STENCIL

STENCIL provides a web templating framework for aggregating, visualizing, and disseminating experimental bioinformatics and genomics datasets to support interpretation and reproducible sharing.

Key Features:

• Customizable Visualization Templates: Defines templates that render a wide range of experimental outcomes and produce interactive visualizations while preserving fidelity to original data sources.
• REST API-based Programmatic Access: Exposes REST APIs for programmatic data access, sharing, and integration with external analysis environments.
• Galaxy Integration and Data Streaming: Integrates with Galaxy to stream analysis outputs directly into templates and workflow contexts.
• Data Integrity and Reproducibility: Produces downloadable, editable figures that preserve links between visual representations and underlying datasets to support reproducibility.
• Lightweight, Scalable Framework: Implements a lightweight framework demonstrated on over 2,400 distinct datasets from two large genomic initiatives.

Scientific Applications:

• Bioinformatics and Genomics Research: Aggregates and visualizes complex genomic and experimental datasets to aid interpretation.
• Data Dissemination and Reporting: Facilitates sharing of analysis outputs and preservation of dataset–figure relationships for reproducible reporting.
• Workflow Integration: Embeds visualization and dissemination steps into bioinformatics workflows by streaming outputs from platforms such as Galaxy.

Methodology:

Users define templates that dictate visualization rendering; the backend exposes REST APIs and integrates with Galaxy to stream data into those templates.