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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:

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