Case study for MEtabolic Regulation Rule INference (MERRIN) on Covert's model

This repository contains the data and notebook to reproduce the inference of regulatory rules of the core regulated metabolic networks of Covert et al (2001) from dynamic regulatory FBA (d-rFBA) simulations, performed with FlexFlux.

The notebooks can be visualized at https://nbviewer.org/github/bioasp/merrin-covert/tree/main/.

They can be executed interactively:

• online, using
• or on your computer, provided you have Docker and Python installed:

  docker pull bioasp/merrin:v1
  docker run -it --rm -p 8888:8888 bioasp/merrin:v1
  

  then point your browser to http://127.0.0.1:8888.

The ground-truth models are specified in the data repository, e.g., https://github.com/bioasp/merrin-covert/tree/main/data/covert:

• metablic_network.xml specifies the metabolic network in SBML format
• regulatory_network.bnet specifies the regulation rules, in BoolNet format
• interactions.txt list the putative regulations (PKN - Prior Knowledge Network)