- adapt spelling SEDML -> SED-ML
- choose ".sedml" rather than ".xml" so as not to confuse our users as to which files to open / import
- added two examples of SED-ML files (with SBML files) to the testsuite/distribution folder
- fix import of SED-ML plots, so that phase plots can be imported, as well as log plots
- allow import of SED-ML documents, that explicitly define what level / version of SBML they include
- do not overwrite models of other files without warning, rather use a non-existing filename for the exported model
- modify SED-ML export to allow export of phase plots
- modify SED-ML export to not default to model1.xml for SBML file names
Bug 1981. Updated fix. The problem was in the calculation of the Link
matrix which did not correctly update all values if no species or no
reactions where present.
Bug 1902. The start values are now remembered at the beginning of an
optimization ore parameter estimation task and are correctly displayed and
saved in the GUI.
Added SED-ML examples to package.
Added export of the environment variable COPASIDIR to CopasiUI shell
script executed under Linux instead of the CopasiUI binary which has been
moved to a non standard location.
Added missing model files required for the SED-ML examples to the Windows
installer packages.
Fixed SED-ML example files.
The Eigen value and Eigen vector calculations of the Fisher Information
Matrix are now production ready.
Fixed saving and display of Model Parameter Sets.
- added SED-ML scan example
- fix SED-ML import of plots: typo, that used the same display name on all curves.
- also import the name given in the SED-ML file for a trace (taking first the one from the curve definition, then the one from the datagenerator, and finally the Objects Displayname).
- Bug2006: ignore SedInvalidNamespaceOnSed, if issued wrongly
- fix for Bug1984: clarification of histograms, the right axis is now enabled when histograms are used, and the Y values represent percent values
- allow import of SED-ML models that specify the full path to a model file
- give a warning, if a SED-ML description involves multiple models