meneco

A tool for the completion of metabolic networks

Metabolic network completion

Large-scale metabolic networks as well as measured data sets suffer from substantial incompleteness. meneco is a tool for metabolic network completion. It can be used to check whether a network provides the synthesis routes to comply with the required functionality described by the producibility of metabolites. In particular, it tests whether it is possible to synthesize so called target metabolites from a set of seed metabolites. For networks that fail this test meneco can attempt to complete the network by importing reactions from a metabolic reference database such that the resulting network provides the required functionality. meneco can identify unproducible target metabolites and computes minimal extensions to the network that satisfy the producibility constraints. Additionally, it can compute the union and intersection of all minimal networks extensions without enumerating all minimal network extensions. meneco builds upon a formal method for analyzing large-scale metabolic networks. This qualitative approach describes the bio-synthetic capacities of metabolic networks. Implementing this approach, meneco maps its principles into Answer Set Programming to express the producibility constraints for a set of metabolites.

Installation

You can install meneco by running:

$ pip install --user meneco

On Linux the executable script can then be found in ~/.local/bin

and on MacOS the script is under /Users/YOURUSERNAME/Library/Python/3.2/bin.

Usage of Command line interface

You can download the meneco user guide. Typical usage is:

$ meneco.py draftnetwork repairnetwork seeds targets

For more options you can ask for help as follows:

$ meneco.py --h
    usage: meneco.py [-h] [--enumerate] draftnetwork repairnetwork seeds targets

    positional arguments:
      draftnetwork   metabolic network in SBML format
      repairnetwork  metabolic network in SBML format
      seeds          seeds in SBML format
      targets        targets in SBML format

    optional arguments:
      -h, --help     show this help message and exit
      --enumerate    enumerate all minimal completions

Usage of library

For a guided example, see a demonstration IPython Notebook.

Samples

Sample files for the reconstruction of ectocarpus are available here: ectocyc.sbml, metacyc_16-5.sbml, seeds.sbml, targets.sbml.