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Wednesday, October 26, 2016

Launching COPASI on Linux via Desktop icon

COPASI is released on Linux as a zipped tarball, to make it as easy as possible to get started with it. You simply extract it and run the executables. However, sometimes that is not enough, or if you don't like to launch your programs from the command line, then you want an alternative. Even worse some distributions launch the CopasiUI shell script in an editor, rather than the application instead.

So enough! Here you will find a shell script that you invoke once, and once done it generates a COPASI.desktop file that your Distribution ought to pick up and launch for you.

so you simply download this shell script:

create-copasi-icon.sh

(choose right click and save, should your browser not download the file) make it executable:

chmod +x create-copasi-icon.sh

and run it with the location where you placed your COPASI installation (and where you will leave it). Say you downloaded COPASI-4.16.104-Linux-64bit and placed it in your home directory, where you want it to stay, then you'd run:

./create-copasi-icon.sh ~/COPASI-4.16.104-Linux-64bit

The script will print the full path of the file it generated, and so if you don't like the results you could simply delete it right away. No other files on your systems will be touched.

Once the script ran, you can go to your application launcher of choice (or simply launch your super key aka windows key) and type COPASI. You should find the COPASI icon right there waiting for you. Let me know (with the name of your linux distro & version) if it does not.

Uninstalling the icon

If at any other point you would like to remove the file you can simply remove the desktop file via:

rm ~/.local/share/applications/COPASI.desktop

Friday, September 16, 2016

libCombine, this time in C++

Today (and just in time for the COMBINE meeting next week) I released the first version of a C++ library supporting the COMBINE archive. The primary purpose of this release is to gather feedback about the API and look what additional features people might need from it. To get a glimpse at what is possible right now you could have a look at:

Should you have any feedback, please use the
to let me know, so it won't get lost. 

Thursday, May 8, 2014

LibSBML Python Bindings 5.10.1

We have just updated the libSBML standalone python package, both on PyPI as well as on the Open Build Service. This includes a critical bug fix, when reading SBML Level 3 files using approved packages.
The new versions are available immediately from PyPI, and can be installed by running

pip install python-libsbml

or

pip install python-libsbml-experimental

if you need all packages. Otherwise linux binaries are available from OBS:

There we added now also binaries for Ubuntu 14.04 and Fedora 20.

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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:
http://www.copasi.org/

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:

https://github.com/fbergmann/libSEDML/releases/tag/v0.3.0

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:

https://github.com/fbergmann/libSEDML/issues

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.

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Thursday, April 10, 2014

libSBML 5.10.0 Released

As of now libSBML 5.10.0 is available for download:

http://sourceforge.net/projects/sbml/files/libsbml/5.10.0/

as well as the python source packages in pypi:

https://pypi.python.org/pypi/python-libsbml/5.10.0
https://pypi.python.org/pypi/python-libsbml-experimental/5.10.0

and additional linux python packages from the OBS:

python-libsbml
python-libsbml-experimental

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’.

 

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Sunday, March 2, 2014

Release of the Systems Biology Workbench 2.10.0

We are proud to finally announce a new release of the Systems Biology Workbench 2.10.0. You can download this release directly from SourceForge. This version provides updates to all components:

  • Jarnac comes up with an altered front-end, that will make it easier to work with it. It features also additional script commands .
  • JDesigner has been updated to work on newer Windows versions (7-8.1). It also can now load and save model parameters from / to external files. And it features a new plugin system.

Since our last official release, the SBML Level 3 Layout Package has finally been officially accepted, this release supports that final version as well. Similarly, SED-ML Level 1 Version 2 has been released, and with the Simulation Tool those files can be executed. Broken down into individual applications we have:

  • Layout Viewer / SBW Auto Layout: Support for SBML Level 3 Layout Package.
  • SBW Simulation Tool: Support for all SBML levels, and SED-ML Level 1 Version 2. First experiments such as Parameter Scans can also be exported. It also automatically displays targets of SBML Events / Rules in the list of selected elements, when loading models. The Simulation Tool also supports loading files from the COMBINE archive.
  • SBML Support Library: SBML models using the Hierarchical Model Composition package will be automatically flattened, when possible (The file has to be valid, and all submodels have to be reachable.).
  • JarnacLite / RoadRunner / SBML Support Library / JDesigner: A number of custom annotations have been added to allow the specification / simulation of distribution functions, or referencing the rate of change of a species. I've written about that before: distribution and rateOf.

As some of you know, Frank has joined the COPASI team. This made it possible to write a translator for COPASI, and now there is a new SBW import category that enables calling modules, to have a specific format converted into SBML, which can then be consumed. Current bidirectional translators are available for COPASI and JARNAC format. Practically that means that COPASI and JARNAC files can now be directly imported into: Simulation Tool, Auto Layout and others.

Of course there have been many more changes, bug fixes and improvements, so have a look at our full changelog.