System Requirements and Usage

System Requirements

1. Operating System: Transflux is written in Python and can be run on any Linux/UNIX environment (32/64 bit).
   Recommended OS: We recommend Fedora or Ubuntu Linux for optimal performance.
2. Dependencies :
   1. Transflux depends on CobraPy (>=cobra 0.3.0b3). The detailed set of instructions for installing CobraPy can be accessed here

Usage Instructions

All the files needed to run Transflux are bundled in a compressed (zip) package available for download here.

Run TransFlux using the following syntax-

python transflux_v1.py <model_file> <Gene/protein_expression_file>

The program will generate a Results folder containing the following files:

constrainment_summary.txt: File containing the statistics of the constrainment process.

reaction_flux: A tab-delimited file constainig reaction name, description, pathway and flux through the reaction before and after integrating expression data.

[Details of the requisite file formats for input as well as help on interpreting the results are provided in the README file bundled with the download package; sample input files are also include in the download bundle.]