extracts assertions from 849 papers across theory, tools, and domains, structuring them as nanopublications. By mapping these into a citation-weighted knowledge graph, this project provides a reproducible, living review of hypothesis-level consensus.
Knowledge engineering tools and workflows — ontology alignment, concept mapping, and structured knowledge-base construction for Active Inference
Lean 4 / Mathlib4 formalization of FEP-related mathematics — 50-topic sorry-free catalog, Hermes/OpenGauss LLM drafting, zero-mock verification, manuscript pipeline · paper · Zenodo
Active Inference with RxInfer.jl — Julia-based reactive message passing for efficient Bayesian inference in Active Inference models
PyMCP — Model Context Protocol bridge for PyMDP, enabling Active Inference agents to interoperate with MCP-compatible AI tooling
GEN-24 working project — collaborative generative systems research from the 2024 active inference cohort
NoOrg is a Real Org — experimental organizational infrastructure and governance frameworks for decentralized scientific institutions
UltraLink — framework for linking, rendering, and transforming richly cross-referenced documents across multiple output formats
Learning and exploring probabilistic inference — beginner-accessible Jupyter notebooks for Active Inference from first principles
Question-Oriented Pattern Languages for Knowledge Management — structured templates for navigating complex scientific knowledge spaces
Deterministic Codebase-to-GNN Translation — evidence compiler converting repositories into Generalized Notation Notation Active Inference artifacts via a 22-rule fixpoint engine; dual Python/Rust · paper · Zenodo · Zenodo
On-Policy Distillation and Active Inference — finite variational-model correspondence with deterministic witnesses, reproducibility artifacts, and paired publication release · paper · Zenodo · Zenodo
Institute bot infrastructure — automation, notification, and community management bots for the Active Inference Institute's platforms
Interactive visualization garden — generative art and data-visualization experiments exploring Active Inference dynamics
GEN-25 working project — generative systems and collaborative research from the 2025 active inference cohort
Generalized Notation Notation v2 — next-generation GNN specification with extended model classes and improved toolchain
International Society for the Systems Sciences collaboration — joint research and educational materials bridging Active Inference and systems science
The Open Problems Project — curated registry of open scientific problems in Active Inference and the free energy principle
Robust belief sharing in federated Active Inference — recovery-tested generalized-variational consensus · paper · Zenodo
Validated prerequisite graph, computational claim registry, and SkillTree delivery contract for Active Inference · paper · Zenodo