eQuilibrator overview

equilibrator-api is a command-line API with minimal dependencies for calculation of standard thermodynamic potentials of biochemical reactions using the same data found on eQuilibrator website. It can be used without a network connection (after installation and initialization).

Current Features

• Calculation of standard Gibbs potentials of reactions (together with a represnetation of uncertainties by a full covariance matrix).

• Calculation of standard Gibbs potentials of transport reactions (i.e. between cellular compartments).

• Calculation of standard reduction potentials of half-cells.

• Adjustment of Gibbs free energies to pH, ionic strength, and pMg (Magnesium ion concentration).

• Pathway analysis tools such as Max-min Driving Force and Enzyme Cost Minimization (requires the equilibrator-pathway package).

• Adding new compounds that are not among the 500,000 currently in the MetaNetX database (requires the equilibrator-assets package).

How to cite us

If you plan to use results from equilibrator-api in a scientific publication, please cite our paper: Consistent Estimation of Gibbs Energy Using Component Contributions [1]

How to install

You can simply pip install equilibrator-api and start eQuilibrating. For more details, see Installation.

How to use

For all newcommers, we recommend reading the Tutorial and even taking a look at the API Reference for a full list of classes and functions.

Alternatively, if you are looking for a quick-and-dirty guide, you can take a look at the Code examples section.

References

[1]

Elad Noor, Hulda S. Haraldsdóttir, Ron Milo, and Ronan M. T. Fleming. Consistent Estimation of Gibbs Energy Using Component Contributions. PLOS Computational Biology, 9(7):e1003098, July 2013. URL: http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003098 (visited on 2017-12-13), doi:10.1371/journal.pcbi.1003098.