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libsbmljs-Enabling web-based SBML tools.
Biosystems ( IF 2.0 ) Pub Date : 2020-04-24 , DOI: 10.1016/j.biosystems.2020.104150
J Kyle Medley 1 , Joseph Hellerstein 2 , Herbert M Sauro 1
Affiliation  

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 server-side 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.



中文翻译:

libsbmljs-启用基于Web的SBML工具。

许多在线存储库中都使用SBML标准来存储系统生物学模型,但是目前尚没有支持Web的JavaScript库可以读取和写入SBML格式。这是一个严重的局限性,因为Web已成为一种通用的软件分发手段,并且现代Web浏览器的图形功能为构建丰富的交互式应用程序提供了强大的手段。而且,越来越多的开发人员致力于Web技术,他们准备利用Web的通用性来构建系统生物学和其他领域的下一代工具。但是,当前的解决方案需要服务器端处理为了支持建模中的现有标准。我们提供libsbmljs,一个适用于Node.js和Web的JavaScript / WebAssembly库,并全面支持所有SBML扩展。我们的库是用于在线SBML编辑器,模型构建工具和基于Web的模拟器的启用技术,并且完全在浏览器中运行,而无需任何专用的服务器资源。我们提供NPM软件包,大量示例,JavaScript API文档以及在线演示,允许用户阅读和验证BioModels和BiGG数据库中任何模型的SBML内容。我们还提供了说明和脚本,以允许用户针对任何libSBML版本构建libsbmljs的副本。尽管我们的库支持所有现有的SBML扩展,但是我们将介绍如何在将来的包装中添加其他扩展。为了演示此实现的实用性,我们还在https://libsbmljsdemo.github.io/上提供了一个演示,其中包含概念验证的SBML模拟器,该模拟器支持ODE和SBML核心模型的随机模拟。我们的项目托管在https://libsbmljs.github.io/,其中包含示例链接,API文档以及所有用于创建libsbmljs的源代码文件和构建脚本。我们的源代码已获得Apache 2.0开源许可证的许可。

更新日期:2020-04-24
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