Friday, September 16, 2016
Thursday, May 8, 2014
The new versions are available immediately from PyPI, and can be installed by running
pip install python-libsbml
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.
Saturday, April 19, 2014
- 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.
- 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.
Tuesday, April 15, 2014
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:
- Support for SED-ML L1V2
- Support for Notes / Annotations in both versions
- Support for AddXML / ChangeXML
- 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
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’.
Sunday, March 2, 2014
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.
Friday, December 20, 2013
The first package that I looked into was python. The idea would be to create two flavors of the source packages, one with libSBML core + accepted packages (dubbed python-libsbml), and another that includes also all proposed packages (dubbed python-libsbml-experimental).
With these source packages, installing the python bindings is as simple as running:
Thanks to the Open Build Service this also makes it possible to provide binaries for a variety of linux distributions for them. They provide even repositories, so that the packages could be automatically updated, when a new version has been released.python setup.py install
Hopefully in time for the next release we want to add these packages to the standard repositories (like pypi) over. And so I would like to ask you for feedback on the packages so far. Thanks!