EFMlrs is a Python package combined with a designated workflow that makes it easy for users to calculate elementary flux modes (EFMs) using a new approach in metabolic modeling - the mplrs algorithm. Besides this new approach also efmtool is supported, as it uses the most common and established algorithm for calculating EFMs - the double description method. The mplrs algorithm can make use of up to two thousand threads in parallel so that for the first time EFMs can be calculated for models that are too big to be calculated using tools e.g. efmtool that are based on the double description method. Furthermore, the EFMlrs package provides a method that makes it possible to integrate reaction bounds from the sbml files, so that subsets of EFMs can be calculated. This feature is compatible with both algorithms, the mplrs algorithm and the efmtool. EFMlrs can be used as a stand-alone console python program but is flexible enough to be integrated in already established workflows.


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5 months, 4 weeks ago passed




python, bioinformatics, metabolism, flux, cobrapy, systems-biology, biochemistry, computational-biology, sbml, metabolic-network, metabolic-models, sbml-model, mplrs, efmtool, lexicographic-reverse-search, elementary-flux-modes

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