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A Web Tool for Generating High Quality Machine-readable Biological Pathways
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SBMLDiagrams: a python package to process and visualize SBML layout and render.

Jin Xu1, Jessie Jiang2, Herbert M Sauro1

  • 1Department of Bioengineering, University of Washington, Seattle, WA 98195, USA.

Bioinformatics (Oxford, England)
|November 12, 2022
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Summary
This summary is machine-generated.

A new Python package, SBMLDiagrams, simplifies adding and retrieving pathway diagram information from Systems Biology Markup Language (SBML) models. This tool enhances biochemical model visualization and data exchange capabilities.

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Area of Science:

  • Systems Biology
  • Computational Biology
  • Bioinformatics

Background:

  • Systems Biology Markup Language (SBML) is a standard for biochemical models.
  • SBML Layout and Render package allows pathway diagram representation.
  • Limited tools exist for managing SBML layout and render information.

Purpose of the Study:

  • Introduce SBMLDiagrams, a Python package for SBML layout and render information.
  • Provide a straightforward API for adding and retrieving diagram data.
  • Facilitate easier visualization and data management in systems biology.

Main Methods:

  • Developed a Python package named SBMLDiagrams.
  • Integrated skia-python for diagram rendering.
  • Enabled export to common formats like PNG and PDF.

Main Results:

  • SBMLDiagrams offers a user-friendly Python API for SBML diagram data.
  • The package supports rendering and exporting pathway diagrams.
  • Successfully implemented layout and render information management for SBML.

Conclusions:

  • SBMLDiagrams simplifies the handling of SBML layout and render information.
  • The package enhances the usability of SBML for biochemical model visualization.
  • Promotes wider adoption and easier management of SBML pathway diagrams.