Describe Visualizations with Vega
Author declarative Vega visualization specifications for simulation results, or automatically convert pathway maps and network diagrams (Escher, GINsim, SBGN) into interactive, publication-ready figures packaged directly within COMBINE/OMEX archives.
Declarative Visualization via Vega
Interactive, publication-quality graphics driven directly by simulation datasets
BioSimulations standardizes on Vega, a declarative visualization grammar in JSON syntax. Rather than bundling static bitmap charts (PNG, JPEG), Vega allows modelers to articulate visual mappings, scales, axes, legends, and multi-view interactive dashboards.
Vega datasets dynamically reference SED-ML report tasks and HDF5 output streams using URI dataset identifiers.
Save as *.vg.json inside the COMBINE archive and register with format URI combine.specifications/vega.
Supports pan, zoom, dynamic tooltips, coordinate crosshairs, and multi-series brushing natively in the browser.
biosimulators-utils CLI
Automated command-line conversion & COMBINE archive packaging
Install the BioSimulators utilities package with diagram visualization and conversion dependencies.
pip install biosimulators-utils[visualizations]Diagram & Network Format Converters
Convert existing biological pathway layouts and regulatory networks directly into Vega figures
Escher Metabolic Pathways
Flux Balance Analysis (FBA) visualization
Escher is the community standard for building metabolic pathway maps. BioSimulators utilities convert Escher JSON pathway layouts into Vega specifications.
Simulation flux distributions calculated via FBA, pFBA, or flux variability analysis (FVA) can be projected onto metabolic reaction arrows (scaling width, color temperature, and hover labels).
GINsim Logical Networks
Qualitative gene & signaling networks
GINsim (Gene Interaction Network simulation) specifies discrete logical and multi-valued regulatory networks.
Converts .ginml files into interactive node-link Vega network diagrams. Node activation states, inhibitory interactions, and discrete state transitions are reflected dynamically as simulations execute.
SBGN Process Diagrams
Standard biological process notation
The Systems Biology Graphical Notation (SBGN) provides standardized graphical languages for biochemistry.
Converts SBGN-ML Process Description (PD) and Activity Flow (AF) maps into vector Vega glyphs. Kinetic concentration trajectories and state variables are dynamically bound to species glyphs and transition nodes.
Best Practices for COMBINE/OMEX Visualization Packaging
When authoring custom Vega visualizations, ensure that the "data" blocks in your Vega specification declare names that match the SED-ML report tasks (e.g. report_1). Register the file in your archive manifest as http://identifiers.org/combine.specifications/vega to enable automatic rendering in the BioSimulations experiment dashboard.