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Welcome to MetQuest's documentation!

MetQuest is a dynamic programming based algorithm for identifying all possible pathways from metabolic networks between the source and the target metabolites. MetQuest requires the genome-scale metabolic reconstructions, set of seed, source and target metabolites and the pathway length cut-off. MetQuest is compatible with Python 3 and is OS-independent. An extensive documentation can be found here.

Citation

Ravikrishnan, A., Nasre, M. & Raman, K. Enumerating all possible biosynthetic pathways in metabolic networks. Sci. Rep. 8:9932 (2018).

Authors

Acknowledgments

Installation

Use pip3 to install metquest from PyPI:

Via Python Package

pip3 install metquest

Direct installation

  1. Install Python 3.4 or higher
  2. Clone this repository to your computer using git or download the repository and decompress it.
  3. Navigate to the folder where metquest is downloaded and type
python3 setup.py install

(Elevated sudo rights may be required depending on the platform)

Required python packages

  1. cobra >= 0.11.3
  2. numpy >= 1.14.3
  3. scipy
  4. python-libsbml
  5. networkx >= 2.1

Input

Folder whose structure is as shown:

mainfolder/
|-Example1/
|   |-- SBML model(s) of metabolic networks # XML files of the metabolic networks(COBRA-compatible)
|   |-- seed_mets.txt       # Text file containing the seed metabolites separated by a newline
|   |-- source_mets.txt     # Text file containing the source metabolites separated by a newline
|   |-- target_mets.txt     # Text file containing the target metabolites separated by a newline
|   |-- cutoff.txt          # Text file containing the size cut-offs separated by a newline  
|-Example2/
|   ...

Kindly ensure that the SBML model has the field <model id> and the metabolites are prefixed with the model identifiers, for instance, if the model identifier is 'ecoli_core_model', and the seed metabolite is 'fum_c', the input text file should contain ecoli_core_model fum_c

Running MetQuest

From command line

MetQuest can be directly run from the terminal as

metquest.sh <path containing the input folder>

Navigate to the folder where metquest is installed and type

python3 execute_metquest.py <path containing the input folder>

From python console

>>> import metquest
>>> metquest.execute_all_codes()

When prompted, enter the path containing the folder with all the data files

Running examples

In the python console, type the following

>>> import metquest
>>> metquest.example.run_this_example()

This will run the example files.

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