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A Web Tool for Generating High Quality Machine-readable Biological Pathways
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libsbmljs-Enabling web-based SBML tools.

J Kyle Medley1, Joseph Hellerstein2, Herbert M Sauro1

  • 1Department of Bioengineering, University of Washington, Box 355061, Seattle, WA 98195-5061, United States of America.

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|April 28, 2020
PubMed
Summary
This summary is machine-generated.

A new JavaScript/WebAssembly library, libsbmljs, enables direct browser-based reading and writing of Systems Biology Markup Language (SBML) models. This facilitates the development of online tools for systems biology without server-side processing.

Keywords:
SBMLSystems biologyWeb

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Area of Science:

  • Systems Biology
  • Computational Biology
  • Bioinformatics

Background:

  • Systems Biology Markup Language (SBML) is a standard for storing biological models in online repositories.
  • Current limitations prevent direct web-based manipulation of SBML models, necessitating server-side processing.
  • A growing developer community skilled in web technologies is poised to advance systems biology tools.

Purpose of the Study:

  • To introduce libsbmljs, a JavaScript/WebAssembly library for reading and writing SBML models directly in web browsers.
  • To enable the development of web-native SBML editors, model-building tools, and simulators.
  • To eliminate the need for server-side processing for SBML-related web applications.

Main Methods:

  • Development of a JavaScript/WebAssembly library (libsbmljs) with full support for all SBML extensions.
  • Provision of NPM packages, API documentation, and an online demo for user accessibility.
  • Integration with existing databases like BioModels and BiGG for model validation.

Main Results:

  • libsbmljs runs entirely in the browser, supporting all SBML extensions.
  • The library enables online SBML editors, model-building tools, and web-based simulators.
  • A proof-of-concept simulator for ODE and stochastic simulations of SBML core models is demonstrated.

Conclusions:

  • libsbmljs removes barriers to web-based systems biology tool development.
  • The library empowers a wider developer community to contribute to the field.
  • libsbmljs enhances accessibility and interactivity for SBML model manipulation and simulation.