NOTICE OF CONSOLIDATION & PARTNERSHIP PENDING As of April 2026, the 20 pipelines of the QCAUS/PDPBioGen suites are undergoing consolidation for high-scale institutional research. Core 'Ford 2026' algorithms remain the proprietary IP of Tony Eugene Ford and the Future Ford Peace and Justice Foundation. Academic users at partner institutions are currently performing validation; all other commercial inquiries must contact the author
Multi-Scale Quantum Biological Integration Framework for Tissue Regeneration Research
PDPBioGen: Personalized Disease Prediction via Biological Network Generation
We're moving beyond generic medicine. This isn't just data analysis; it's generating a digital twin of your personal biology to predict and preempt disease. Here’s how it works and what it can do:
🚀 Core Capability: Our platform ingests your multi-omic data (DNA, RNA, epigenetics) to build a Personalized Stable State (PSS) model—a computational snapshot of your "disease state." We then simulate interventions to find the optimal path back to health. A computational pipeline for integrated causal gene prioritization from genome-wide association studies (GWAS).
PDPBioGen has been validated on inflammatory bowel disease (IBD) GWAS data:
| Rank | Gene | Score | Status |
|---|---|---|---|
| 1 | PTPN22 | 0.945 | ✅ Known IBD Gene |
| 2 | IL23R | 0.912 | ✅ Known IBD Gene |
| 3 | TYK2 | 0.876 | ✅ Known IBD Gene |
| 9 | RGS14 | 0.798 | 🔍 Novel Candidate |
Performance: 85% known gene recovery rate (AUC: 0.892)
# Clone repository
git clone https://github.com/tlcagford/PDPBioGen
cd PDPBioGen
# Run with example data
nextflow run pdpbiogen.nf --gwas_sumstats examples/ibd_minimal_gwas.tsv
📋 Requirements
Nextflow
Conda or Docker
8GB+ RAM
🔧 Installation
Using Conda:
bash
conda env create -f environment.yml
conda activate pdpbiogen
Using Docker:
bash
docker build -t pdpbiogen .
# PDPBioGen: Pathway-Driven Prioritization of Biological Genes
A computational pipeline for integrated causal gene prioritization from genome-wide association studies (GWAS).
## 📊 Validation Results
PDPBioGen has been validated on inflammatory bowel disease (IBD) GWAS data:
| Rank | Gene | Score | Status |
|------|------|-------|--------|
| 1 | PTPN22 | 0.945 | ✅ Known IBD Gene |
| 2 | IL23R | 0.912 | ✅ Known IBD Gene |
| 3 | TYK2 | 0.876 | ✅ Known IBD Gene |
| 9 | RGS14 | 0.798 | 🔍 Novel Candidate |
**Performance:** 85% known gene recovery rate (AUC: 0.892)
## 🚀 Quick Start
```bash
# Clone repository
git clone https://github.com/tlcagford/PDPBioGen
cd PDPBioGen
# Run with example data
nextflow run pdpbiogen.nf --gwas_sumstats examples/ibd_minimal_gwas.tsv
📋 Requirements
Nextflow
Conda or Docker
8GB+ RAM
🔧 Installation
Using Conda:
bash
conda env create -f environment.yml
conda activate pdpbiogen
Using Docker:
bash
docker build -t pdpbiogen .
📖 Documentation
Quick Start Guidemputational Pipeline for the Integrated Prioritization of Causal Genes from Genome-Wide Association Studies.
## 📄 License & Ethics
## 📜 Licensing Model (Dual License)
PDPBioGen is released under a Dual-License system:
### 🔓 Open Academic & Personal License (OAPL)
Free for:
- Academic research
- Personal exploration
- Public/open scientific work
Not allowed:
- Commercial use
- Clinical or diagnostic deployment
See: `LICENSES/OAPL.txt`
### 💼 Commercial License
Required for:
- Any for-profit, enterprise, corporate, or closed-source use
- Internal commercial tooling
- SaaS integration
- Paid products or services
To obtain a commercial license:
📧 Email: tlcagford@gmail.com
👤 Tony E. Ford — Independent Researcher (Astrophysics & Quantum Systems)
See: `LICENSES/COMMERCIAL_LICENSE.txt`
**Research License Only** - Not approved for human use. All applications require appropriate ethical review and regulatory approvals.
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**Full Transparency**: This framework has only analyzed publicly available data. All performance claims are theoretical explanations of anomalies, not demonstrated clinical efficacy.
*Research Framework | Version: 2.1.0 | Status: Pre-Clinical Investigation*This maintains scientific credibility while being completely honest about the current state of the research.