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:
(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.
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
pip install python-libsbmlpip install python-libsbml-experimental
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:
Bug fixes:
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.
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 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:
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:
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.
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
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:
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 …
The SBML Online Validator, currently represents the most comprehensive validator for SBML files. While we are working on a standalone version of it, it will be some time before it will be released. In the meantime I came across a nice Web Automation Framework (see http://watin.org/). That makes it very easy to test web applications. It was easy enough to wrap it into an SBW module, so that now all SBML files can be easily validated right from your favorite SBW Application:
I’ve pushed the project over to http://fbergmann.github.io/LaunchOnlineValidator/ if you like to see how that was done. Or grab the module right from SourceForge: SetupSBMLValidator_1.0.exe.
Its official the new libSBML 5.9.0 is available immediately from source forge:
http://sourceforge.net/projects/sbml/files/libsbml/5.9.0/
There have been a number of changes. In the past months both the SBML Level 3 Qualitative Modeling Package, and the SBML Level 3 Layout Package have been released. From now on, they will be enabled and fully validated by every libSBML binary release.
And while there are many great new features (such as a converter that promotes all local reaction parameters to global ones, or a converter that attempts to infer units of elements), there are two new API introductions that I want to highlight below. Please see also the full release announcement.
LibSBML 5.9.0 also introduces a new API, that makes it easier to search for specific elements in the SBML documents. You might be familiar with the SBase::getAllElements method, that until now would have returned all SBase elements below a certain element. So if you called it on a Event you would get a list containing of Trigger, Delay and EventAssignments. New is now, that getAllElements can optionally take an ElementFilter. In order to use the ElementFilter you would create a new class, that inherits from ElementFilter and implements one method:
virtual bool filter(const SBase* element);
This function can inspect an SBase element for its properties, and if it should be returned by getAllElements it would return true and false otherwise. This also works in the bindings languages, such as Python, Java or C#. So for example in C# if you would like a filter that filters for elements that contain Notes, you would implement the method like so:
public override bool filter(SBase element)
{
// return in case we don't have a valid element
// or the element contains no notes.
if (element == null || !element.isSetNotes())
return false;
// otherwise include it in the result
return true;
}
Then you simply pass that class into the call to getAllElements, and you would only receive elements with notes. Examples for this are in the examples folder of libSBML:
Another new concept included in 5.9.0 is the IdentifierTransformer class. This was initially motivated by the comp package, where often identifiers (SIds / METAIDs) would have to be renamed during flattening. Of course when you rename things, then you have to go through all references, to ensure that these would be corrected as well. To make this easier we included the IdentifierTransformer class. Similar as to the ElementFilter you would again inherit from that class and implement:
virtual int transform(SBase* element);
in order to use the transformer, you would first call getAllElements with the appropriate filter, to get a hold of all elements you would want to transform. and then go through them applying the transformer to the items. Of course this is useful even outside of comp. As example we include a transformer, that will updated all SBML Ids, to be as close as possible to their elements Name (by ensuring that all invalid characters such as spaces are removed from the name to represent a valid id):
Of course these transformers don't have to be used at all in the context of renaming identifiers. The general API also allows them to do pretty much any manipulations of the elements that you would like.
Today I want to announce a new version of the FluxBalance tool. New in this version is that it works better with SBW. By adding a new entry to the menu bar “Export L2”, it is now possible to export the Flux Balance problem designed to other SBW modules as SBML Level 2 Version 4 files with the FluxBalance annotation. Is the button not pressed the SBML Level 3 File with the official Flux Balance Constraints Package will be exported. The new installer is available immidiately from SourceForge under:
http://sourceforge.net/projects/sbw/files/modules/FluxBalance/
Unfortunately, we are still not quite there for the next SBW release, last changes on JDesigner are in the process. In the meantime there is a new update for SBW please feel free to download the latest version.
I’ve just finished a one hour Rosa & Co webinar, and thought to post the slides below. You might also be interested in their other webinars, you can find the webinar archive here.
We are still working on the next release for SBW. Some users commented, that the last release candidate did not work for them, having issues in JDesigner. As of right now a new Windows build is available, from the Update tool or:
http://128.208.17.26/fbergman/files/latest/SetupSBW.exe
Thank you again for all the reports so far, please keep them coming.
The COMBINE meeting has just started, and we finally made the release candidate for the SED-ML Level 1 Version 2 specification available. SED-ML L1V2 finally extends the simulation experiments covered by SED-ML to include any kind of repeat and perturbation experiment. Apart from that it also includes the possibility to fully parameterize simulations, by specifying algorithm specific parameters like relative and absolute tolerances of integrators. The specification is available online from:
http://tinyurl.com/sed-ml-l1v2-rc
On my end I’ve updated the libSedML, and the SED-ML Script editor and of course SBW to be able to simulate L1V2. Another major change has been applied to the SED-ML Web Tools that now also support L1V2, and are now also capable of simulating the repeatedTask concept with CellML additionally to SBML.
As always any feedback is appreciated.
As hinted at, a couple of days ago, we are shortly before the release of the next version of SBW with enhancements for all associated programs. Today I want to announce a new release candidate. On SourceForge you will find installers for Windows, OSX as well as Linux (x86 & x64). You can download them from:
http://sourceforge.net/projects/sbw/files/sbw/2.10.0/rc1/
I’ve also created virtual machines & live images with SUSE studio, that are available online:
32bit OpenSUSE 12.3,
64bit OpenSUSE 12.3
Any feedback is appreciated.
It has been some time since the last release. Of course we never stopped working, as you can tell if you look at the change log:
Apart from major upgrades to JDesigner and Jarnac, there is full support for the newly released Layout package. Additionally, Level 3 models using the Hierarchical Modeling (i.e. comp) Package can be automatically flattened for use in our simulators. Also an import option has been added to many modules, so that COPASI files can be opened.
The new windows installer can be downloaded from:
Or obtained from the update program.
Finally, after a good 10 years since the first presentation of a layout extension to SBML, the specification has been sent to the SBML editors for approval. One might think it is actually quite easy to describe where something is, and it should not take all that long to agree on a bare minimum for a standard, but be that as it may, we are now in the final stretches. If you like, you could have a look at the specification:
It is of course fully supported by libSBML. Now that the specification is in the approved format for L3 packages, including a whole number of validation rules, validation is currently added to libSBML and will be available from the Online Validator with the acceptance of the package. In the meantime you could use the
Software support is shaping up: SBW has been supporting SBML Layout since 2005, and COPASI has it enabled in publicly released builds since last year. Both software tools also import CellDesigner annotations! At last years HARMONY meeting the layout specification has received its biggest change, by adding a GeneralGlyph, that makes it possible to also layout elements, that previously where not possible. Support for that is available in the latest SBW builds,
And within the COPASI codebase, to be released sometime soon.Here a screenshot, showing the exchange between COPASI & SBW of an SBML Level 3 model with a GeneralGlyph that represents an SBML Event, including Trigger and Event Assignment:
Don't you hate all these long compile times? I've head of Ninja a long time ago, but never gave it much thought. In case you don't feel like following the page, Ninja is a replacement for make / nmake. So today I gave it a try:
Couldn't be simpler. I cloned the git repository, opened a VS command line, called bootstrap.py with python 2.7, and added the directory to the path.
I figured libSBML makes for a great test project, at least on my machine a build of it with tests takes forever. So I configured a new build of libsbml, release, static runtime, with tests. Thus the configuration line is:
cmake -G Ninja -DWITH_CHECK=ON -DWITH_STATIC_RUNTIME=ON -DLIBSBML_DEPENDENCY_DIR=..\..\vs11_dependencies_32_static-release ..\..
and the build is ready to go. To collect timing information, i run using time:
\cygwin\bin\time.exe ninja
And *drumroll*, time reported: 0.00user 0.00system 2:29.59elapsed 0%CPU. If you know Windows C++ builds (on non SSD drives), you know they take forever, so having all these projects build in two and a half minutes is amazing.
Just so you know, here the counter example, of using NMake as distributed by VS11. Here the configure line is:
cmake -G "NMake Makefiles" -DWITH_CHECK=ON -DWITH_STATIC_RUNTIME=ON -DLIBSBML_DEPENDENCY_DIR=..\..\vs11_dependencies_32_static-release -DCMAKE_BUILD_TYPE=Release ..\..
running timed build again leaves gives us: 0.00user 0.00system 8:31.14elapsed 0%CPU. A whole 6 minutes more!
So I couldn’t stop there, a compilation of libSBML on OSX took (again with tests) 1m55.769 (vs. 4m4.568 for the regular make, and 2m2.698 for make –j 4). With universal binaries (i386 + x86_64) that time doubles as expected. Not too much of a difference. But this is made up by the fact that the output of ninja displays all critical things like warnings an errors nicely.
Today I used ninja for COPASI. Just as example: CopasiSE + CopasiUI + java bindings builds in just 4 minutes, 28! As compared to the 24m28 that nmake was using.
It seems obvious that using Ninja definitely saves a bunch of time, especially when compiling on Windows. The next thing to try is to use it as external build tool in VS!
