SBML (the Systems Biology Markup Language) is an XML-based format for communicating and storing representations of biological processes. Its aim is to be a lingua franca for representing models in biology. SBML is suitable for models commonly found in research on a number of topics, including cell signaling pathways, metabolic pathways, biochemical reactions, gene regulation, and many others.
JSBML is a community-driven project to create a free, open-source, pure Java™ library for reading, writing, and manipulating SBML files (the Systems Biology Markup Language) and data streams. It is an alternative to the mixed Java/native code-based interface provided in libSBML.
ModelPolisher accesses the BiGG Models knowledgebase to annotate SBML models.
A Java-based software for visualizing and translating the KEGG PATHWAY database. Conversion of KGML files into BioPAX, SBML, GraphML, GML, and various other formats.
A standalone program that reads files created with the graphical network editor Escher and converts them to files in community standard formats.
cy3sbml: SBML for Cytoscape 3
Cross platform highly-extensible JavaFx based application which provides functions for reading, writing, manipulating, and validating SBML files.
Encoding ME models in SBML
Translation between CellDesigner-flavoured SBML and SBGN-ML
JSim is a Java-based simulation system for building quantitative numeric models and analyzing them with respect to experimental reference data. JSim's primary focus is in physiology and biomedicine, however its computational engine is quite general and applicable to a wide range of scientific domains.
Translation between CellDesigner-flavoured SBML and SBGN-ML
SBMLreporter provides a way to read the contents of XML-based SBML files. This is helpful and important for, e.g., error detection, proofreading and model communication. SBMLreporter is a new implementation of SBML2LaTeX.
An efficient Java™ solver implementation for SBML
Easily usable JavaFx-based inSilico module for dynamic Systems Biology Markup Language (SBML) model simulation visualization. Provides an intuitive Graphical User Interface for dynamic processing based on SBSCL.
A convenient library that greatly simplifies application development with Java™
JSBML is a community-driven project to create a free, open-source, pure Java™ library for reading, writing, and manipulating SBML files (the Systems Biology Markup Language) and data streams. It is an alternative to the mixed Java/native code-based interface provided in libSBML.
A graphical editor for systems biology models.
the SBML module of BiVeS