# $Id: ChangeLog,v 1.9.2.9 2008/09/10 08:42:12 rodrigue Exp $ version 1.3.4 Added support for SBML level 2 version 4. Added a keyboard shortcut to add a MIRIAM annotation to an element. Added support for newer libsbml-3.x and libsbml-4.0.0 License headers updated Miriam file updated, now parameter, rules, event and other can be annotated. Updated libSBML dll to include the latest libSBML-4.0.0 for windows. Updated the data folder to include the fifteenth release of BioModels Database. Added libSBML linux 32bit and 64bit libraries, to allow user to use all the functionalities of SBMLeditor without having to do any compilation and/or shell script edition. Corrected and put back the shortcut for SBMLeditor for Linux on the menu and desktop Corrected the installation package to allow it to be started from the browser download page on windows. Linux still to chmod +x, before launching the setup Source repository moved to the SBML sourceforge project : http://sbml.svn.sourceforge.net/viewvc/sbml/trunk/sbmleditor/ version 1.3.3 Correction to the Miriam annotations. In SBMLeditor-1.3.2, I replaced http://xxxx#ID by urn:miriam:xxxx#ID but it should have be urn:miriam:xxxx:encode(ID) No annotations are lost, when you load a model in SBMLeditor, whichever of the 3 methods you are using to store the miriam annotations, everything will be transformed to the correct one. Use the variable USERPROFILE for the window .bat file instead of HOMEDRIVE and HOMEPATH to store the sbml.properties file. Updated libSBML dll to include the latest libSBML-3.2.0 for windows. Updated the data folder to include the eleventh release of BioModels Database. version 1.3.2 Allow creation of SBML level 2 version 3 only. Older version can still be used normally but cannot be created from scratch inside the SBMLeditor. Conversion to level 2v3 now available. Keyboard shortcut are shown in the menu item when possible. Update of some of the menu names. Disable deprecated or deleted attributes like species.charge. Add an option to switch it on or off. unit.offset --> removed from any SBML level and version Celcius unit --> removed from any SBML level and version Added an help menu with some documentation (draft). The documentations are display in separate frames that can be left open while using SBMLeditor. Added some MIRIAM qualifiers: isEncodedBy, encodes and occursIn. Added an option (enable.sbw) in sbml.properties to enable or not SBW. Is is disable by default. Select by default the compartment when you edit/create a species and there is only one compartment define in the model Update the Miriam export file to use the new uri scheme and the new XML schema Write a converter for the old URI/URLs, when you open a model in SBMLeditor, the uri would be replace to the official URN. Corrected a bug when deleting a MIRIAM annotation. Since we use the bqbiol and bqmodel namespace, when you were trying to remove one MIRIAM annotation on an other SBML element than the model, it would delete the whole RDF element with any remaining annotations. version 1.3 (build 20080507) Added support for SBML l2v2 and l2v3 Added support for libsbml-3.x. There is now a libsbml-utils jar file that you have to include in your classpath The windows installer now include directly the libSBML dlls to allow the user to have several libSBML installed on their computers. version 1.2 There is a properties file where you can specify if you want to save invalid model. You can also use the options menu to change this value. The last open and save locations are kept with other properties like the display/hide and if you want to save invalid model or not. The qualifier "hasPart" was missing in the add relation dialog. Fixed now. The dates stored in the RDF annotation inside element is checked to comply to he pattern http://www.w3.org/TR/NOTE-datetime. The timezone is added if it was missing. A new date is created if the old date is not recognized. version 1.1.1 Release (build 20070212) The equation editor is now correctly handling the empty mathML String created by the SBMLeditor when new SBML elements are created. The equation editor is now correctly handling the infix formula containing the substring ci or cn inside SBML element names or ids. version 1.1 Release (build 20070207) You have now a dialog opening to tell you that your model is valid and if libSBML was used to validate. If you open SBMLeditor without libSBML installed, there will be a dialog box opening to tell you about the limitations. All the "edit math" menuitem should be disable, when you press the E key to edit, you go to the normal edit dialog and not the graphical equation editor if libSBML is not present. When you create an element, the check box "Open mathML editor" is disabled and it is not possible any more to open the graphical equation editor if libSBML is not present. When you use undo/redo button in the equation editor, the coloring is conserved (the two green arrows button, eg: to the left to undo what you have just done) When you are doing a copy,cut/paste in the equation editor, I am trying to keep the coloring when possible. version 1.0 Release (build 20061211) Update the title of the SBMLeditor window according to the model name. Validate the id and add a tooltip also when editing a relation. Added the correct XML schema for SBML level 2 version 2 fron the sbml.org web site. Upaded version of the Miriam URIs. Acces to the System Biology Workbench. version 1.0 build 20060922 Remove any empty lists. Working with the new annotations schema. Added a menu under options to hide or display notes, annotation and math. Check missing namespace inside rdf element. Hide constant text field for local parameter, following the SBML specs. You can create SpeciesRef (Reactant, Product, Modifier) inside the equation editor with the "add new.." button or via shortcut (same as in the main windows : Ctrl-A, Ctrl-B, Ctrl-D respectively). The focus is now back to the equation editor after adding a new element. If annotations lenovere/finney are found, they are transformed to the new schema defined in sbml l2v2. Sample models include only latest biomodel DB. Added id and name at the element level in the tree to have some basic info when the nodes are collapsed. The build number is automaticaly generated and added inside the about window and the installer xml file. version 1.0 build 20060413-1709 Put the cross-platform Look&Feel to have a nice display on Mac Added two configurable options to change the display in the list of name/id no default value put for spatialDimension on the compartment element version 1.0 build 20060411-0940 Put back a check on the parameter id during the creation of the element Correct the local parameter creation inside the mathML editor version 1.0 build 20060106 Addition of a math editor, using the libsbml to transform MathML to infix formula.