SBMLDiagrams: A python package to process and visualize SBML layout and render

TL;DR

SBMLDiagrams is a Python package that simplifies adding, retrieving, and visualizing SBML layout and render information, supporting diagram export in common formats for biochemical models.

Contribution

It introduces a new Python API for SBML layout and render data, with rendering support via skia-python and easy export options.

Findings

Enables easy addition and retrieval of SBML layout data

Supports rendering and exporting diagrams as PNG or PDF

Open-source and platform-independent

Abstract

Summary: The Systems Biology Markup Language (SBML) is an extensible standard format for exchanging biochemical models. One of the extensions for SBML is the SBML Layout and Render package. This allows modelers to describe a biochemical model as a pathway diagram. However, up to now there has been little support to help users easily add and retrieve such information from SBML. In this application note, we describe a new Python package called SBMLDiagrams. This package allows a user to add layout and render information or retrieve it using a straightforward Python API. The package uses skia-python to support the rendering of the diagrams, allowing export to commons formats such as PNG or PDF. Availability: SBMLDiagrams is publicly available and licensed under the liberal MIT open-source license. The package is available for all major platforms. The source code has been deposited at GitHub (github.com/sys-bio/SBMLDiagrams). Users can install the package using the standard pip installation mechanism: pip install SBMLDiagrams. Contact: hsauro@uw.edu.