MagmaFlow v10.0.6 MagmaFlow: A desktop platform for artificial intelligence-driven expression analysis 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. What's New in v10.0.6 Enrichr pathway enrichment databases updated to the latest available versions: Gene Ontology updated to 2026 (GO_Biological_Process_2026, GO_Molecular_Function_2026, GO_Cellular_Component_2026) KEGG confirmed at 2026, WikiPathways at 2024, Reactome at 2024, MSigDB Hallmark at 2020 All database versions aligned with the latest Enrichr library releases as of May 2026 Files in This Release File Platform Architecture Compatibility Signing Status MagmaFlow-MacOsSilicon-arm64-10.0.6.dmg macOS Apple Silicon (arm64) macOS 11 Big Sur or later — M1, M2, M3, M4 chips (2020 and later) Signed and notarized MagmaFlow-MacOs-MacOsIntel-x86_64_10.0.6.dmg macOS Intel (x86_64) All Intel Macs — macOS 10.12 Sierra or later Unsigned (see note below) MagmaFlow-10.0.6_Windows.exe Windows x86_64 Windows 10 (64-bit) or later Unsigned How to Identify Your Mac Go to Apple menu → About This Mac: If Chip shows Apple M1/M2/M3/M4 → your Mac is Apple Silicon (2020 or later) → download the arm64 DMG If Processor shows Intel Core → your Mac is Intel → download the Intel DMG Important Note on the Intel Build The MagmaFlow-MacOs_x86_64_10.0.6.dmg is intentionally distributed without Apple notarization. This is due to a fundamental and unresolvable incompatibility between Apple's notarization requirements and the JVM memory model on Intel Macs running older macOS versions. Apple's notarization process requires the hardened runtime flag, which restricts executable memory allocation. The Java Virtual Machine requires dynamic executable memory mapping for its code cache, a requirement that cannot be disabled without breaking the application. This conflict affects Intel Macs on macOS 10.14 Mojave and earlier, where Apple had not yet updated the memory management model. To maximize compatibility across all Intel Macs regardless of macOS version, we distribute a single unified Intel build without notarization. To open the Intel build when macOS displays a security warning: Right-click the DMG file and select Open Click Open in the security dialog that appears Drag MagmaFlow to your Applications folder and launch normally This is a standard one-time override for trusted third-party software and is fully documented in Apple's official Gatekeeper guidance. Key Features Interactive Volcano Plot Visualization Feature Description Double-Click Gene Selection Instantly add/remove target genes by double-clicking data points Drag and 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 and 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 and 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 https://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 (default: 2020 onwards, customizable) 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 2026 (BP, MF, CC), KEGG 2026, Reactome 2024, WikiPathways 2024, MSigDB Hallmark 2020. Database release versions are explicitly specified in each API call to ensure reproducibility of enrichment results across MagmaFlow versions Species Support Human, Mouse, Zebra fish 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 System Requirements macOS — Apple Silicon (arm64) Chip: Apple M1, M2, M3, or M4 (Mac purchased 2020 or later) macOS 11 Big Sur or later (macOS 13 Ventura or later recommended) 4 GB RAM minimum — 8 GB recommended for datasets >30,000 genes 1280 × 720 display minimum — Full HD recommended macOS — Intel (x86_64) Chip: Intel Core i5, i7, or i9 (64-bit) — any Intel Mac macOS 10.12 Sierra or later 4 GB RAM minimum — 8 GB recommended for datasets >30,000 genes 1280 × 720 display minimum — Full HD recommended Windows Windows 10 (64-bit) or later — Windows 11 recommended 4 GB RAM minimum — 8 GB recommended for datasets >30,000 genes 1280 × 720 display minimum — Full HD recommended Installation macOS — Apple Silicon Download MagmaFlow-MacOs_arm64-10.0.6.dmg Open the DMG and drag MagmaFlow to your Applications folder Launch from Applications — no security prompts expected macOS — Intel Download MagmaFlow-MacOs_x86_64_10.0.6.dmg Right-click the DMG and select Open Click Open in the security dialog Drag MagmaFlow to your Applications folder Launch from Applications Windows Download MagmaFlow-10.0.6_Windows.exe Run the installer and follow the setup wizard Launch from Start Menu or desktop shortcut 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 (default: 2020 onwards, customizable) https://eutils.ncbi.nlm.nih.gov/entrez/eutils/ Enrichr Over-Representation Analysis https://maayanlab.cloud/Enrichr/ License MagmaFlow is distributed under the MagmaFlow Academic Binary End-User License Agreement (EULA v1, October 2025). The binary is freely available for academic and non-commercial use without registration or fee. The source code is maintained as closed-source under the stewardship of the Knowledge and Technology Transfer Office (KTO) of the Université libre de Bruxelles (ULB). Commercial use requires prior written consent from ULB. Commercial licensing inquiries: carlos.eduardo.buss@ulb.be Related Resources GitHub Repository: https://github.com/carlosbuss1/MagmaFlow MagmaFlowR Package: https://github.com/carlosbuss1/magmaflowR Main Publication: Buss CE, Li A, Gilglioni EH, Bansal M, Singh SP, Bakiri L, Cardozo AK, Gurzov EN. MagmaFlow: A desktop platform for artificial intelligence-driven expression analysis. FEBS Open Bio. 2026 Jun 3. doi: 10.1002/2211-5463.70288.