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
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