Software Open Access

JSBML 1.1

Rodriguez, Nicolas; Dräger, Andreas

We are pleased to announce the release of JSBML-1.1, which is now
available for downloading from

https://sourceforge.net/projects/jsbml/files/jsbml/1.1

JSBML is a community-driven project to create a free, open-source, pure
Java library for reading, writing, and manipulating SBML files and data
streams. It is an alternative to the mixed Java/native code-based
interface provided in libSBML.

For more details, please visit

http://sbml.org/Software/JSBML

Thank you for your interest and support of JSBML and SBML in general.

The JSBML team.

 


User-visible new features and bug fixes since 1.0.

Version 1.1 (09-12-2015)
New Features:

Implemented the ability to support multiple version of SBML Level 3
package definitions.

Improved the Maven pom files, and changed the Maven group ids and
artifact ids. They should be stable now. With these changes in place,
we can update the Maven repository much more quickly and easily. Next
steps are to make JSBML available in Maven Central.

Added some utility classes to improve support for SBML files written by
the Cobra toolbox before the SBML Level 3 FBC package was created. The
CobraFormulaParser class can parse properly the Cobra gene associations
String into an ASTNode. The CobraUtils class contain a method to parse
the SBML notes into a Java Properties object.

Updated the implementation of the SBML Level 3 Groups package to the
Groups version 0.7 specification.

Bug Fixes:

The compartment 'units' attribute was not written in SBML L1. This is
corrected now.

SBML L1 rules were not correctly written: the wrong XML element name
was used. Now it uses the correct L1 names and attributes.

The clone constructor for the Species class did not copy the
speciesType attribute. Thanks to Olivier Martin who reported the
problem.

The clone constructor for the FunctionDefinition class did not copy the
id attribute.

Since the merge with the astnode2 branch in 1.1-beta1, the attributes on mathML elements where processed before calling the main processAttributes method and as a consequence, some of them where not processed at all, like 'sbml:units'. Thanks to Matthias König who reported the problem.

 

 

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