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BMC Syst Biol. 2018 Sep 26;12(1):84. doi: 10.1186/s12918-018-0607-5.

Escher-FBA: a web application for interactive flux balance analysis.

Author information

1
Department of Bioengineering, University of California, San Diego, La Jolla, USA.
2
Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, USA.
3
Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
4
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kongens, Lyngby, Denmark.
5
Department of Bioengineering, University of California, San Diego, La Jolla, USA. zaking@ucsd.edu.

Abstract

BACKGROUND:

Flux balance analysis (FBA) is a widely-used method for analyzing metabolic networks. However, most existing tools that implement FBA require downloading software and writing code. Furthermore, FBA generates predictions for metabolic networks with thousands of components, so meaningful changes in FBA solutions can be difficult to identify. These challenges make it difficult for beginners to learn how FBA works.

RESULTS:

To meet this need, we present Escher-FBA, a web application for interactive FBA simulations within a pathway visualization. Escher-FBA allows users to set flux bounds, knock out reactions, change objective functions, upload metabolic models, and generate high-quality figures without downloading software or writing code. We provide detailed instructions on how to use Escher-FBA to replicate several FBA simulations that generate real scientific hypotheses.

CONCLUSIONS:

We designed Escher-FBA to be as intuitive as possible so that users can quickly and easily understand the core concepts of FBA. The web application can be accessed at https://sbrg.github.io/escher-fba .

KEYWORDS:

Constraint-based modeling; Escher; Flux balance analysis; Metabolism; Visualization; Web application

PMID:
30257674
PMCID:
PMC6158907
DOI:
10.1186/s12918-018-0607-5
[Indexed for MEDLINE]
Free PMC Article

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