Dataset Information

SBML2L(A)T(E)X: conversion of SBML files into human-readable reports.

ABSTRACT:

Summary

The XML-based Systems Biology Markup Language (SBML) has emerged as a standard for storage, communication and interchange of models in systems biology. As a machine-readable format XML is difficult for humans to read and understand. Many tools are available that visualize the reaction pathways stored in SBML files, but many components, e.g. unit declarations, complex kinetic equations or links to MIRIAM resources, are often not made visible in these diagrams. For a broader understanding of the models, support in scientific writing and error detection, a human-readable report of the complete model is needed. We present SBML2L(A)T(E)X, a Java-based stand-alone program to fill this gap. A convenient web service allows users to directly convert SBML to various formats, including DVI, L(A)T(E)X and PDF, and provides many settings for customization.

Availability

Source code, documentation and a web service are freely available at (http://www.ra.cs.uni-tuebingen.de/software/SBML2LaTeX).

SUBMITTER: Drager A

PROVIDER: S-EPMC2682517 | biostudies-literature | 2009 Jun

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

SBML2L(A)T(E)X: conversion of SBML files into human-readable reports.

Dräger Andreas A Planatscher Hannes H Motsou Wouamba Dieudonné D Schröder Adrian A Hucka Michael M Endler Lukas L Golebiewski Martin M Müller Wolfgang W Zell Andreas A

Bioinformatics (Oxford, England) 20090323 11

<h4>Summary</h4>The XML-based Systems Biology Markup Language (SBML) has emerged as a standard for storage, communication and interchange of models in systems biology. As a machine-readable format XML is difficult for humans to read and understand. Many tools are available that visualize the reaction pathways stored in SBML files, but many components, e.g. unit declarations, complex kinetic equations or links to MIRIAM resources, are often not made visible in these diagrams. For a broader unders ...[more]

PMID: 19307240

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Project description: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.

Dataset Information

SBML2L(A)T(E)X: conversion of SBML files into human-readable reports.

Summary

Availability

Publications

SBML2L(A)T(E)X: conversion of SBML files into human-readable reports.

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