Some time ago I developed libSedML a C# library that fully supports SED-ML for SBML as well as CellML models for creation of the description just as for the execution of Simulation Experiments. However, frequently the question to a C++ based library comes up. This project makes use of libSBML XML layer as well as code generation as starting point to produce a library for reading and writing of SED-ML models.
This library requires libSBML to be present, as its XML parsing layer will be used. for that either expat, xerces-c or libXML2 needs to be available. Additionally libSEDML makes use of libnuml. All dependencies are available as git submodule.
Building Python wheels
Since all dependencies are included as submodules, be sure to checkout the project with submodules:
git clone --recurse-submodules https://github.com/fbergmann/libSEDML
Then a build is as easy as:
cd libSEDML python src/bindings/python/setup.py build
or install, if you prefer. It requires cmake and swig installed.
This library uses CMake to build the library, so from an initial checkout all you would need todo is to run:
mkdir build cd build cmake -DLIBSBML_LIBRARY=< path to libsbml lib> -DLIBSBML_INCLUDE_DIR=< path to includes > ... -DEXTRA_LIBS= < comma separated list of xml libraries> make make install
Should libSBML be installed in a default location it will be found automatically. Note that you do need to list the xml libraries that libSBML was linked against. In most cases libSBML is compiled against libXML and have compression enabled, so your
EXTRA_LIBS would be:
note the semicolon denoting the listing of several libraries. Of course you could also enter the full path to each individual file, just to give an example, on windows I use:
for linking against
expat and indicating, that libSBML was compiled without compression.
This project is open source and freely available under the Simplified BSD license. Should that license not meet your needs, please contact me.
Copyright (c) 2013-2021, Frank T. Bergmann
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