moped - A Python package for metabolic modelling and topological analysis [article]

Nima Philipp Saadat, Marvin van Aalst, Oliver Ebenhoeh
2020 bioRxiv   pre-print
Mathematical modeling of metabolic networks is a powerful approach to investigate the underlying principles of metabolism and growth. Such approaches include, amongst others, differential equations based modeling of metabolic systems, constraint based modeling and topological analysis of metabolic networks. Most of these methods are well established and are implemented in numerous software packages, but these are scattered between different programming languages, packages and syntaxes. This
more » ... syntaxes. This complicates establishing straight forward pipelines integrating model construction and simulation. We present the Python package moped which serves as an integrative hub for constructing, modifying and analysing metabolic models. moped supports the de novo construction of models directly from genome sequences and pathway/genome databases, providing a completely reproducible model construction and curation process. Alternatively, existing models published in SBML format can be easily imported. Models are represented as Python objects, for which a wide spectrum of easy-to-use modification and analysis methods exist. The model structure can be manually altered by adding, removing or modifying reactions, and gaps can be filled automatically. This greatly supports the development of curated models. Moreover, moped provides several analysis methods, in particular including the calculation of biosynthetic capacities using metabolic network expansion. The integration with other Python based tools is facilitated through various model export options. For example, a model can be directly converted into a cobrapy object for constraint-based analyses. Likewise, conversion into a modelbase object supports dynamic simulations using ordinary differential equations. moped is a fully documented and expandable Python package. We demonstrate the capability to serve as a hub for integrating model construction, database import, topological analysis and export for constraint-based and kinetic analyses.
doi:10.1101/2020.12.04.411512 fatcat:xz3zbrfsq5bgfoj7335ozmn4fu