# AGENTS.md — A template/ approach to Reproducible Generative Research

**Paper**: A template/ approach to Reproducible Generative Research: Architecture and Ergonomics from Configuration through Publication (2026)
**Area**: Computational, Reproducible Research, Open Science
**Authors**: Daniel Ari Friedman

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## Agent Roles

### 📖 Research Agent
**Focus**: Deep analysis of reproducible research infrastructure and build pipeline design
**Tasks**:
- Analyze core argument: Infrastructure as Code applied to the research lifecycle creates deterministically buildable, independently verifiable research artifacts
- Evaluate: Two-Layer Architecture separating infrastructure from project workspaces
- Evaluate: Zero-Mock testing policy enforcing real operations over mocks
- Evaluate: Documentation Duality standard (README.md + AGENTS.md + SKILL.md)

### 🔬 Methods Agent
**Focus**: Methodological rigor and pipeline verification
**Tasks**:
- Assess and document: Eight-stage build pipeline architecture
- Assess and document: SHA-256 cryptographic hashing with steganographic watermarking
- Assess and document: Coverage enforcement (90% project / 60% infrastructure)
- Assess and document: Comparative analysis against 9 peer tools across 14 dimensions

### 📚 Citation Agent
**Focus**: Citation context and scholarly impact
**Tasks**:
- Track citations and downstream adoptions of the template/ framework
- Map connections to related reproducibility literature (Snakemake, Nextflow, CWL, Quarto, DVC)
- Identify citing papers and community adoption patterns

### 🔗 Synthesis Agent
**Focus**: Cross-paper and cross-domain connections
**Tasks**:
- Connect themes: reproducible research, Infrastructure as Code, AI-agent documentation, Model Context Protocol
- Link to related works in the docxology corpus (GNN, CEREBRUM, MDKV, ActiveInferAnts)
- Identify synergies with Active Inference, cognitive security, and computational frameworks

### 💼 Consultant Agent
**Focus**: Practical application and knowledge transfer
**Tasks**:
- Evaluates practical adoption strategies for research groups and institutions
- Maps the template/ framework to industry CI/CD and DevOps workflows
- Facilitates knowledge transfer for open-source research infrastructure

## Extraction Log

- **Source PDF**: `template_daf_v1_03202026.pdf` (1,153,790 bytes)
- **PDF Status**: ✅ Available
- **Documentation Quality**: Curated from Zenodo metadata and user-provided abstract
- **DOI**: [10.5281/zenodo.20669283](https://doi.org/10.5281/zenodo.20669283)

## Related Papers

- [GNN](../2023_GNN/) — Generalized Notation Notation for Active Inference models
- [CEREBRUM](../2025_CEREBRUM/) — Case-Enabled Reasoning Engine with Bayesian Representations
- [MDKV](../2025_MDKV/) — Multitrack Markdown Container for Structured Documents

See [BIBLIOGRAPHY.md](../../pages/BIBLIOGRAPHY.md) for the full publication catalog.