RBApy is a open-source Python package for automated generation of bacterial Resource Balance Allocation (RBA) models. RBA models have been developed for Bacillus subtilis 168 (wild type), Escherichia coli K-12 (wild type) and CO2-fixing Escherichia coli K-12 (engineered strain). You can find these models here: https://github.com/SysBioInra/Bacterial-RBA-models.
For a complete documentation on RBApy installation and usage, please visit the website: https://sysbioinra.github.io/RBApy/
For all details on installation and usage of code, please refer to the RBApy website https://sysbioinra.github.io/RBApy/. Make sure that you have scipy version <= 1.2.1, as the changes that have recently been introduced in the version 1.3.0 are not yet compatible with RBApy.
For more detailed instructions on usage, please refer to the RBApy website https://sysbioinra.github.io/RBApy/.
Put the SBML file containing the GSMM of your organism of interest in the input directory and fill in the parameter file input/params.in. Then open a console at the root of the repository and run:
`
python generate_rba_model.py input/params.in
`
or, more generally:
`
python generate_rba_model.py path/to/params.in
`
The script will generate several files used as an input for the RBA solver.
By default, they will be written to the output directory.
Warning: for the first run, the script will download and parse Uniprot data as best it can. Unfortunately, numerous values cannot be parsed properly and are replaced with default values. The script will generate many helper files to replace these default values with hand-curated values. You should fill in these helper files and rerun the script to obtain more relevant output (see instructions below).
Once the RBA model was generated, you can solve it using:
`
python solve_rba_model.py path/to/model
`
where the path points to the directory containing the XML files defining the RBA model.
The SBML file must be a valid SBML file, with gene-reaction associations. RBApy assumes that the boolean relation is always “or”s of “and”s, e.g. (g1 and g2) or (g3 and g4) Moreover, the words “or” and “and” must be written in lowercase letters. Empty fields in Gene-association will be interpreted as a diffusion reaction.
Copyright (c) 2018 INRA - MaIAGE - France. S. Fischer, A. Bulovic, A. Goelzer, M. Dinh
RBApy is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
RBApy is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with RBApy. If not, see <https://www.gnu.org/licenses/>
If you wish to cite this work, please refer to https://doi.org/10.1016/j.ymben.2019.06.001 .