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

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

Elliot Rowe  1 , Bernhard O Palsson  1   2   3   4 , Zachary A King  5
Affiliations

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

Elliot Rowe et al. BMC Syst Biol. .

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.

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Conflict of interest statement

Ethics approval and consent to participate

Not applicable.

Consent for publication

Not applicable.

Competing interests

The authors declare that they have no competing interests.

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Figures

Fig. 1
Fig. 1
A screenshot of Escher-FBA. Buttons inside the tooltip for each reaction allow for quick modifications to be made to the network by the user with immediate visual updates to the network. At the bottom of the screen the current objective function, flux through the objective, and a reset button for the whole map can be seen
Fig. 2
Fig. 2
Examples of Escher-FBA simulations. (a) Simulated growth with succinate as sole carbon source. (b) Simulated anaerobic growth on a glucose minimal medium. (c) Maximizing ATP yield in the default model. (d) Growth of the iMM904 model of S. cerevisiae. Note that arrow widths were increased in the settings menu to make changes more obvious
Fig. 3
Fig. 3
Pathway usage for two heterologous routes to 1-propanol production in E. coli. The pentose phosphate pathway (PPP) flux necessary for each heterologous production pathway can be compared by, first, forcing production of 1-propanol to be 99% of the maximum value (by setting the lower bound of the 1-propanol exchange reaction) and, second, minimizing flux through the first step in the PPP. (a) The 1-propanol pathway reported by Atsumi et al. [22] uses a single path to achieve 1-propanol production. It requires significant PPP flux and has a lower overall yield. (b) The pathway reported by Shen and Liao [23] uses two pathway synergistically to achieve higher yield. The pathway is stoichiometrically balanced with glycolysis, so it requires no PPP flux
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References

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