precursor

Compute minimal precursors sets that enable the production of target metabolites

Minimal nutrition sets to produce target metabolites

A qualitative approach to elaborating the bio-synthetic capacities of metabolic networks. Given a set of desired target metabolites, this approach applies a notion of bio-chemical producebility to metabolic reaction networks and allows to identify the minimal sets of precursors that are required to produce the target metabolites.

Installation

You can install precursor by running:

$ pip install --user precursor

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

and on MacOS the script is under /Users/YOURUSERNAME/Library/Python/2.7/bin.

Usage

Typical usage is:

$ precursor.py --autoseeds network targets 

For more options you can ask for help as follows:

$ precursor.py --help
usage: precursor.py [-h] [--autoseeds] net inputs

positional arguments:
  net          metabolic network in SBML format
  inputs       targets in XML format

optional arguments:
  -h, --help   show this help message and exit
  --autoseeds  compute possible seed metabolites

Samples

An archive with sample files is available here: precursor_data.tar.gz