Project for the translation of SBML files into BNGL files. You can find more information about the project here.
These builds are the from the head of master and are not guaranteed to be stable. Use at your own risk.
You should use Python 3.5 or later. A number of Python libraries need to be installed, but these can be automatically installed in a Python virtual environment, which is exactly what the makefile does under Linux and OSX or what the PowerShell script does for Windows.
sudo apt-get install -y python3-dev
sudo apt-get install -y python3-venv
You'll need to install Python 3. We recommend using Anaconda for this.
If you want to run ./atomizer/SBMLparser/sbmlTranslator.py
directly, you can
install all the Python requirements at the system level by doing:
cd SBMLparser
sudo pip3 install -r requirements.txt
Alternatively, you can do this at the user level:
cd SBMLparser
pip3 install --user -r requirements.txt
From the top-level directory, type the following:
make; make install
This will create an sbmlTranslator
binary in ./atomizer/bin
. This is made
using PyInstaller.
Right click on ./atomizer/build_sbmlTranslator_win.ps1
and select Run with PowerShell
.
./sbmlTranslator -i /path/to/sbml/file [-a] [-o output.bngl]
Optional arguments
Directory Structure:
SBMLparser: Directory containing the main project.
sbmlTranslator.py: Entry level file
atomizer: Contains the main implicit assumption extraction code
utils: contains several utility scripts used during the atomization process