Meneco

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

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

Typical usage is:

$ meneco.py draftnetwork.sbml repairnetwork.sbml seeds.sbml targets.sbml

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

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

1.5.3

Mar 1, 2019

1.5.2

Mar 29, 2017

1.5.0

Feb 23, 2016

This version

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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