CheckerBoardR.shiny (v2.0.0)

Modernized Shiny Webportal for Multi-Model Drug Combination Synergy & Antagonism Analysis

CheckerBoardR.shiny is a high-performance, premium web portal and modeling platform designed to perform drug combination synergy, antagonism, and dose-response curve fitting. It supports relative cell viability normalization, percent inhibition mapping, and robust mathematical synergy models.

Online Portal: http://chemgrid.org:3838/checkerboardr/

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🚀 Key Features in v2.0.0

1. Unified Synergy Modeling Engine

• 4-Parameter Logistic (4PL) Hill Curves: Fits dose-response levels natively, computing $EC_{50}$, Slope (Hill coefficient), $E_{max}$, and $E_{min}$ using R's numeric optimization.
• Synergy Models: Computes Highest Single Agent (HSA), Bliss Independence, Loewe Additivity, and Zero Interaction Potency (ZIP) synergy landscapes.
• Monotonic Linear Interpolation: Fallback routines guarantee calculation completion even under highly noisy or partial data fits.

2. Premium Publication-Quality Visualization Layouts

• 3D Interactive Plotly Surface: Features dynamic 3D camera controls (Rotation/Azimuth, Elevation, Zoom/Distance) to allow researchers to view and export figures at identical angles.
• 2D ggplot Heatmap: A beautifully formatted, contoured grid heatmap with exact text score annotations and clear legends.
• 1D Single-Agent Fit Curves: Side-by-side dose-response curve fits for quick visual inspection.
• Classic 3D persp Fallback (Base R): Uses your publication-ready Blue-Green-Yellow gradient color scheme, automatically matching the chosen theme.
• Style Guide Presets: Integrates Nature (Classic Grey/Arial), Science (High-Contrast White/Helvetica), The Economist (Sleek Blue/Trebuchet MS), and Financial Times (Warm Salmon/Georgia) style templates.

3. Axis Flips & Bliss Valley Perspective Toggles

• Interactive checkboxes let you flip the X-axis (Drug A), Y-axis (Drug B), or Z-axis (Invert score heights).
• Enables researchers to seamlessly "look into the Bliss inhibition valleys".
• Absolute Formatting: Negated metrics remain mathematically correct, but their tooltip hovers, tick values, and legend ranges dynamically absolute-format as positive numbers to maintain high visual clarity.

4. Click-to-Load Sample Data Expansion & Paste Auto-Detect

• Click-to-load samples for JSON Chemotherapy Grids, XML Antifungal Grids, Excel spreadsheets (.xlsx), and Delimited CSV/TAB formats.
• Includes a pasted text area with an intelligent auto-detector that decodes XML or JSON payloads dynamically and updates GUI input choices automatically.

5. Stdio Python MCP Server

• Integrated checkerboardr_mcp_server.py, allowing LLM coding assistants to perform calculations, compute scores, and generate publication-ready plots programmatically.

6. Docker Containerization

• Ships with a pre-configured Dockerfile to build and deploy the R Shiny application in any containerized environment instantly.

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📦 Getting Started & Docker Deployment

To build and run the entire CheckerBoardR portal locally inside a container:

# Build the Docker image
docker build -t checkerboardr .

# Run the container (exposes R Shiny on port 3839)
docker run -p 3839:3839 checkerboardr

Access the app in your browser at http://localhost:3839.

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🛠 Contributing

1. Fork it!
2. Create your feature branch: git checkout -b my-new-feature
3. Commit your changes: git commit -am 'Add some feature'
4. Push to the branch: git push origin my-new-feature
5. Submit a pull request :D