The py_emra package

I’m pleased to announce the py_emra package for Ensemble Modeling Robustness Analysis (EMRA). EMRA is a tool for modeling metabolic systems which I have worked on through my PhD.

The crux of EMRA is to use dynamic stability as a criteria for model selection and simulation in metabolic systems (e.g. bacterial metabolism). This depends on using what’s called a kinetic model of metabolism, one which uses a rate law to represent the amount of flux through any given reaction. Stability can be analyzed mathematically based on the specifics of these rate laws and how the reaction network is connected.

Understanding the stability of metabolic systems is important for redirecting them towards products of interest like biofuels. In the longer term, stability could be an interesting concept to explore in more complex cases like human diseases, particularly those with a metabolic component like diabetes or cancer.

As an exercise in Python coding and version control with Git, I decided to translate the existing EMRA code base from MATLAB into Python. Luckily, most of the features, including symbolic math and numerical integration, are available.

The Python package and readme is available on Github.

A paper about the package is available on biorXiv.

For more about EMRA see my Google Scholar page.

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