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A Web Tool for Generating High Quality Machine-readable Biological Pathways
Published on: February 8, 2017
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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.
Bio Systems
|April 28, 2020
Summary
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.
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.
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