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
- 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
- https://www.metabolic-economics.de/enzyme-cost-minimization/
- 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
- Flamholz, E. Noor, A. Bar-Even, R. Milo (2012) eQuilibrator - the biochemical thermodynamics calculator, Nucleic Acids Res, DOI: 10.1093/nar/gkr874
1 maintainer
Release files for equilibrator-pathway 0.8.1
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| equilibrator_pathway-0.8.1.tar.gz | 24.0 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| equilibrator_pathway-0.8.1-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 59.0 kB
Release files / equilibrator_pathway-0.8.1.tar.gz
| Download URL | equilibrator_pathway-0.8.1.tar.gz |
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| Size | 24.0 kB |
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