---
title: "SOFTWARE - Daniel Ari Friedman"
description: "Daniel Ari Friedman's SOFTWARE - AI, Active Inference, and Cognitive Security."
keywords: "Daniel Ari Friedman, active inference, SOFTWARE"
---
# π» Software β Open-Source AI, Scientific Computing & Research Tools
> **Navigation**: [π Home](../README.md) | [π Bibliography](BIBLIOGRAPHY.md) | [π» Software](SOFTWARE.md) | [π Links](LINKS.md) | [π§ Discovery](DISCOVERY.md) | [π€ Profile](PROFILE.md) | [π€ Collaborators](COLLABORATORS.md) | [π₯ Media](MEDIA.md) | [πΊ Videos](VIDEOS.md) | [π¦ Resources](RESOURCES.md) | [π Wikipedia](WIKIPEDIA.md)
**Open-Source Repositories by Daniel Ari Friedman, PhD ([@docxology](https://github.com/docxology))**
*Python Β· Rust Β· Go Β· TypeScript Β· Julia β Active Inference frameworks, cryptographic tools, computational biology, and AI infrastructure*
*48 original repositories Β· 32 catalogued Active Inference Institute contributions Β· AII organization: 50 public repositories*
*Available for [research consulting & collaboration](../README.md#-available-for-consulting--tutoring) Β· [All links](LINKS.md) Β· [Full profile](PROFILE.md)*
---
## Table of Contents
- [Repositories Owned by docxology](#repositories-owned-by-docxology)
- [Repositories docxology Contributes To](#repositories-docxology-contributes-to)
- [Active Inference Institute](#active-inference-institute)
---
## 𧬠Repositories Owned by docxology
> Original repositories created and maintained under [@docxology](https://github.com/docxology), sorted by star count. Excludes profile repo, test repos, and forks. For 286 total public repos including forks see the [full profile](https://github.com/docxology?tab=repositories).
| Repository | Description | Language | β | Updated |
|---|---|---|:---:|---|
| [QuadCraft](https://github.com/docxology/QuadCraft) | Minecraft variant built on tetrahedral geometry β voxels replaced by Quadray-coordinate tetrahedra, exploring Buckminster Fuller's synergetics in an interactive 3D world | JavaScript | 8 | 2026-03 |
| [template](https://github.com/docxology/template) | Multi-project research template with 10-stage CI/CD pipeline, Ruff linting, multi-Python-version testing, issue/PR templates, and security scanning | Python | 7 | 2026-03 |
| [MetaInformAnt](https://github.com/docxology/MetaInformAnt) | Meta-framework integrating computational entomology, Active Inference, and information theory for modeling ant colony cognition and beyond Β· [π](../papers/2021_ActiveInferants/) | Python | 5 | 2026-03 |
| [codomyrmex](https://github.com/docxology/codomyrmex) | AI-native modular coding workspace β 127 modules, 424 MCP tools, 21K+ zero-mock tests, multi-agent orchestration (Claude/Gemini/GPT), PAI integration | Python | 3 | 2026-03 |
| [cognitive-engine](https://github.com/docxology/cognitive-engine) | Hybrid neuro-symbolic AI combining fractal symbolic representations with probabilistic neural models for enhanced reasoning; includes Unipixel fractal building blocks and PEFF ethical reasoning | Python | 3 | 2026-03 |
| [opentir](https://github.com/docxology/opentir) | Comprehensive toolkit analyzing 250+ Palantir open-source repositories (6.2M+ lines of code) β automated discovery, multi-language analysis, dependency mapping, statistical profiling, and professional visualizations | Python | 3 | 2025-11 |
| [timeline_generator](https://github.com/docxology/timeline_generator) | Networked Life Encoding β interactive D3 knowledge graph of human intellectual history; 24 relationship types, Perplexity AI enrichment; seeded around R. Buckminster Fuller's network | TypeScript | 3 | 2026-03 |
| [FORMINDEX](https://github.com/docxology/FORMINDEX) | Analysis and tooling around FORMIS, the world's largest ant-literature database; bibliometric mining and structured index generation | Rich Text Format | 3 | 2024-10 |
| [ActiveInferAnts](https://github.com/docxology/ActiveInferAnts) | Active Inference for ants β multi-language implementations (Python) for modeling ant-colony cognition as Bayesian agents minimizing free energy Β· [π](../papers/2021_ActiveInferants/) | Python | 2 | 2024-04 |
| [crescent-city](https://github.com/docxology/crescent-city) | End-to-end pipeline for ingesting, parsing, and querying the Crescent City, CA municipal code; TypeScript-based legal-text processing | TypeScript | 2 | 2026-02 |
| [ivm-xyz](https://github.com/docxology/ivm-xyz) | Python library for 3D and 4D Quadray/IVM (Isotropic Vector Matrix) geometry β coordinate conversion, volume calculations, and polyhedral operations | Python | 2 | 2025-11 |
| [Markov_Blanket_Detection](https://github.com/docxology/Markov_Blanket_Detection) | Dynamic Markov Blanket Detection (DMBD) β PyTorch-accelerated framework for identifying causal relationships in complex systems; static and temporal modes with cognitive-structure labeling | Python | 2 | 2025-06 |
| [QuadMath](https://github.com/docxology/QuadMath) | Mathematical exposition of Quadray coordinate systems (4-vector tetrahedral coordinates); LaTeX documentation and computation library | TeX | 2 | 2026-02 |
| [active_inference](https://github.com/docxology/active_inference) | Active Inference for, with, and by Generative AI β Python implementations of free-energy-minimizing agents integrated with modern AI tooling Β· [π](../papers/2020_BehaviorEngineering/) | Python | 1 | 2025-11 |
| [AgenticMesh](https://github.com/docxology/AgenticMesh) | Active Inference & Agentic Mesh β modular Python infrastructure for building agentic systems using free-energy-minimizing Active Inference principles | Python | 1 | 2025-02 |
| [curriculum](https://github.com/docxology/curriculum) | Curriculum development framework for interdisciplinary education in Active Inference, biology, and computational science | HTML | 1 | 2026-01 |
| [lean_niche](https://github.com/docxology/lean_niche) | Lean/minimal niche-construction modeling β formal computational representations of ecological niche dynamics | Python | 1 | 2025-08 |
| [literature](https://github.com/docxology/literature) | Literature collection and analysis tools for structured ingestion, annotation, and exploration of scientific publications | Python | 1 | 2025-12 |
| [obsidian-construction-from-text](https://github.com/docxology/obsidian-construction-from-text) | Automated Obsidian vault construction from unstructured text β NLP pipelines to generate bidirectionally-linked knowledge graphs | Python | 1 | 2025-03 |
| [qr_live_protocol](https://github.com/docxology/qr_live_protocol) | QR code-based live protocol system for real-time data exchange and interactive session management | Python | 1 | 2025-10 |
| [ultralink-docx](https://github.com/docxology/ultralink-docx) | UltraLink document format tooling β linking, rendering, and transformation utilities for rich hyperlinked documents | HTML | 1 | 2025-03 |
| [cognitive](https://github.com/docxology/cognitive) | Cognitive Ecosystem Modeling Framework β Active Inference agents with Obsidian-compatible knowledge management, bidirectional graph validation, belief updating, and network visualization | Python | 13\* | 2025-09 |
| [active_torchference](https://github.com/docxology/active_torchference) | PyTorch-based Active Inference implementations β GPU-accelerated variational inference and free energy minimization | Python | 0 | 2025-10 |
| [ant-pheromone](https://github.com/docxology/ant-pheromone) | Computational simulation of ant pheromone trail dynamics and stigmergic communication | Python | 0 | 2022-09 |
| [ant_stack](https://github.com/docxology/ant_stack) | The Ant Stack β layered computational model of collective ant-colony intelligence Β· [π](../papers/2025_AntStack/) | Python | 0 | 2025-09 |
| [ento_linguistics](https://github.com/docxology/ento_linguistics) | Ento-Linguistics corpus pipeline β term extraction, terminology networks, semantic entropy, CACE scoring Β· [π](../papers/2026_EntoLinguistics/) | Python | 0 | 2026-04 |
| [cognitive_case_diagrams](https://github.com/docxology/cognitive_case_diagrams) | Compositional linguistic case for cognitive modeling β categorical case systems, DisCoCat/DisCoCirc diagrams, tests and figures for the Active Inference Journal manuscript Β· [π](../papers/2026_CognitiveCaseDiagrams/) | Python | 0 | 2026-04 |
| [Autonomous-Drone-Navigation-in-AirSim-With-Active-Inference](https://github.com/docxology/Autonomous-Drone-Navigation-in-AirSim-With-Active-Inference) | Active Inference-driven autonomous drone navigation in Microsoft AirSim simulation environment | β | 0 | 2025-04 |
| [biol-1](https://github.com/docxology/biol-1) | BIOL-1: General Biology course materials β College of the Redwoods; lectures, labs, and interactive HTML content | HTML | 0 | 2026-03 |
| [biol-8](https://github.com/docxology/biol-8) | BIOL-8: Human Biology course materials β College of the Redwoods; lectures, labs, and interactive HTML content | HTML | 0 | 2026-03 |
| [cascadia](https://github.com/docxology/cascadia) | Cascadia bioregion modeling and data analysis tools | Python | 0 | 2025-08 |
| [course](https://github.com/docxology/course) | Course materials framework for structured interdisciplinary learning modules | Python | 0 | 2025-12 |
| [enactive_inference_model](https://github.com/docxology/enactive_inference_model) | Three-level hierarchical enactive inference model of mental action β focused-attention meditation with expert/novice profiles; reproducible simulations and figures Β· [π](../papers/2025_Thoughtseeds/) | Python | 0 | 2026-02 |
| [EvoJump](https://github.com/docxology/EvoJump) | Comprehensive Framework for Evolutionary Ontogenetic Analysis β modeling developmental trajectories and evolutionary dynamics Β· [π](../papers/2025_EvoJump/) | Python | 0 | 2025-10 |
| [flick](https://github.com/docxology/flick) | Lightweight Python tooling for rapid data flicking and processing pipelines | Python | 0 | 2025-03 |
| [fuller-obsidian](https://github.com/docxology/fuller-obsidian) | Obsidian vault dedicated to R. Buckminster Fuller's ideas β synergetics, geodesics, and design science | β | 0 | 2025-02 |
| [godel_ivm](https://github.com/docxology/godel_ivm) | GΓΆdel numbering meets the IVM (Isotropic Vector Matrix) β formal encoding of geometric objects as prime products | Python | 0 | 2025-10 |
| [goference](https://github.com/docxology/goference) | Active Goference β production-ready Go framework for Active Inference autonomous agents; genuine variational inference, free energy minimization, POMDP policy planning via gonum | Go | 0 | 2025-09 |
| [hhs-opendata](https://github.com/docxology/hhs-opendata) | Analysis of HHS (Department of Health and Human Services) open data β policy analytics and public-health data pipelines | Python | 0 | 2026-02 |
| [infra-calc](https://github.com/docxology/infra-calc) | Infrastructure calculator for estimating resource requirements and costs in multi-agent and AI systems | JavaScript | 0 | 2025-05 |
| [markdown_decision_process](https://github.com/docxology/markdown_decision_process) | Framework for Probabilistic Document Analysis β Markov Decision Process over Markdown artifacts for structured document reasoning Β· [π](../papers/2025_MarkdownDecisionProcess/) | Python | 0 | 2025-10 |
| [mdkv](https://github.com/docxology/mdkv) | MKV-like key-value format and methods for Markdown β structured metadata embedding in plain-text documents Β· [π](../papers/2025_MDKV/) | Python | 0 | 2025-08 |
| [p3if](https://github.com/docxology/p3if) | Properties, Processes, and Perspectives Inter-Framework (P3IF) β multiplexing interdisciplinary requirements frameworks to manage information risk and foster cognitive security Β· [π](../papers/2023_P3IF/) | Python | 0 | 2026-01 |
| [service](https://github.com/docxology/service) | Service-layer infrastructure and API tooling for Python-based research applications | Python | 0 | 2025-05 |
| [snake](https://github.com/docxology/snake) | Classic snake game implemented in Python β used for testing multi-agent and reinforcement learning algorithms | Python | 0 | 2025-11 |
| [steganographer](https://github.com/docxology/steganographer) | 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 | Rust | 0 | 2026-03 |
| [symergetics](https://github.com/docxology/symergetics) | Symbolic Synergetics β computer algebra and formal symbolic systems for Buckminster Fuller's synergetics mathematics | Python | 0 | 2025-09 |
| [transformer](https://github.com/docxology/transformer) | Transformer architecture explorations β attention mechanisms and architectural variants for Active Inference research | Python | 0 | 2025-10 |
> \* Note: a same-named repository exists at [`ActiveInferenceInstitute/cognitive`](https://github.com/ActiveInferenceInstitute/cognitive) (β18); `docxology/cognitive` (β13) is an **original** repository β these are distinct projects.
---
## π€ Repositories docxology Contributes To
> Repositories under other organizations or owners where docxology has made substantial contributions, primarily as **Officer and Director of the Active Inference Institute**. Sorted by star count. Forks of external projects are marked **[fork]**.
### ποΈ Active Inference Institute
| Repository | Description | Language | β | Year |
|---|---|---|:---:|---|
| [ActiveInferenceJournal](https://github.com/ActiveInferenceInstitute/ActiveInferenceJournal) | Content hub for the Active Inference Journal β 500+ video transcripts, stream archives, and multimedia publishing infrastructure for the Institute's primary educational output | HTML | 42 | 2024 |
| [ActiveBlockference](https://github.com/ActiveInferenceInstitute/ActiveBlockference) | Active Inference agents in cadCAD block-based simulation β formal agent-based modeling using complex-systems simulation framework | Jupyter | 32 | 2023 |
| [ActiveInferAnts](https://github.com/ActiveInferenceInstitute/ActiveInferAnts) | Active Inference models for/of ants across 32+ programming languages β multi-language reference implementation of stigmergic Active Inference | Python | 28 | 2024 |
| [GeneralizedNotationNotation](https://github.com/ActiveInferenceInstitute/GeneralizedNotationNotation) | GNN β formal notation standard for specifying Active Inference generative models; JSON/YAML schema, validators, and transpilers to Python, Julia, and MATLAB Β· [Zenodo software](https://doi.org/10.5281/zenodo.19600217) | Python | 24 | 2024 |
| [FEP_Lean](https://github.com/ActiveInferenceInstitute/FEP_Lean) | Lean 4 / Mathlib4 formalization of FEP-related mathematics β 50-topic sorry-free catalog, Hermes/OpenGauss LLM drafting, zero-mock verification, manuscript pipeline Β· [π](../papers/2026_FEPLean/) | Python | 3 | 2026 |
| [cognitive](https://github.com/ActiveInferenceInstitute/cognitive) | Cognitive modeling and simulation tools β multi-agent Active Inference environments, benchmarks, and visualization | Python | 18 | 2025 |
| [Active_Inference_Ontology](https://github.com/ActiveInferenceInstitute/Active_Inference_Ontology) | Formal OWL/RDF ontology for Active Inference β defines classes, properties, and axioms for free energy principle concepts | β | 13 | 2023 |
| [Journal-Utilities](https://github.com/ActiveInferenceInstitute/Journal-Utilities) | Transcription, processing, and publishing pipelines for the Active Inference Journal β Whisper-based download, transcription, RAG/knowledge-graph, and export utilities Β· [Zenodo release](https://doi.org/10.5281/zenodo.18686966) | HTML | 11 | 2026 |
| [Symposium](https://github.com/ActiveInferenceInstitute/Symposium) | Applied Active Inference Symposium materials β talks, workshops, proceedings, and collaborative session artifacts from annual Applied AIF symposia | Python | 11 | 2024 |
| [ActiveInferenceCategoryTheory](https://github.com/ActiveInferenceInstitute/ActiveInferenceCategoryTheory) | Formal categorical foundations for Active Inference β string diagrams, functorial semantics, and compositional models using category theory | β | 10 | 2024 |
| [CEREBRUM](https://github.com/ActiveInferenceInstitute/CEREBRUM) | Case-Enabled Reasoning Engine with Bayesian Representations for Unified Modeling β grammatical case framework for compositional cognitive models | Python | 12 | 2025 |
| [GEO-INFER](https://github.com/ActiveInferenceInstitute/GEO-INFER) | Geospatial Active Inference β applying free energy minimization to geographic systems, spatial planning, and bioregional intelligence | HTML | 9 | 2024 |
| [AEOS](https://github.com/ActiveInferenceInstitute/AEOS) | Active Entity Ontology for Science β OWL ontology for representing active entities, their actions, and causal relationships in scientific models | β | 8 | 2022 |
| [courses](https://github.com/ActiveInferenceInstitute/courses) | Structured Active Inference learning courses β cohort-based curriculum materials, exercises, and collaborative learning artifacts | HTML | 8 | 2024 |
| [Research-Discovery-Engine](https://github.com/ActiveInferenceInstitute/Research-Discovery-Engine) | AI-driven research synthesis and navigation β semantic search, citation graph analysis, and cross-domain connection discovery across the Active Inference literature | HTML | 6 | 2024 |
| [Parr_et_al_2022_ActInf_Textbook](https://github.com/ActiveInferenceInstitute/Parr_et_al_2022_ActInf_Textbook) | Active Inference Textbook Study Group β code, exercises, and reading notes accompanying Parr, Pezzulo & Friston (2022) | Julia | 6 | 2023 |
| [Biofirm](https://github.com/ActiveInferenceInstitute/Biofirm) | Bioregional Active Inference for organizational stewardship β applying free energy minimization to ecological and community governance systems | Python | 5 | 2024 |
| [Start](https://github.com/ActiveInferenceInstitute/Start) | Institute onboarding hub β getting-started guides, contributor pathways, project index, and orientation materials for new participants | Python | 5 | 2024 |
| [Knowledge-Engineering](https://github.com/ActiveInferenceInstitute/Knowledge-Engineering) | Knowledge engineering tools and workflows β ontology alignment, concept mapping, and structured knowledge-base construction for Active Inference | Jupyter | 4 | 2022 |
| [ActInf_RxInfer](https://github.com/ActiveInferenceInstitute/ActInf_RxInfer) | Active Inference with RxInfer.jl β Julia-based reactive message passing for efficient Bayesian inference in Active Inference models | β | 2 | 2024 |
| [pymcp](https://github.com/ActiveInferenceInstitute/pymcp) | PyMCP β Model Context Protocol bridge for PyMDP, enabling Active Inference agents to interoperate with MCP-compatible AI tooling | Python | 2 | 2025 |
| [GEN24](https://github.com/ActiveInferenceInstitute/GEN24) | GEN-24 working project β collaborative generative systems research from the 2024 active inference cohort | Jupyter | 1 | 2024 |
| [NoOrg](https://github.com/ActiveInferenceInstitute/NoOrg) | NoOrg is a Real Org β experimental organizational infrastructure and governance frameworks for decentralized scientific institutions | HTML | 1 | 2024 |
| [ultralink](https://github.com/ActiveInferenceInstitute/ultralink) | UltraLink β framework for linking, rendering, and transforming richly cross-referenced documents across multiple output formats | β | 1 | 2025 |
| [ActiveInferenceImplementations](https://github.com/ActiveInferenceInstitute/ActiveInferenceImplementations) | Learning and exploring probabilistic inference β beginner-accessible Jupyter notebooks for Active Inference from first principles | Jupyter | 0 | 2022 |
| [ATLAS](https://github.com/ActiveInferenceInstitute/ATLAS) | Question-Oriented Pattern Languages for Knowledge Management β structured templates for navigating complex scientific knowledge spaces | Python | 0 | 2025 |
| [Bots](https://github.com/ActiveInferenceInstitute/Bots) | Institute bot infrastructure β automation, notification, and community management bots for the Active Inference Institute's platforms | β | 0 | 2022 |
| [Garden-of-Iris](https://github.com/ActiveInferenceInstitute/Garden-of-Iris) | Interactive visualization garden β generative art and data-visualization experiments exploring Active Inference dynamics | Python | 0 | 2023 |
| [gen25](https://github.com/ActiveInferenceInstitute/gen25) | GEN-25 working project β generative systems and collaborative research from the 2025 active inference cohort | β | 0 | 2025 |
| [gnn](https://github.com/ActiveInferenceInstitute/gnn) | Generalized Notation Notation v2 β next-generation GNN specification with extended model classes and improved toolchain | β | 0 | 2024 |
| [ISSS](https://github.com/ActiveInferenceInstitute/ISSS) | International Society for the Systems Sciences collaboration β joint research and educational materials bridging Active Inference and systems science | Python | 0 | 2024 |
| [topp](https://github.com/ActiveInferenceInstitute/topp) | The Open Problems Project β curated registry of open scientific problems in Active Inference and the free energy principle | TeX | 0 | 2024 |
---
## π Summary
| Category | Owned | Highlighted Repos |
|----------|:-----:|---|
| Active Inference & Modeling | 12 | `active_inference`, `active_torchference`, `goference`, `AgenticMesh`, `enactive_inference_model`, `Markov_Blanket_Detection`, `cognitive`, `cognitive-engine`, `ActiveInferAnts`, `EvoJump`, `markdown_decision_process`, `transformer` |
| Entomology & Biology | 7 | `ento_linguistics`, `MetaInformAnt`, `ant_stack`, `ant-pheromone`, `FORMINDEX`, `biol-1`, `biol-8` |
| Synergetics & Geometry | 5 | `QuadCraft`, `QuadMath`, `ivm-xyz`, `godel_ivm`, `symergetics` |
| Cognitive Security | 2 | `p3if`, `opentir` |
| Developer Tools | 10 | `codomyrmex`, `template`, `steganographer`, `timeline_generator`, `qr_live_protocol`, `obsidian-construction-from-text`, `mdkv`, `ultralink-docx`, `infra-calc`, `snake` |
| Data & Policy | 2 | `hhs-opendata`, `crescent-city` |
| Education | 4 | `literature`, `curriculum`, `course`, `lean_niche` |
| Other | 5 | `cascadia`, `fuller-obsidian`, `transformer`, `service`, `flick` |
| **docxology subtotal** | **48** | |
| AII Contributions (non-fork) | 32 | Catalogued repositories with docxology contributions |
| **Grand Total** | **80** | |
> *For 286 total public repositories including personal forks, see the [full profile](https://github.com/docxology?tab=repositories). AII catalog count includes source repositories with docxology contributions; the [AII GitHub API](https://api.github.com/users/ActiveInferenceInstitute) returned 50 public organization repositories on 2026-05-13, including org-level forks and adjacent projects. See [BIBLIOGRAPHY.md](BIBLIOGRAPHY.md) for the full publication catalog and [DISCOVERY.md](DISCOVERY.md) for source-discovery queries.*
---
*See also [BIBLIOGRAPHY.md](BIBLIOGRAPHY.md) for the full publication catalog Β· [DISCOVERY.md](DISCOVERY.md) for public-source discovery Β· [README.md](../README.md) for profile overview Β· [LINKS.md](LINKS.md) for all web presences Β· [COLLABORATORS.md](COLLABORATORS.md) for research network*
---
*Maintained by Daniel Ari Friedman | [β Back to Home](../README.md)*