MagmaFlow_v10.0.3: Interactive Volcano Plot Application

MagmaFlow: Interactive Volcano Plot Application (v10.0.1)

MagmaFlow is a **JavaFX-based scientific visualization tool** for creating **publication-ready volcano plots**.
It enables researchers to **explore, annotate, and export** differential expression results interactively, ensuring high-quality figures for papers, presentations, and data exploration.

---

Features

- Interactive volcano plot exploration
- Drag-and-drop and double-click gene annotation with labels
- Customizable thresholds (log2FC, p-value, adjusted p-value)
- Export-ready plots (PNG, SVG, PDF)
- Persistent project save/load (JSON format)
- Publication-quality styling with white backgrounds and clean legends
- Cross-platform (Windows, macOS, Linux)

---

Installation

Download

The latest release is available here:
https://github.com/carlosbuss1/MagmaFlow/releases/tag/magmaflow

macOS

1.  Download the `.dmg` by zenodo
2.  Open the downloaded `.dmg` file and drag the **MagmaFlow** icon into your **Applications** folder.
3.  Try launching the app. If macOS blocks it:
    *   Go to **System Settings** → **Privacy & Security** → **Security**
    *   Scroll down to **"Allow accessories to connect"**
    *   Click **"Allow"** to approve MagmaFlow
    *   Then re-open the app
    > *This step is needed because macOS sometimes restricts apps from unidentified developers.*

---

Usage

*   No pre-manipulation of data is required. You can use the direct output from your DEA (RNA-seq, proteomics, or phosphoproteomics).
*   Import your results (CSV/TSV).
*   The app automatically recognizes the required columns:
    *   `Gene`
    *   `log2FC`
    *   `p-value`
    *   `adj-pvalue` (optional but recommended)
*   Adjust thresholds for log2 fold-change and p-value.
*   Explore interactively: click on points to annotate genes.
*   Export figures for your manuscript.

**Example input format:**

| Gene    | log2FC | p-value | adj-pvalue |
| :------ | :----: | :-----: | :--------: |
| PTPRF   |  1.2   |  0.004  |   0.007    |
| PTPN12  |  -0.8  |  0.012  |   0.025    |

---

Citation

If you use MagmaFlow in your research, please cite:

> Carlos Eduardo Buss. MagmaFlow: Interactive Volcano Plot Application. Signal Transduction and Metabolism Laboratory (STML), Free University of Brussels (ULB). DOI: 10.5281/zenodo.17011630

A `CITATION.cff` file is included for GitHub’s citation support.

---

License

MagmaFlow – Academic Binary License

Copyright (c) 2025 Carlos Buss

Permission is hereby granted to download, install, and use the MagmaFlow 
executable (DMG, MSI, JAR, or other compiled distributions) for academic 
and research purposes only, provided that all publications or presentations 
resulting from its use include an appropriate citation of the authors and DOI.

You may:
- Use the executable for academic and research purposes.
- Share the unmodified executable with colleagues for non-commercial use.

You may not:
- Use the executable for commercial purposes without prior written permission.
- Reverse engineer, decompile, or modify the executable.
- Redistribute modified versions or integrate into other applications.

Citation:
Academic use requires citation of the following DOI:10.5281/zenodo.17107683

Disclaimer:
This software is provided “as is,” without warranty of any kind, express 
or implied, including but not limited to the warranties of merchantability, 
fitness for a particular purpose, and noninfringement.

---

Author

Carlos Eduardo Buss
Senior Bioinformatician, Signal Transduction and Metabolism Laboratory (STML),  
Free University of Brussels (ULB)  
📧 [carlos.eduardo.buss@ulb.be](mailto:carlos.eduardo.buss@ulb.be)