E coli Core

The Core E. coli Model

The core E. coli metabolic model is a subset of the genome-scale metabolic reconstruction iAF1260. It is described in EcoSal Chapter 10.2.1 - Reconstruction and Use of Microbial Metabolic Networks: the Core Escherichia coli Metabolic Model as an Educational Guide by Orth, Fleming, and Palsson (2010) link

Downloads

ecoli_core_model.xls

  • A Microsoft Excel file that describes the reactions and metabolites in the core E. coli model. This file includes the full S matrix.

core_regulatory_rules.xls

  • A Microsoft Excel file that gives the Boolean regulatory rules for every gene in the regulated model.

ecoli_core_model.mat

  • A MATLAB data file that contains the core E. coli model (without regulation) in a format that can be used with the COBRA Toolbox.

modelReg.mat

  • A MATLAB data file that contains the regulated core E. coli model for the COBRA Toolbox.

optimizeRegModel.m

  • A new COBRA Toolbox function that is needed to run simulations using the regulated model. This function uses flux balance analysis to determine the state of the network while considering regulatory constraints.

dynamicRFBA.m

  • A new COBRA Toolbox function that performs dynamic flux balance analysis using the regulated model.

solveBooleanRegModel.ma

  • A COBRA Toolbox function that is required by both optimizeRegModel.m and dynamicRFBA.m.

ecoli_core_model.xml

  • An SBML file for the core E. coli model without regulation. COBRA Toolbox users with the SBML Toolbox can load this file using the function readCbModel.m.

Location

Location

417 Powell-Focht Bioengineering Hall

9500 Gilman Drive La Jolla, CA 92093-0412

Contact Us

Contact Us

In Silico Lab:  858-822-1144

Wet Lab:  858-246-1625

FAX:   858-822-3120

Website Concerns: sbrgit@ucsd.edu

User Login