Gallery

Here we showcase some of the principal visualization capabilities of SBMLNetwork: SBGN-style rendering, style template application, reaction alignment & layout refinement, and simulation data overlays.

Note

All visualization data (Layout + Render) are embedded directly inside the distributed SBML files and the link to those files is provided for each example.

Contents

SBGN-Compliant Network

SBGN-Compliant iNOS Pathway. Rendered with SBGN-like glyphs: multi-compartment support, reaction centers, multi-segment curves, empty species, multiple labels, and customized arrowheads.

Feature focus: Standards-based reproduction of an SBGN map within SBML Layout/Render.

Resources: SBML file | Source script

Escher-Style Template Application

Escher Style on the E. coli Core Model. An SBML model (with Layout) styled using an Escher-inspired template via SBMLNetwork’s Render utilities.

Feature focus: Applying a predefined style template across an entire network.

Resources: SBML file | Source script

Reaction Alignment and Layout Refinement

Reaction Alignment in the TCA Cycle. Core TCA reactions arranged on a circular arc with a vertically aligned upstream step; alias species reduce edge crossings. Color encodings differentiate metabolite classes.

Feature focus: High-level geometric alignment (circular + vertical) for pathway logic.

Resources: SBML file | Source script

Simulation Data Overlays (Flux Encoding)

Reaction Flux Gradient on Glycolysis Pathway. Reaction fluxes at a selected simulation time point encoded as a continuous color gradient on reaction curves (vivid → high flux; muted → low).

Feature focus: Mapping simulation output (fluxes) to visual attributes (color; also supports thickness, node size, etc.).

Resources: SBML file | Source script