# EoE pMHC-II Therapeutics Website Deployment Guide

## Quick Start for Netlify Deployment

Your website is ready to deploy to **https://ruthannepai.netlify.app/**

### What's Included

```
eoe_program_website/
├── index.html                           # Main landing page (perturbseq-integrated)
├── reports/
│   ├── EoE_Business_Scientific_Strategy.md    # Full integrated report
│   └── Deliverables_Summary.md               # Quick reference
├── docs/                                 # Supplemental materials (if needed)
└── assets/                               # Images/PDFs (if needed)
```

### Deployment Steps

#### Option 1: Netlify Web Interface (Easiest)

1. Go to https://app.netlify.com/
2. Sign in with your GitHub account
3. Click "Add new site" → "Deploy manually"
4. Drag and drop the `eoe_program_website/` folder (or all contents) into the deploy area
5. Netlify will auto-publish to `ruthannepai.netlify.app`

#### Option 2: Git Deployment (Recommended for Updates)

1. Create a GitHub repository for your EoE project:
   ```bash
   mkdir eoe-phmhc-therapeutics
   cd eoe-phmhc-therapeutics
   git init
   ```

2. Copy the `eoe_program_website/` contents into your repo root:
   ```bash
   cp -r eoe_program_website/* .
   ```

3. Create a `.gitignore`:
   ```
   .DS_Store
   node_modules/
   *.swp
   ```

4. Push to GitHub:
   ```bash
   git add .
   git commit -m "Initial EoE pMHC-II therapeutics program documentation"
   git push origin main
   ```

5. On Netlify:
   - Click "Add new site" → "Import an existing project"
   - Select your GitHub repository
   - Set build command: (leave blank — static site, no build needed)
   - Set publish directory: `.` (root)
   - Deploy!

### What's Updated in This Version

✅ **Perturbseq Integration:**
- SIK3 kinase target (Program B=0.815) added to Path B rationale
- Dual-track commercial strategy: Path A (monotherapy) vs. Path B (combination + SIK3i)
- Phase 1b de-risking experiment: iTreg/Tr1 co-culture with EoE PBMC
- SIK3i partner selection strategy (AstraZeneca, Pfizer, Schrödinger options)

✅ **Budget Consistency:**
- Phase 1 expanded from $20–35k to $40–65k (killer experiments + Phase 1b)
- Total preclinical budget: $275–457k base / $300–500k with 10% contingency
- All sections reconciled and consistent

✅ **Molecular Mechanism Section:**
- New Section 3.2 on perturbseq convergence to LKB1→AMPK/SIK→CREB axis
- Mechanistic rationale for why SIK3 inhibition synergizes with pMHC-II Tr1 induction

### Content Structure

**index.html** (landing page) includes:
- Program overview with perturbseq findings highlighted
- Epitope selection & structural validation data
- Nanoparticle architecture specs
- Dual-track commercial strategy (Path A vs. Path B)
- 5-phase preclinical roadmap with milestones
- IP attribution framework
- About section (citizen scientist context, Built with Claude Hackathon)

**Reports/ (Markdown):**
- Full business & scientific strategy (2.7 KB markdown)
- Deliverables summary with quick reference tables
- Can be viewed on GitHub or converted to PDF via pandoc

### Customization Tips

If you want to customize the site further:

1. **Change colors:** Edit the `<style>` section in `index.html`
   - `#c2185b` = magenta (eosinophilic disease awareness color)
   - `#7b1fa2` = purple (complementary)

2. **Add more pages:** Create additional `.html` or `.md` files in the root or subdirectories

3. **Add images:** Save PNG/PDF files to `assets/` folder; reference in HTML as `assets/filename.png`

4. **PDF conversion:** Convert markdown to PDF:
   ```bash
   pandoc reports/EoE_Business_Scientific_Strategy.md -o EoE_Business_Scientific_Strategy.pdf
   ```

### Netlify Environment Variables (Optional)

If you plan to add Netlify CMS or forms:
- Go to Site settings → Build & deploy → Environment
- Add any variables (not needed for static site)

### Custom Domain (Optional)

To use your own domain instead of `.netlify.app`:
1. In Netlify: Site settings → Domain management
2. Add your custom domain
3. Follow DNS configuration steps provided by Netlify

### Support & Troubleshooting

**Site not updating after push?**
- Check Netlify Deploy log (Site settings → Deploys)
- Clear browser cache (Ctrl+Shift+Delete)

**Links not working?**
- Use relative paths: `reports/filename.md` not `/reports/filename.md`

**Markdown not rendering in browser?**
- Markdown files display as text by default
- Convert to HTML or use a markdown viewer plugin
- Or share the raw markdown links to GitHub

### Next Steps

1. **Deploy to Netlify** (any option above)
2. **Share the link** (https://ruthannepai.netlify.app/) with potential biotech partners
3. **Consider adding:**
   - Interactive figures (if figures exist, upload to `assets/`)
   - Contact form (Netlify Forms)
   - Video clips (if biotech pitch videos created, embed in new page)
   - CV / about page link

---

**Questions?** Reference Netlify docs: https://docs.netlify.com/