MetQuest

MetQuest is a dynamic programming based algorithm for identifying all possible pathways from metabolic networks between the source and the target metabolites.

Getting started

1. Clone this repository to your computer using git or download the repository and decompress it. All the executable codes can be found in the folder Codes.
2. Install Python 2.7.14

Ensure that the following packages (with the specified version) are installed: NetworkX 1.9.1, cobrapy 0.5.4 and libSBML 5.13.0

Use the following commands on Terminal (Mac and Linux) to install the packages pip install cobra==0.5.4

pip install scipy==0.13.3

pip install networkx==1.9.1

pip install python-libsbml==5.13.0

On windows, navigate to folder C:\Python27\Scripts\, type cmd in Win + R. Type

pip.exe install cobra==0.5.4

pip.exe install scipy==0.13.3

pip.exe install networkx==1.9.1

pip.exe install python-libsbml==5.13.0

Input

Folder whose structure is as shown:

   
    ├── Example                 # Folder  
    │   ├── 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
    └── ...

Running MetQuest

On Mac and Linux

Go to terminal and navigate to the directory where the codes are downloaded. For instance, if the codes are downloaded in Desktop, go to terminal and type cd Desktop/MetQuest/Codes/

To run MetQuest, type

python exec_metquest.py

Follow the instructions on the screen.

On Windows

Open Python IDE, open the exec_metquest.py and execute it. Follow the instructions on the screen.

Output

The output pathways get saved as text files in a new folder called Results. The output in the files follow the format:

Reaction #

Reaction Name: reaction

Example

Authors

• Aarthi Ravikrishnan
• Meghana Nasre
• Karthik Raman

License

1. By using the software enclosed in this package (MetQuest), you agree to become bound by the terms of this license. 
2. This software is for your internal use only. Please DO NOT redistribute it without the permission from the authors.
3. This software is for academic use only. No other usage is allowed without a written permission from the authors. It cannot be used for any commercial interest.
4. The authors appreciate it if you can send us your feedback including any bug report.
5. The authors do not hold any responsibility for the correctness of this software, though we cross-checked all experimental results.

Acknowledgments

This work was supported by the Indian Institute of Technology Madras grant ERP/1314/004/RESF/KARH to KR and the INSPIRE fellowship, Department of Science and Technology, Government of India to AR.