Metabolic Network Completion. Compute minimal completions to your draft network with reactions from a repair network.

Project description

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 Command line interface

Typical usage is:

> meneco.py -d draftnetwork.sbml -s seeds.sbml -t targets.sbml -r repairnetwork.sbml

For more options you can ask for help as follows:

> meneco.py --h
usage: meneco.py [-h] -d DRAFTNET -s SEEDS -t TARGETS [-r REPAIRNET]
                 [--enumerate]

optional arguments:
  -h, --help            show this help message and exit
  -d DRAFTNET, --draftnet DRAFTNET
                        metabolic network in SBML format
  -s SEEDS, --seeds SEEDS
                        seeds in SBML format
  -t TARGETS, --targets TARGETS
                        targets in SBML format
  -r REPAIRNET, --repairnet REPAIRNET
                        perform network completion using REPAIRNET a metabolic
                        network in SBML format
  --enumerate           enumerate all minimal completions

Usage 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

Project details

Release history Release notifications | RSS feed

2.0.2

Apr 28, 2022

2.0.1

Mar 23, 2022

2.0.0

Mar 5, 2020

This version

1.5.3

Mar 1, 2019

1.5.2

Mar 29, 2017

1.5.0

Feb 23, 2016

1.4.3.1

Nov 23, 2015

1.4.3

Nov 23, 2015

1.4.2

May 21, 2014

1.4.1

Mar 5, 2014

1.4

Mar 4, 2014

1.3.2

Jan 21, 2014

1.3.1

Jan 17, 2014

1.3

Jan 16, 2014

1.2

Jan 9, 2014

1.1

Jul 5, 2013

1.0dev pre-release

Dec 4, 2012

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