[jsbml-team] jsbml-rc2 to test
17 Apr '12 03:41
We are pleased to announce the second release candidate of JSBML-0.8
which is available for download from
This will be a short release and we are planning to do the final 0.8
during the next few weeks if no major problems are found.
Version 0.8-rc2 (11-04-2012)
Please try it and report any problems you encounter using JSBML either
to the mailing list firstname.lastname@example.org or using the issue
tracker for JSBML at
Below is a summary of the changes visible to the users :
* User visible changes :
- Major improvements of the reading and writing speed for large
* Bug Fixes:
- It was forgotten to implement an unsetSubstanceUnits method on the
Model class. Thanks to Robert Byrnes for reporting this problem.
- In the Reaction class, the setReversible method only accepted
Boolean, no boolean.
- Several bug fixes and improvements to units derivation, merging and
- There was a bug in KineticLaw that prevented a correct iteration
through all child elements.
- When cloning JSBML wrongly assigned the same TreeNodeChangeListeners
to the new data structure. Now, the TreeNodeChangeListeners are not
copied when cloning a JSBML object.
- The clone methods were corrected to register properly all entities
with an id.
- QuantityWithUnit did not fire update events when changing its value
because of an incorrect comparison between the previous and the new
- Corrected a bug that made it impossible to set a kinetic law with an
existing list of local parameters as the new kinetic law in a
- Meike Aichele detected and fixed the problem that some Listeners
were set too soon in the Model class, so that no Event was detected.
- One rdf namespace declaration was missing when creating an History
element from scratch.
- [Tracker item #3511439] : Model.getSpeciesType(String) was
corrected and it's speed improved. Thanks to Thomas Bernard who
noticed and reported the problem.
- Annotation elements that are missing a proper namespace declaration
will be correctly read and not considered as improper SBML elements.
- [Tracker item #3487517] : If one empty rdf Bag element was present
in an annotation read by jsbml, an XML element was not closed
properly, resulting in an invalid generated SBML. Thanks to Anna
Zhukova to report this problem.
- [Tracker item #3434930] : The parsing of a Message as an XML String
was incorrect as the method was expecting only a notes element to
enclose the HTML.
* Known issues :
- Reading of more than one RDF Description elements in the RDF
annotation block (the official SBML annotation scheme) is not
supported at the moment. Planned for the next major release.
- The RDF block at the top level of the annotation is considered to
be the official SBML annotation.
- SBML L3 packages are not supported and not kept.
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