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Roadmap

Big Picture

Visualization Studio

Phase 1: Foundation ✅

Interactive dashboards with modern web components and real-time data binding

Data Ingestion

Phase 1: Foundation ✅

Multiple tabular formats with Delta Lake storage and data provenance

MultiQC Integration

Phase 2: Specialized Components ✅

Seamless integration with bioinformatics quality control reports

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Image Grid Component

Phase 2: Specialized Components ✅

S3-backed image galleries with configurable thumbnails and grid layout

Geospatial Map Component

Phase 2: Specialized Components ✅

Scatter, density, and choropleth maps with cross-filtering and GeoJSON / Map-capable Table DCs (v0.12.0)

Advanced Biology Visualizations

Phase 2: Specialized Components 🔄

Omics plots extending the v0.12 DC-level type-config pattern — Volcano, Manhattan, Sunburst, and more

Templates & Community

Phase 3: Templates ✅

Reusable dashboard templates for standard bioinformatics workflows, nf-core integration, and nf-core plugin for automatic data ingestion

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React (Beta) Viewer

Phase 3.5: UI Modernization 🔄

Vite + Mantine SPA rewrite — ships in Beta at /*-beta routes in v0.12.0, graduates onto canonical URLs in v0.15.0 when the legacy Dash frontend is removed

Citable Science

Phase 4: Reproducibility 📋

DOI-backed snapshots and sample-to-viz provenance on top of the existing Serve hosting

AI & Intelligence

Phase 5: Intelligence 📋

Smart dashboard creation & AI-assisted analysis

Reproducibility & FAIR

Built with FAIR principles in mind. v0.12 ships YAML-defined dashboards, Cross-DC linking, nf-core/ampliseq templates, and hosting via SciLifeLab Serve ✅. Citable DOI snapshots, persistent IDs, and data lineage land in Phase 4.

Challenge Status
Reproducibility requires setup nf-core/ampliseq templates shipped (docs); nf-core plugin planned
Can't reproduce visualizations YAML-defined dashboards + traceable data (docs)
Siloed experiment data Cross-DC linking (docs)
Dashboards disappear Hosted on SciLifeLab Serve (changelog)
Not citable / no sample-to-viz traceability Phase 4 — DOI snapshots via SciLifeLab Serve + LabID provenance
No data lineage Phase 4 — Delta Lake time travel, auditing

Current Features

Data Ingestion

  • YAML-based data ingestion via CLI (docs)
  • Polars-compatible formats (Parquet, CSV, JSON, TSV) → Delta Lake
  • S3/MinIO storage with backup/restore commands (docs)
  • MultiQC report integration (docs | #626)
  • MultiQC data lifecycle — append / replace / clear runs from the viewer with uniformity validation (v0.12.0, docs)
  • DC-level type configuration — Map-capable Table DCs (lat/lon column detection on upload, DCTableCoordinatesConfig); extensible to advanced-viz types (v0.12.0, docs)
  • Client-side table joining in CLI ( #634)
  • Recipe-based data transformation — Python recipes with 4-checkpoint validation (docs)
  • Template-based project setup — one-command project creation with {DATA_ROOT} substitution (docs)

Dashboard Components

Specialized components share a common pattern: a DC-level type-config (introduced for Map in v0.12.0) declares the columns that drive the visualization, so every figure built on top inherits the config — no per-figure boilerplate. Advanced biology visualizations extend the same pattern.

  • Generic components: Figure, Table, Card, Interactive (docs)
  • MultiQC components for QC reports (docs)
  • Image grid with S3/MinIO integration and configurable thumbnails ( #664)
  • Geospatial map component: scatter, density, choropleth with GeoJSON DC support + Map-capable Table DCs (v0.12.0, docs)
  • Figure code mode with live preview ( #639)

Dashboard Interactivity

  • Two-panel layout with tabs ( #616)
  • Cross-DC filtering via universal linking (docs)
  • Cross-DC links UI — Create / Edit / Delete links from the React Beta viewer with resolver picker and sample-mapping preview (v0.12.0, docs)
  • Interactive selection filtering: scatter/table/map selections
  • YAML dashboard import/export (docs)

Infrastructure

  • Docker + Kubernetes with Helm charts (docs)
  • SciLifeLab Serve hosting via values-serve.yaml overlay (changelog)
  • Celery/Redis background processing
  • Authentication: local, Google OAuth, unauthenticated mode

Frontend

  • React (Beta) viewer — Vite + Mantine SPA shipped at /*-beta routes (v0.12.0); graduates onto canonical URLs in v0.15.0
  • Multi-app architecture (Management, Viewer, Editor) — Dash, legacy; removal in v0.15.0

Planned Features

Phase 3: Templates & Community

Reusable dashboards for standard bioinformatics workflows, with a focus on nf-core community adoption.

Infrastructure (shipped)

  • Depictio templates system — one-command project setup via depictio run --template, with {DATA_ROOT} substitution, template provenance tracking, and automatic dashboard import (docs)
  • Recipe-based data transformation — versioned Python recipes with 4-checkpoint validation, co-located with templates (docs)

Shipped templates — peer-reviewed by developers, ready to use

Template Pipeline Versions Recipes
nf-core/ampliseq 16S/ITS amplicon sequencing 2.14.0, 2.16.0 Alpha diversity, rarefaction, taxonomy composition, relative abundance, differential abundance (ANCOM-BC)

Planned

  • nf-core plugin — automatically registers nf-core pipeline outputs in Depictio at run time, no manual CLI step required
  • nextflow.config template — embed Depictio ingestion directly in your Nextflow config so data collection happens at pipeline runtime
  • Snakemake report plugin — Depictio as a drop-in replacement for Snakemake's built-in HTML report, with interactive dashboards instead of static outputs

Phase 3.5: React (Beta) viewer graduation — v0.15.0

The React (Beta) viewer ships in v0.12.0 alongside Dash; in v0.15.0 it takes over the canonical URLs and the Dash frontend is removed. Track contribution paths in Contributing → Frontend Guidelines.

  • React (Beta) viewer shipped under /*-beta paths (v0.12.0) — /dashboards-beta, /dashboard-beta/{id}, /dashboard-beta-edit/{id}, /projects-beta, /projects-beta/{id}, /profile-beta, /admin-beta, /cli-agents-beta, /about-beta
  • URL graduation (v0.15.0) — React Beta takes over /dashboards, /dashboard/{id}, /dashboard-edit/{id}, /projects and the legacy Dash frontend is removed
  • Component parity audit — every Dash editor feature has a React equivalent before cutover

Phase 4: Citable Science

DOI-backed citability and sample-to-viz provenance on top of the existing SciLifeLab Serve hosting.

  • DOI snapshots — persistent stable URLs per dashboard version, citable in publications
  • Sample-to-viz provenance — LabID linking sample → pipeline run → Delta table → visualization
  • Static export — Quarto for publication supplements

Phase 5: AI & Intelligence (12+ months)

  • Smart dashboard creation — describe the analysis you need; AI proposes a layout and component configuration
  • AI-assisted analysis — automated anomaly detection, visualization recommendations, and plain-language report narration
  • MCP server — expose Depictio as a tool for AI agents to create dashboards, query data, and manage projects programmatically

Visualization Modules

  • Reusable chart configurations catalog
  • High-dimensional methods (UMAP, PCA, t-SNE)
  • JBrowse2 genome browser component
  • Advanced biology visualizations — Volcano, Manhattan, Sunburst, and more (see the Advanced Biology Visualizations tile in the timeline)

UI & Components

  • Markdown component for documentation
  • Extended interactive components (radio buttons, improved sliders, …)
  • Project creation wizard with workflow selection