Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2022:2349:339-365.
doi: 10.1007/978-1-0716-1585-0_15.

A Beginner's Guide to the COBRA Toolbox

Ali Navid  1
Affiliations

A Beginner's Guide to the COBRA Toolbox

Ali Navid. Methods Mol Biol. 2022.

Abstract

COBRA toolbox is one of the most popular tools for systems biology analyses using genome-scale metabolic reconstructions. The toolbox permits the use of many constraint-based analytical methods for examining characteristics of metabolism in the biosystems ranging in complexity from single cells to microbial communities and ultimately multicellular organisms. The toolbox has a number of different variants that can be used depending on a user's choice of programming language. Here, I provide a basic tutorial for beginners that plan to use the original MATLAB version of the toolbox.

Keywords: Systems biology, Genome-scale models, Constraint-based analysis, FBA, Metabolic networks, COBRA toolbox.

PubMed Disclaimer

References

    1. Fang X, Lloyd CJ, Palsson BO (2020) Reconstructing organisms in silico: genome-scale models and their emerging applications. Nat Rev Microbiol 18:731–743 - PubMed - PMC - DOI
    1. Chaudhury S, Abdulhameed MDM, Singh N, Tawa GJ, D’haeseleer PM, Zemla AT et al (2013) Rapid countermeasure discovery against francisella tularensis based on a metabolic network reconstruction. PLoS One 8(5):e63369 - PubMed - PMC - DOI
    1. Navid A, Almaas E (2009) Genome-scale reconstruction of the metabolic network in Yersinia pestis, strain 91001. Mol Biosyst 5(4):368–375 - PubMed - DOI - PMC
    1. Navid A (2011) Applications of system-level models of metabolism for analysis of bacterial physiology and identification of new drug targets. Brief Funct Genomics 10(6):354–364 - PubMed - DOI - PMC
    1. Burgard AP, Pharkya P, Maranas CD (2003) Optknock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization. Biotechnol Bioeng 84(6):647–657 - PubMed - DOI

Publication types

LinkOut - more resources