equilibrator-pathway

Pathway analysis tools based on thermodynamic and kinetic models. This package can run two different pathway analysis methods:

• Max-min Driving Force (MDF)¹: objective ranking of pathways by the degree to which their flux is constrained by low thermodynamic driving force.
• Enzyme Cost Minimization (ECM)^{2, 3}: estimating the specific cost in enzymes for sustaining a flux, given a kinetic model.

Installation

The easiest way to install equilibrator-pathway is PyPI (and we recommend using a virtual environment):

virtualenv -p python3 equilibrator
source equilibrator/bin/activate
pip install equilibrator-pathway

The plot_* methods of the results need matplotlib, which is an optional dependency (versions up to 0.8.0 always installed it). To plot, install the plot extra:

pip install 'equilibrator-pathway[plot]'

or, if you prefer installing with conda:

conda install -c conda-forge equilibrator-pathway

The following example Jupyter notebook can help you get started.

If you only want to try out MDF or ECM without installing anything locally, we have a simple web interface for you at eQuilibrator ⁴.

References

1. E. Noor, A. Bar-Even, A. Flamholz, E. Reznik, W. Liebermeister, R. Milo (2014), Pathway Thermodynamics Highlights Kinetic Obstaclesin Central Metabolism, PLOS Comp. Biol., DOI: 10.1371/journal.pcbi.1003483
2. https://www.metabolic-economics.de/enzyme-cost-minimization/
3. E. Noor, A. Flamholz, A. Bar-Even, D. Davidi, R. Milo, W. Liebermeister (2016), The Protein Cost of Metabolic Fluxes: Prediction from Enzymatic Rate Laws and Cost Minimization, PLOS Comp. Biol., DOI: 10.1371/journal.pcbi.1005167
4. Flamholz, E. Noor, A. Bar-Even, R. Milo (2012) eQuilibrator - the biochemical thermodynamics calculator, Nucleic Acids Res, DOI: 10.1093/nar/gkr874