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

Elliot Rowe, Bernhard O. Palsson, Zachary A. King*

*Corresponding author for this work

Research output: Contribution to journalJournal articleResearchpeer-review

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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.
Original languageEnglish
Article number84
JournalBMC Systems Biology
Volume12
Number of pages7
ISSN1752-0509
DOIs
Publication statusPublished - 2018

Bibliographical note

This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/)

Keywords

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

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