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rbatools

rbatools is a programming interface for Resource Balance Analysis (RBA) models (https://rba.inrae.fr) based on the RBApy package (https://github.com/SysBioInra/RBApy). It includes methods to solve, modify, and analyse RBA models and to export model information and simulation results into various formats.

Usage remark

rbatools is based on linear-programming and therefore requires a linear-optimization package. We strongly suggest using the (propriatary) CPLEX tool, which is available under a free academic license.

Nonetheless we included functionality with the freely available swiglpk solver, however this sometimes is not able to obtain satisfactory solutions.

Installation

Install this package locally:

After cloning this repository, in your terminal navigate into the base directory of rbatools locally on your computer and execute:

pip install .

Install this from PyPI:

pip install rbatools

--------------------> Please note that installation of rbatools is required to run the tutorial.

Tutorials

MyBinder Tutorial

We generated a short tutorial, to be provided online with mybinder.

Please follow this link: https://mybinder.org/v2/gh/obodeit/rbatools_mybinder/main?labpath=tutorial_mybinder.ipynb

Instructional Jupyter notebooks

This repository includes various instructional jupyter notebooks, exemplifying the use of rbatools.

They are located in this repositories' subdirectory:

/tutorials/jupyter_notebooks

--------------------><--------------------

We included a sample model in the tutorial folder and added a loader module, to import it into the notebook. However we only included the model of B.Subtilis. In order to run the other models. We suggest to obtain them from our repository and store them in the same directory as this repository. (see section "Model availability")

Requirements to run jupyter notebooks:

The jupyter notebooks use additional functionality provided by libraries, not defined as dependencies of rbatools. The user therefore should install those to be able to run the tutorial-notebooks. Please execute the following commands in your terminal:

pip install notebook

pip install ipywidgets

pip install seaborn
Instructions to run jupyter notebooks:

In order to lauch the jupyter notebook interface, please execute the following command in your terminal:

jupyter notebook

Once a file browser opens in your web browser, please navigate in to the "/tutorials/jupyter_notebooks" directory and doubleclick one of the following notebooks.

Example_workflows_rba_tools.ipynb

This is a Jupyter notebook with example applications and workflows of rbatools with B.subtilis model.

Model_components_information_access.ipynb

This is a Jupyter notebook with example applications on how to access information on model-components and their relationships in the B.subtilis model.

Example_workflows_rba_tools_Ecoli.ipynb

Example applications and workflows with E.coli model. (Please note significantly longer computation times, than with B.subtilis model)

Running

scripts

We provided scripts with basic functionalities of rbatools in the subdirectory "scripts":

run_growth_rate_optimization.py

This script runs a growth-rate optimisation and stores the obtained results as sbtab. The arguments to provide are an rba-model and the optional arguments for the used lp-solver (default: swiglpk, alternative: cplex) and the path where the results should be stored. To run it, execute the following command in your terminal:

python run_growth_rate_optimization.py path/to/rba/model --lp-solver swiglpk --output-dir ...

generate_sbtab_of_model_for_html.py

This script imports an rba-model and exports its component-structure as tabular sbtab (as presented on https://rba.inrae.fr/models) The arguments to provide are an rba-model and the optional argument for the path where the results should be stored. To run it, execute the following command in your terminal:

python generate_sbtab_of_model_for_html.py path/to/rba/model --output-dir ...

run command-line tool

If the rbatools packaage is installed properly, the aforementioned scripts can also be executed as command-line tools The respective commands (with identical arguments as scripts) for the terminal are:

run-growth-rate-optimization path/to/rba/model --lp-solver swiglpk --output-dir ...

and

generate-sbtab-of-model-for-html path/to/rba/model --output-dir ...

Documentation

A full api-reference documentation can be found at: https://sysbioinra.github.io/rbatools/api_ref

Model availability

RBA models can be obtained from the repository https://github.com/SysBioInra/Bacterial-RBA-models

The Example_workflow_rba_tools notebook requires the previosly mentioned Bacterial-RBA-models repository to be placed in the same location, as this repository.

Authors

Bodeit, O., Liebermeister, W. and Goelzer A.

Citation

If you use RBAtools for scientific publications, please cite our article: Bodeit O., Ben Samir I., Karr J.R., Liebermeister W., Goelzer A. (2023), "RBAtools: a programming interface for Resource Balance Analysis models", Bioinformatics Advances 3 (2023). https://doi.org/10.1093/bioadv/vbad056

License

Copyright (c) 2022 INRAE - MaIAGE - France.

rbatools 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.

rbatools 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 rbatools. If not, see https://www.gnu.org/licenses/