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).

Fig. 1.

Example workflow using the SBML2L^aT_EX web service and SBML file BIOMD0000000003.xml (available at http://www.ebi.ac.uk/biomodels) After upload of an SBML file, several options allow customizing the output: MIRIAM annotations, an SBML consistency check or predefined unit declarations can be excluded, the desired file format can be selected; the paper size can be set to the US formats letter, legal or executive as well as to the European formats DIN A0-9 and the page orientation can be switched to landscape (especially important if the report contains fractions with very long denominators, where no automatic line break can be inserted). Several other options influence the layout of the report, e.g. names can be used in equations instead of identifiers, which can be displayed in typewriter or roman font. When the user clicks on the ‘convert’ button, the report file is generated and accessible for download.