sybil-SBML

This SBML (Systems Biology Markup Language) integration provides SBML support for sybil.

If you're facing any problems, please open an issue or a discussion.

Installation

The guide below has worked with R 4.1.2 on Linux Mint 21, which is based on Ubuntu 22.04 LTS.

Start by installing the dependencies. Follow the installation instructions from libSBML. Below is a shortcut of the instructions adapted to Ubuntu, thus might require some tweaking for your system.

Start by fetching the latest libSBML and R interface from the official location:

wget https://sourceforge.net/projects/sbml/files/libsbml/5.18.0/stable/Linux/64-bit/libSBML-5.18.0-Linux-x64.deb
wget https://sourceforge.net/projects/sbml/files/libsbml/5.18.0/stable/R%20interface/libSBML_5.18.0.tar.gz

Then install libSBML as a system library:

sudo apt install ./libSBML-5.18.0-Linux-x64.deb 

If the previous step failed, it might be that some libSBML dependencies (such as lixbml2) might need for the previous step to work:

sudo yum install libxml2-devel

Finally, proceed to install the R interface to libSBML (will take a while):

R CMD INSTALL libSBML_5.18.0.tar.gz

For various reasons, sybil-SBML is temporarily not available on CRAN anymore. Until then, it needs to be installed straight from this GitHub repository:

Use the following commands in the R console to install this package:

install.packages("remotes")
remotes::install_github("SysBioChalmers/sybil-SBML")

If the above fails because of failing to load libsbml.so, try adding the path to this file before starting R:

LD_LIBRARY_PATH=/usr/lib64 R

If the fix worked, make this permanent by changing this variable in your .bashrc file.

Remove the installation files::

rm libSBML-5.18.0-Linux-x64.deb libSBML_5.18.0.tar.gz 

Note: This repository was previously hosted at https://gitlab.cs.uni-duesseldorf.de/general/ccb/sybilSBML .