sn248/r2sbml

R interface to the SBML library

r2sbml

R interface to the SBML library

This is a work in progress. The aim of this project is to provide an interface to read in SBML models in R. Eventually, I want to be able to read in an SBML file and convert it into a model which can be simulated in R/MATLAB/Julia. Currently the package only contains example R scripts from libsbml library.

Installation

Installation of this package from source requires that libsbml is installed on your system (for Unix and macOS). On Windows, the library is downloaded from its rwinlib location and installed. There are no additional steps on Windows.

Installation of libsbml on macOS from source

Installation of libsbml from source is easy. Download the source files from https://github.com/sbmlteam/libsbml/archive/refs/tags/v5.19.5.tar.gz

Extract and install the library using the following commands in the terminal

tar -xzf libsbml-5.19.5.tar.gz 
cd libSBML-5.19.0-Source
./configure
make
sudo make install

This should install the library at default location /usr/local/lib and the header files at usr/local/include

Check that the library is present at its location using the following command at the terminal. On my system it shows the following output

libsbml-static.a
libsbml.5.18.0.dylib
libsbml.5.19.0.dylib
libsbml.5.dylib
libsbml.a
libsbml.dylib
libsbml.la
libsbml2matlab.dylib
libsbmlj.jnilib

The presence of libsbml-static.a and libsbml.a should indicate successful installation of the libsbml library. If you have pkg-config installed, you can also check the installation of the library using the following command

pkg-config --libs libsbml

which should give the following output

-L/usr/local/lib -lsbml

You can also install libSBML using macports on macOS. See more instructions here.

Installation of libsbml on Unix systems

Installation from source can done on most Unix systems following exactly the same steps as note above for macOS. In addition, distribution packages are available for the different linux OS. For Ubuntu, the following commands can be used in the terminal

sudo apt-get update
sudo apt-get install libsbml5 libsbml5cli libsbml5-dev

Installation of the library can be checked using the pkg-config library as discussed above.