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Published October 18, 2024 | Version v2
Model Open

iCH360: a compact model of Escherichia coli core and biosynthesis metabolism

Creators

  • 1. ROR icon University of Oxford
  • 2. ROR icon Max Planck Institute for Terrestrial Microbiology
  • 3. ROR icon Weizmann Institute of Science
  • 4. ROR icon Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement

Description

iCH360 manuscript: code and data

This repository contains code and data required to reproduce all results in:
 
A compact model of  Escherichia Coli core and biosynthetic metabolism
available at
 
Note:
This Zenodo record is a copy of the following github repository:
https://github.com/marco-corrao/iCH360_paper/tree/9b205e65e193f070e0d714e6c515f8d9da2d6de7
but additionally contains some heavy files (namely, the enumerated EFMs for each condition and a local EQuilibrator cache used for thermodynamic constant estimation) that were above the github file size limit.

Using iCH360

This repository is only intended to provide the files and tools to reproduce all results in the paper. If you wish to use iCH360 for your own work, please go to the model repo:
 
https://github.com/marco-corrao/iCH360
 
where you'll find the most up-to-date version of the model and its variants.

Navigating the repository

 ./Model

Contains the metabolic models (in `JSON` and `SBML` formats) mentioned in the paper, namely:
- The main stoichiometric model, *i*CH360
- The enzyme-constrained model variant, EC-*i*CH360
- The reduced model variant *i*CH360red

./Visualisation

Contains all the relevant metabolic maps, ready to be loaded in Escher for visualisation [1]:
- The full model map
- The compressed model map
- The maps for each metabolic subsystem
- The maps for the pathways not included in the model, but used to compute the equivalent biomass reaction used in the model.

./Annotation

Contains annotation maps to the EcoCyc database [2].

./Knowledge_graph

Contains the computational pipeline used to build the knowledge graph complementing the stoichiometric model, as well as the final graph structure in GML (.gml) and cytoscape (.cyjs) formats

./Analysis

Contains the Python scripts required to reproduce all analyses mentioned in the paper. More specific details are provided in each subfolder

./EFM

Contains the pipeline for creating the reduced model variant *i*CH360red, as well as counting and enumerating its elementary flux modes (EFMs).

./Enzyme_Constraints

Contains the data and scripts used to construct the enzyme constrained model EC-*i*CH360 and fit its turnover numbers to measured enzyme abundances.

./Thermodynamics

Contains the file and script required to compute the estimates of thermodynamic constants for the reactions and metabolites in the model

./Experimental_data

Contains experimental data (proteomics, metabolomics, and fluxomics) from other works, mapped to the model.

./External_database_data

Contains mappings between genes and polypeptides retrieved from the EcoCyc database [2].

./Manuscript_Figures

Contains all the notebooks (in Python and R) required to reproduce the figures in the paper.
 

Dependencies

The following packages are used throughout the repo:
```
# General dependencies (used throughout)
cobra==0.29.0
numpy==1.24.0
scipy==1.10.1
pandas==1.5.3
matplotlib==3.7.1
seaborn==0.12.2
networkx==3.0
tqdm==4.65.0
requests==2.28.2

 

Additional dependencies are required to reproduce some analyses:
 
# EFM enumeration
efmtool==0.2.1

 

# turnover number fitting procedure:
gurobipy==11.0.1 #requires a valid GUROBI licence
casadi==3.6.3

 

# MDF analysis
gurobipy==11.0.1 #requires a valid GUROBI licence

 

# Thermodynamic constant estimation
equilibrator-api==0.4.7
equilibrator-assets==0.4.1
cvxpy==1.5.2
```

 

References

 1. King, Z. A. et al. Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways. PLOS Computational Biology 11, e1004321 (2015).
 2. Keseler, I. M. et al. The EcoCyc database: reflecting new knowledge about _Escherichia coli_ K-12. Nucleic Acids Res 45, D543–D550 (2017).

Files

iCH360_paper_zenodo_record.zip

Files (1.1 GB)

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Additional details

Dates

Updated
2024-10-18
Code and files required to reproduce all analyses and figures in the manuscript supporting the model