libsbmljs—Enabling web-based SBML tools

Abstract

The SBML standard is used in a number of online repositories for storing systems biology models, yet there is currently no Web-capable JavaScript library that can read and write the SBML format. This is a severe limitation since the Web has become a universal means of software distribution, and the graphical capabilities of modern web browsers offer a powerful means for building rich, interactive applications. Also, there is a growing developer population specialized in web technologies that is poised to take advantage of the universality of the web to build the next generation of tools in systems biology and other fields. However, current solutions require serverside processing in order to support existing standards in modeling. We present libsbmljs, a JavaScript / WebAssembly library for Node.js and the Web with full support for all SBML extensions. Our library is an enabling technology for online SBML editors, model-building tools, and web-based simulators, and runs entirely in the browser without the need for any dedicated server resources. We provide NPM packages, an extensive set of examples, JavaScript API documentation, and an online demo that allows users to read and validate the SBML content of any model in the BioModels and BiGG databases. We also provide instructions and scripts to allow users to build a copy of libsbmljs against any libSBML version. Although our library supports all existing SBML extensions, we cover how to add additional extensions to the wrapper, should any arise in the future. To demonstrate the utility of this implementation, we also provide a demo at https://libsbmljsdemo.github.io/ with a proof-of-concept SBML simulator that supports ODE and stochastic simulations for SBML core models. Our project is hosted at https://libsbmljs.github.io/, which contains links to examples, API documentation, and all source code files and build scripts used to create libsbmljs. Our source code is licensed under the Apache 2.0 open source license.

MakeSBML: a tool for converting between Antimony and SBML

“…For educators, embedding interactive SBML models in their online learning materials will be invaluable, allowing the students to explore the behavior of chemical networks such as metabolic and signaling networks. Besides the Antimony library discussed here, the SBML library (libSBML) [ 10 ] has been converted to a JavaScript/WebAssembly version for use in a web browser ( https://github.com/sys-bio/libsbmljs ) [ 11 ]. This work includes a proof of concept simulator for existing SBML models ( https://libsbmljs.github.io/ ).…”

SyBLaRS: A web service for laying out, rendering and mining biological maps in SBGN, SBML and more

“…SyBLaRS mainly depends on the Cytoscape.js library to draw graphs and manage graph operations. It uses sbgnml-to-cytoscape [ 26 ] and libsbmljs [ 27 ] packages and the cytoscape-graphml extension to convert SBGNML, SBML and GraphML files, respectively, into JSON format as accepted by Cytoscape.js. Cytosnap , which is a package to render graphs on the server side with Cytoscape.js, is used to apply layout and/or generate images of pathway graphs.…”