  eQuilibrator (equilibrator.weizmann.ac.il) is a calculator for biochemical
equilibrium constants and Gibbs free energies, originally designed as a
web-based interface. While the website now counts ${\sim}1000$ distinct monthly
users, its design could not accommodate larger compound databases and it lacked
an application programming interface (API) for integration in other tools
developed by the systems biology community. Here, we report a new python-based
package for eQuilibrator, that comes with many new features such as a 50-fold
larger compound database, the ability to add novel compound structures,
improvements in speed and memory use, and correction for Mg2+ ion
concentrations. Moreover, it adds the ability to compute the covariance matrix
of the uncertainty between estimates, for which we show the advantages and
describe the application in metabolic modeling. We foresee that these
improvements will make thermodynamic modeling more accessible and facilitate
the integration of eQuilibrator into other software platforms.
