Resource Balance Analysis

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Downloads

RBAtools

RBAtools can be installed via pip. The python programming interface RBAtools includes high-level methods to solve, manipulate and analyse RBA-models and to export model and simulation results into different file formats. A detailed description and code documentation can be found on github. To install RBAtools via pip, run

  pip install rbatools

RBAtools source code can be also obtained from github. The repository contains further installation instructions and documentation, including a number of jupyter notebooks.

Jupyter notebooks

RBAtools comes with some instructional jupyter notebooks. A slim jupyter notebook tutorial can be directly run on mybinder without installing any RBA code on your machine. This notebook demonstrates the main high-level simulation methods and generates all plots from our future article on RBAtools. In addition, three jupyter notebooks are available at the RBAtools git repository. To run these notebooks, the following python packages must be installed:

  pip install notebook
  pip install ipywidgets
  pip install seaborn

For running the notebooks, the Bacillus subtilis RBA model must be available on your machine. Before running the notebooks, download the RBA models git repository (see above) and place it in the same directory as the RBAtools folder.

RBApy

The python package RBApy for model construction and basic simulation can be installed via pip. RBApy source code and documentation is also available on github.com. Detailed documentation, installation instructions, and usage examples can be found at the RBApy homepage on github. For further details, see our article Bulović A. et al. (2019), Metabolic Engineering, 55, 12-22 [pdf]. To install RBApy via pip, run

  pip install rbapy

To run simulations with RBApy, numerical solvers to be installed in your system. RBApy supports three different solvers: the proprietary solvers CPLEX and Gurobi and the free solver GLPK. You can install RBApy together with your preferred solver via one of the following:

  pip install rbapy[cplex]
  pip install rbapy[swiglpk]
  pip install rbapy[gurobi]

swiglpk stands for "GLPK". Note that for the proprietary solvers CPLEX and Gurobi require a valid license. Please note that RBA simulations are numerically demanding. To our experience GLPK is not fully reliable when simulating large models like our E coli model (where GLPK gets sometimes stalled).

Command-line interface and docker image for RBApy

BioSimulators is a registry of biosimulation tools, developed by the Center for Reproducible Biomedical Modeling, the Karr Lab at the Icahn School of Medicine at Mount Sinai, and the Center for Cell Analysis & Modeling at the University of Connecticut Health Center. A docker image and a standardized command-line interface for RBApy, following the BioSimulators framework, are available as a python package at PyPi. Please note that you need a valid CPLEX license.

RBA model download

For downloading RBA models, please see our models page.