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@Mythmaker28 Mythmaker28 released this 23 Oct 00:13
· 11 commits to main since this release
v1.1
9bb0c73

Molecular Arrest Framework v1.1.0

DOI

First public release of the Molecular Arrest Framework - A unifying theoretical framework for natural compounds with dampening effects on biological regulation.

📦 What's in this Release

Core Scientific Content

  • Manuscript (v6) - Complete theoretical framework with IMRAD structure (1,943 lines)
  • Structured data package - FAIR² compliant research data
  • 10 paradigmatic compounds - Spanning arrest-oscillation continuum
    • 6 core arrest agents (Salvinorin A, Paclitaxel, Rapamycin, Capsaicin, Tetrodotoxin, Resveratrol)
    • 4 continuum compounds (Ibogaine, Noribogaine, Psilocybin, LSD)

Metrics & Calculations

  • API (Arrest Potency Index) - Quantitative framework for arrest potency
  • EMC (Entropy Modulation Coefficient) - Neural complexity metric
  • NCR (Network Connectivity Reduction) - Brain network impact
  • PARI (Post-Arrest Resilience Index) - Hormetic benefit quantification
  • Monte Carlo uncertainty quantification - Full Python implementation with reproducible seed

Data Package (FAIR² Compliant)

  • Compound_Properties_Database.csv - 10 compounds × 36 parameters with PubMed sources
  • Confidence_Grading_Matrix.csv - 44 quantitative predictions stratified by evidence level
  • API_Calculations_Full.xlsx - Step-by-step calculations with Monte Carlo simulations
  • Experimental_Protocols_Summary.csv - 3 validation experiments with power calculations
  • Case_Studies_Supplement.md - 5 extended case studies

Code & Reproducibility

  • Python_Code_API_Monte_Carlo.py - Fully documented script (MIT License)
    • Fixed seed=42 by default for reproducibility
    • Option for independence tests with variable seeds
    • 10,000 Monte Carlo iterations per compound
  • R_Code_Figures_S2.R - Publication-quality figure generation
  • requirements.txt - Explicit Python dependencies with versions
  • test_api_calculations.py - Unit tests for API calculations

Documentation

  • Data_Dictionary.md - Complete variable definitions, units, quality control
  • Literature_Search_Strategy.md - PRISMA-compliant search protocol (95+ sources)
  • README.md - Comprehensive usage guide with quick start
  • CONTRIBUTING.md - Contribution guidelines
  • CODE_OF_CONDUCT.md - Community standards

Supplementary Materials

  • Figures_Supplementaires.txt - Specifications for Figures S1-S3
  • v6.txt - Full manuscript in structured text format
  • Figure drafts (S1: Molecular Structures, S2: Oscillatory Advantage, S3: API Flowchart)

🔬 Scientific Highlights

Novel Framework

  • First unifying theory for molecular arrest across biological scales
  • Explicit falsifiability - 44 testable predictions with confidence grading
  • Quantitative metrics for dampening vs. oscillatory effects
  • 3 proposed validation experiments with full protocols

Data Quality

  • 95+ primary sources from peer-reviewed literature
  • All parameters traceable to PubMed IDs
  • Confidence stratification - High (41%), Moderate (30%), Low (30%)
  • Monte Carlo uncertainty - 95% confidence intervals for all APIs

Reproducibility

  • ✅ Fixed random seed (seed=42) for exact replication
  • ✅ Explicit software versions (Python 3.8+, R 4.0+)
  • ✅ Public databases only (DrugBank 5.1.10, ChEMBL v31, PubChem)
  • ✅ Step-by-step calculation documentation

📊 Key Statistics

Metric Value
Compounds characterized 10
Molecular parameters 36 per compound
Quantitative predictions 44
Literature sources 95+ (PubMed)
Code lines (Python) 562
Monte Carlo iterations 10,000 per compound
Confidence intervals 95% for all metrics

🚀 Quick Start

Installation

git clone https://github.com/Mythmaker28/arrest-molecules.git
cd arrest-molecules
pip install -r Data_Package_FAIR2/requirements.txt

Run API Calculations

cd Data_Package_FAIR2
python Python_Code_API_Monte_Carlo.py --all
# Outputs: API values with 95% CI for all compounds

Verify Predictions

python test_api_calculations.py
# Tests: API formula, Monte Carlo convergence, data integrity

📖 How to Cite

For the Dataset

Lepesteur T. (2025). Molecular Arrest Framework Research Data Package (v1.1.0) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.XXXXXXX

For the Framework

Lepesteur T. (2025). Molecular Arrest in Biological Regulation: A Unifying Framework for Natural Compounds with Dampening Effects. Manuscript in preparation.

For the Code

Lepesteur T. (2025). molecular-arrest-framework: API calculation tools (v1.1.0). GitHub. https://github.com/Mythmaker28/arrest-molecules

📜 License

  • Data & Documentation: CC-BY 4.0 (free to share and adapt with attribution)
  • Code: MIT License (free to use commercially and non-commercially)
  • Synthesis protocols: Controlled access (requires IRB approval, see README)

🔮 Known Items & Future Work

Pending for Next Release

  • ORCID registration confirmed (currently provisional)
  • Publication-quality figures finalized (post-journal acceptance)
  • Experimental validation data (Experiments 1-3 proposed)

Planned Updates

  • v1.2: Add salvinorin A analogs (8 compounds from literature)
  • v2.0: Integrate Experiment 1 results (fMRI entropy validation)
  • v2.1: Integrate Experiment 2 results (oscillatory cellular lifespan)
  • v3.0: Clinical validation from Experiment 3 (TRD trial)

🤝 Contributing

We welcome contributions! Please see CONTRIBUTING.md for guidelines.

Accepted contributions:

  • Novel compound additions (requires literature PMIDs)
  • Bug fixes with tests
  • Documentation improvements
  • Experimental validation data

Major changes require discussion - Open an issue before submitting PRs for:

  • Metric modifications (API, EMC, NCR, PARI)
  • Threshold changes (Level 1/2/3 criteria)
  • New dependencies

📞 Contact & Support

Response time: 7 business days

🙏 Acknowledgments

  • Independent data verification: Dr. Marie Legrand, PharmD (Université de Rennes)
  • Database access: DrugBank, PubChem, ChEMBL (public versions)
  • Community: Open science advocates and reviewers

⚠️ Responsible Research Notice

This framework includes discussion of:

  • Schedule I controlled substances (research context only)
  • Dual-use compounds (synthesis protocols under controlled access)
  • Experimental protocols requiring IRB/DEA approval

All use must comply with local regulations. See Section 4.4.5 of manuscript for dual-use considerations and mitigation strategies.

📋 Changelog (v1.1.0)

Added

  • 4 new compounds (Ibogaine, Noribogaine, Psilocybin, LSD)
  • Case Studies Supplement (5 detailed studies)
  • Extended predictions (42 → 44 total)
  • requirements.txt with explicit versions
  • Harmonized documentation (95+ sources)

Changed

  • Dataset: 6 → 10 compounds (+67%)
  • Version numbering harmonized to v1.1.0
  • GitHub URLs canonicalized (Mythmaker28/arrest-molecules)
  • Enhanced literature search strategy

Fixed

  • Prediction count consistency (now 44 everywhere)
  • Compound count consistency (now 10 everywhere)
  • Version consistency across all files
  • Contact information harmonized

Release Date: October 22, 2025
Maintainer: Tommy Lepesteur
License: CC-BY 4.0 (data) + MIT (code)
Zenodo Archive: Automatic upon release publication

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