Computational Methods & Open Science

Research templates, markdown containers, discovery engines, reproducible workflows, and software infrastructure.

25 Works

Curated works in this domain from the unified bibliography.

9 Related Repositories

Selected software entries connected to this domain.

Collaborator Context

Active Inference Institute contributors, Open-source repository contributors

Selected Works

Newest and most relevant entries for this domain.

Open full bibliography

Related Software

Repository entry points for implementation, data, and teaching work.

template

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

Python · ⭐ 17

mdkv

MKV-like key-value format and methods for Markdown — structured metadata embedding in plain-text documents

Python · ⭐ 0

markdown_decision_process

Framework for Probabilistic Document Analysis — Markov Decision Process over Markdown artifacts for structured document reasoning

Python · ⭐ 0

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 · ⭐ 1

timeline_generator

Networked Life Encoding — interactive D3 knowledge graph of human intellectual history; 24 relationship types, Perplexity AI enrichment; seeded around R. Buckminster Fuller's network

TypeScript · ⭐ 4

codomyrmex

AI-native modular coding workspace — 128 modules, 600 MCP tools, 21K+ zero-mock tests, multi-agent orchestration (Claude/Gemini/GPT), PAI integration

Python · ⭐ 6

biology_textbook

Open generative biology textbook — Markdown source, tested Python modules, programmatic figures; archived at Zenodo

Python · ⭐ 0

biol-1

BIOL-1: General Biology course materials — College of the Redwoods; lectures, labs, and interactive HTML content

HTML · ⭐ 0

biol-8

BIOL-8: Human Biology course materials — College of the Redwoods; lectures, labs, and interactive HTML content

HTML · ⭐ 0

Learning Path

A compact route through the material.

  • Start with the reproducible generative research template.
  • Use MDKV and Markdown Decision Process for structured document work.
  • Use the Discovery Engine and software catalog for agentic research navigation.

Markdown domain map