MagmaFlow_v10.0.4: MagmaFlow An Integrated Desktop Platform for Differential Expression Interpretation Through AI-Powered Literature Annotation and Pathway Network Analysis
Authors/Creators
Description
MagmaFlow
An Integrated Desktop Platform for Differential Expression Interpretation Through
AI-Powered Literature Annotation and Pathway Network Analysis
Overview
MagmaFlow is a cross-platform desktop application combining interactive volcano plot visualization with automated annotation, integrated literature mining, and pathway-level contextual analysis. The platform retrieves relevant PubMed references, pathway memberships, and disease associations directly within an interactive visualization environment, enabling efficient, reproducible, and publication-ready analysis of transcriptomic datasets.
MagmaFlow transforms volcano plot analysis from static display into dynamic biological interpretation, representing the first tool integrating AI-powered literature contextualization with enrichment analysis to convert differential expression data into actionable insights.
Key Features
Interactive Visualization
| Feature | Description |
|---|---|
| Double-Click Gene Selection | Instantly add/remove target genes by double-clicking data points |
| Drag & Drop Labels | Reposition gene annotations with collision avoidance for publication-ready figures |
| Smart Edge Connections | Five layout modes (Auto, Left, Right, Center, Smart) to reduce overlap |
| Advanced Zoom & Pan | SHIFT+drag panning, mouse wheel zooming, one-click fit-to-viewport |
| Real-time Hover Tooltips | Live gene details displaying name, log₂FC, p-value, and adjusted p-value |
Target Gene Management
| Feature | Description |
|---|---|
| Checkbox Control | Synchronized checkboxes for real-time activation/deactivation of annotations |
| File Import | Load target gene lists from text files |
| Manual Entry | Type or paste gene names with smart parsing |
| Smart Positioning | Auto-prevent label overlaps with intelligent spacing |
Color Systems
| Style | Description |
|---|---|
| Gurzov Classic | Traditional blue/red coloring for down/up-regulated genes |
| MagmaFlow Classic 1 | P-value based gradients |
| MagmaFlow Classic 2 | Log₂ fold change based gradients |
| MagmaFlow Classic 3 | Combined p-value and fold change gradients |
| Viridis & Magma | Perceptually uniform, color-blind-friendly scientific palettes |
| Custom Color Pickers | Direct RGB/Hex color refinement with adjustable outlines and transparency |
Precision Customization
| Feature | Description |
|---|---|
| Independent Font Controls | Separate sizes for title, axes, ticks, and annotations |
| Dynamic Thresholds | Real-time p-value and log₂FC cutoff adjustment |
| Smart Tick Spacing | Auto or manual axis intervals for perfect scaling |
| Advanced Dot Styling | Opacity, outlines, sizes with live preview |
| Publication Export | High-resolution PNG (72–1200 DPI) with scalable off-screen rendering |
Project Workflow
| Feature | Description |
|---|---|
| Smart CSV Import | Automatic detection of standard columns via regular expressions; manual mapping dialog for non-standard headers |
| Complete Project Files | JSON format preserving gene data, thresholds, annotations, label positions, and display preferences |
| Auto-save Tracking | Visual indicators for unsaved changes to prevent data loss |
| Session Persistence | Remember your work across application restarts |
R Integration
| Feature | Description |
|---|---|
| MagmaFlowR Package | Companion R package for integration with DESeq2, edgeR, limma, and Seurat pipelines |
| mag_landragem() | Launch MagmaFlow GUI and preload expression data directly from R environment |
| Repository | github.com/carlosbuss1/magmaflowR |
Literature Mining Module
| Feature | Description |
|---|---|
| PubTator3 Integration | AI-powered named entity recognition across 36 million PubMed abstracts and 6 million PMC full-text articles |
| Dynamic Context Definition | Autocomplete for Disease/Condition (required) and Treatment/Chemical (optional) with validated MeSH identifiers |
| Relation Types Configuration | Positive/negative correlation, stimulation, inhibition, or general association to match expression patterns |
| Dual-API Strategy | PubTator3 Relations API for Total and Context papers; NCBI E-utilities for Recent papers and PMIDs |
| Disease Synonym Expansion | Automatic inclusion of abbreviations and related terms for disease-specific searches |
| Log-Scaled Scoring | Composite score (2×log(1+Total) + 8×log(1+Context) + 5×log(1+Recent) + StatsBonus) preventing highly-studied genes from dominating |
| Clickable PMID Links | Direct access to publications sorted by date (newest first) |
Pathway Enrichment and Circle Plot Visualization
| Feature | Description |
|---|---|
| Enrichr API Integration | Over-Representation Analysis across seven pathway databases |
| Supported Databases | Gene Ontology 2023 (BP, MF, CC), KEGG 2021, Reactome 2022, WikiPathways 2023, MSigDB Hallmark 2025 |
| Species Support | Human, Mouse, and Cow (Bos taurus, GO only) |
| Analysis Modes | All significant genes combined, or separate up/down-regulated analyses |
| Circle Plot Visualization | Multi-layer circular diagrams with pathway enrichment, gene expression, and database annotations |
| Cross-Pathway Detection | Curved lines connecting genes appearing in multiple pathways reveal functional relationships |
| Bidirectional Workflow | Pathway discovery informs gene prioritization; volcano visualization contextualizes shared pathway genes |
All Releases
Visit our Zenodo repository for all versions and additional files.
Note: MagmaFlow is distributed as a pre-built application only. Source code is not publicly available.
System Requirements
| Specification | Minimum | Recommended (>30,000 genes) |
|---|---|---|
| RAM | 4 GB | 8 GB |
| Display | 1280 × 720 | Full HD (1920 × 1080) |
| Platform | macOS, Windows | macOS, Windows |
Installation
| Step | Action |
|---|---|
| 1 | Download the DMG (MacOs) or EXE (windows) file from the link above |
| 2 | Open the DMG and drag MagmaFlow to Applications for Mac. Doble-click in EXE in Windows system. |
| 3 | Launch MagmaFlow from Applications folder |
Technical Implementation
| Component | Technology |
|---|---|
| Framework | JavaFX 17.0.2 |
| Compiler | JDK 17 (LTS) |
| Architecture | Model-View-Controller (MVC) |
| Rendering | JavaFX Canvas API with GPU-accelerated GraphicsContext |
| Precision | Double-precision floating-point arithmetic |
External API Integration
| API | Purpose | Endpoint |
|---|---|---|
| PubTator3 | AI-powered named entity recognition | https://www.ncbi.nlm.nih.gov/research/pubtator3-api |
| NCBI E-utilities | Date-filtered publication queries | https://eutils.ncbi.nlm.nih.gov/entrez/eutils/ |
| Enrichr | Over-Representation Analysis | https://maayanlab.cloud/Enrichr/ |
License
MagmaFlow Academic Binary – End-User License Agreement (EULA)
Version Jan-2026
By downloading, installing, or using the MagmaFlow executable (the "Software") you ("Licensee") agree to the terms of this EULA with the Université libre de Bruxelles, Avenue F. Roosevelt 50, B-1050 Brussels, Belgium ("ULB"), which owns all intellectual-property rights in the Software.
Definitions
| Term | Definition |
|---|---|
| Executable / Software | The compiled distribution of MagmaFlow (DMG, MSI, JAR or similar) provided by ULB |
| Academic Use | Use by accredited higher-education or publicly funded research bodies, for teaching, research, or other not-for-profit scholarly purposes |
| Non-Commercial | Any activity not primarily intended for commercial gain and not carried out for the benefit of a for-profit entity |
License Grant
Subject to this EULA, ULB grants Licensee a non-exclusive, non-transferable, royalty-free licence to download, install, and run the Software solely for Academic and Non-Commercial purposes. No right to sublicense is granted.
Restrictions
Licensee shall not:
- Use the Software for any Commercial purpose without prior written consent from ULB
- Modify, adapt, translate, or create derivative works of the Software
- Reverse-engineer, decompile, or disassemble the Software except as permitted by applicable law
- Offer the Software to third parties as a hosted or cloud service (SaaS) or otherwise provide remote access
- Publish the Software or this EULA on public repositories, websites, or mirrors
Warranty Disclaimer
ULB provides the Software "as is" and disclaims all warranties, express or implied, including the warranties of merchantability, fitness for a particular purpose, and non-infringement.
Governing Law
This EULA is governed by Belgian law. Any dispute arising under it shall be submitted to the exclusive jurisdiction of the courts of Brussels.
For Commercial licensing inquiries: carlos.eduardo.buss@ulb.be
Citation
If you use MagmaFlow in your research, please cite:
Buss, C. E. (2026). MagmaFlow_v10.0.4: MagmaFlow An Integrated Desktop Platform for Differential Expression Interpretation Through AI-Powered Literature Annotation and Pathway Network Analysis (v10.0.4). Zenodo. https://doi.org/10.5281/zenodo.18380556
Contact
| Purpose | Contact |
|---|---|
| Questions & Bug Reports | Open an issue on GitHub |
| Commercial Licensing | carlos.eduardo.buss@ulb.be |
Files
Files
(109.4 MB)
| Name | Size | Download all |
|---|---|---|
|
md5:8f75afe41779f4c5cb1eb350523ab368
|
66.0 MB | Download |
|
md5:2ce8cbbc89a4b450a625a63036e20499
|
43.3 MB | Download |
Additional details
Software
- Repository URL
- https://github.com/carlosbuss1/MagmaFlow
- Programming language
- Java