KANNA Project: Sceletium tortuosum Interdisciplinary Thesis

PhD Thesis: Interdisciplinary Analysis of Sceletium tortuosum - From Khoisan Traditional Knowledge to Modern Neuropharmacology

📚 Documentation Navigation: See Documentation Index for complete documentation organization

🚀 Quick Start: For quick setup and basic usage, see Quick Start Guide

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Project Overview

This repository contains all research materials, data, analysis scripts, and writing for a comprehensive interdisciplinary doctoral thesis on Sceletium tortuosum (Kanna), covering:

• Botany & Taxonomy - Phylogenomics, infraspecific structure, biodiversity
• Ethnobotany - Khoisan traditional knowledge, linguistic analysis, cultural transmission
• Phytochemistry - 32+ alkaloids, LC-MS/MS characterization, QSAR modeling
• Pharmacology - SERT/PDE4 mechanisms, molecular docking, ADMET prediction
• Clinical Research - Anxiety, depression, PTSD, addiction applications
• Legal & Ethics - Biopiracy analysis, WIPO Treaty 2024, benefit-sharing frameworks
• Decolonial Studies - Indigenous rights, epistemic justice, collaborative research

Thesis Duration: 42 months (3.5 years) Expected Completion: April 2028 Primary Institution: [To be specified when thesis is submitted]

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📁 Repository Structure

For complete repository structure, see Consolidated Documentation

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🎯 Thesis Structure

For complete thesis chapter overview, see Consolidated Documentation

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🛠️ Technical Stack & Tools

For complete technical stack information, see Consolidated Documentation

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📊 Data Management & Ethics

For complete data management and ethics information, see Consolidated Documentation

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📈 Timeline & Milestones

For current project status and timeline, see Project Status Dashboard

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📝 Usage Instructions

For complete setup and usage instructions, see Consolidated Documentation

🧪 Test Infrastructure Quick Start

The minimal smoke-suite now boots with deterministic fixtures that live under test_data/. Run the following commands from the repository root:

1. make test-infra-smoke – installs the lightweight dependency set and calls scripts/emergency_test_repair.sh --skip-install to rebuild fixtures plus run pytest smoke checks.
2. ./scripts/setup_test_infrastructure.sh – re-runs the same pipeline and prints a manifest of generated artifacts for local verification.
3. Inspect test_data/manifest.json and test_data/README.md to confirm the FAISS index, qrels.json, queries.json, and MinerU samples were refreshed (<160 MB total).

See KANNA_TEST_INFRASTRUCTURE_IMPLEMENTATION_GUIDE.md for detailed validation checkpoints and troubleshooting.

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🚨 Important Reminders

For research ethics, data security, and legal compliance information, see Consolidated Documentation

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📄 License

For licensing information, see original README.md in the root directory.

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Documentation consolidated for clarity and maintainability - last updated October 2025