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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.

Friday, December 20, 2013

libSBML Python Bindings

For a long time we have received reports, that the bindings to some of the supported bindings are hard to build. Usually we would prefer to provide binaries, however in the case of some languages this is not feasible, as there are different versions (that are incompatible with each other) being used. For this reason we have decided to work on creating standalone source packages for python, ruby, perl and r bindings.
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:
python setup.py install
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.

Source:
Linux Binaries:

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!

Thursday, November 28, 2013

Building LibSBML on Windows …

Building libSBML is really straightforward on all platforms. Especially with CMake. All one needs to do is to specify the dependencies. And while one of the parser libraries (libxml, expat or xerces-c) is surely available on every Linux or OS X system. It is sometimes difficult to track those binaries down for windows.

Since I upgraded my machine to use VS2013 today, I released new dependency archives on SourceForge. (for recent releases of Visual Studio (both in 32 and 64 bit and with / without static runtime)). The downloads are available from:

http://sf.net/projects/sbml/files/libsbml/win-dependencies

The binaries included are for the following libraries:

  • bzip2 v1.0.6
  • check v0.9.8
  • expat v2.0.1
  • iconv v1.9.2
  • libxml2 v2.7.7
  • xerces v3.1
  • zlib v1.2.3

Using the dependency archives

Please download the dependency archive, that matches your Visual Studio Version (i.e vs9 files, if you use Visual Studio 2008, vs11 files if you use Visual Studio 2012 ... ) as well as the build type (release / debug) and desired VS runtime (static runtime, vs dynamic (no extension)).

Then extract the file which will contain a folder libSBML Dependencies-1.0.0-b1-win32 for 32 bit, or libSBML Dependencies-1.0.0-b1-win64 for 64bit files.

Now checkout libSBML or download one of the release archives. Next create a build directory from the Visual Studio Command line. Ensure you have cmake in the path and run:

cmake -DLIBSBML_DEPENDENCY_DIR=<dependency dir> -DCMAKE_BUILD_TYPE=Release -DWITH_STATIC_RUNTIME=ON <source dir>

Here <source dir> is the libSBML source directory, and <dependency dir> the extracted directory. If you downloaded the debug archive, replace -DCMAKE_BUILD_TYPE=Release with -DCMAKE_BUILD_TYPE=Debug. In case you downloaded the file with dynamic runtime replace: -DWITH_STATIC_RUNTIME=ON with -DWITH_STATIC_RUNTIME=OFF.


Hope this helps …