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Saturday, April 19, 2014

COPASI 4.12 Released

We have just released a new version of COPASI, and I just wanted to call out my favorite features in this release:
  • We have re-implemented the Rendering backend for network diagrams in Qt and improved the navigation and export of them. That means that all files containing an SBML file supporting the SBML Layout Package and / or the SBML Render Package will displayed properly and could for example be exported as PDF.
  • The same rendering code can now also be used to provide visualization of results for tasks. In this release we just exposed the display of time course results, conserved species, or elementary flux modes. For this visualization the existing rendering information will be altered and not replaced as you can see in the small recording below. Unable to display content. Adobe Flash is required.
  • If you would like to compare, you can switch between the different visualization types, by choosing in the COPASI preferences (Tools/Preferences, or the Preference menu on OSX) to select “Use OpenGL” and give it the Value “YES”.
  • While you are in the Preference menu, have a look at the option “Use Advanced Editing” I encourage you to try it out! If enabled, you can free-type expressions in all the places, where COPASI allows you to enter infix expressions as in for example Event Triggers / Assignments. It also makes it possible to copy expressions from one place to another, something that was not possible before.
  • Speaking about Events, there is a new option in the Time Course Task: “Continue on Simultaneous Events”. Before when two events would be competing and trigger at the same time, COPASI would always interrupt the simulation to make you aware of the fact. By enabling the option, you will just be warned, rather than the simulation stopped. This option is automatically enabled when SBML files are imported. It will not be automatically when opening / creating COPASI files (as it would be a change in behavior as compared to previous versions).
  • SED-ML support: COPASI now has limited support for SED-ML. It is possible to export the Time Course Simulation Task, along with Plots, as well as steady state parameter scans. Other files supporting the same feature set (SED-ML L1V1 / L1V2 without model pre-processing and local SBML sources) can also be imported.
the full release announcement and downloads are as always on the COPASI site:

Tuesday, April 15, 2014

Release of libSEDML 0.3.0

Just in time for HARMONY 2014 I am pleased to announce the release of libSEDML 0.3.0, the source of which is available for download from:

New Features:

  • Support for SED-ML L1V2
  • Support for Notes / Annotations in both versions
  • Support for AddXML / ChangeXML

Bug fixes:

  • sorted issues in supporting both versions and their namespaces
  • numerous improvements

Thanks of course to Sarah Keating, without whom the project would not have been possible, to Bertrand Moreau for helping to improve the CMake build and the Python Bindings.

Please report any issues with libSEDML to:

or directly to me.

Examples for the use of each of the API is available online. If you prefer there to be binaries available for any specific binding language / platform, please let me know.


Thursday, April 10, 2014

libSBML 5.10.0 Released

As of now libSBML 5.10.0 is available for download:

as well as the python source packages in pypi:

and additional linux python packages from the OBS:


The full release announcement is as always on sbml-discuss. Here I would just like to call out a number of changes in this release:

  • We were able to fix a number of memory leaks within libSBML, and would recommend everyone to upgrade.
  • There is now an extensible ASTNode layer implemented, that can be used to add additional math to the set understood by libsbml. This is primarily of importance for SBML Level 3 packages like ‘arrays’ and ‘multi’ that extend math. If your software tool does not use these packages, and is not extending math, then you can use the ‘old’ implementation by specifying  the cmake option ‘LIBSBML_USE_LEGACY_MATH’.
  • The CMake build no longer modifies any files within the source directory, and so it is finally possible to have differently configured build directories side-by-side.
  • It is possible to influence precisely how comp-flattening influences each element in the flattening process. This is made possible by passing along a custom transformer class that will be called on each element by libSBML.
  • The CMake files have also been updated, so that it is possible for others to include the libSBML sources anywhere within their cmake projects and simply add libSBML as subdirectory to their project. All that needs to be done to make this work, is to set CMake variables to the root of the libSBML sources and the root of the libSBML build directory.
  • We have solved several issues with respect to compatibility with OSX Mavericks. The only remaining issue, is that when you install the standalone python packages, you will get an error as the python distutils are pretty much broken with Apples switch to Clang. For now you will have to define the ARCHFLAGS environment variable to include: ‘ARCHFLAGS=-Wno-error=unused-command-line-argument-hard-error-in-future’.