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Open AccessArticle

The Metano Modeling Toolbox MMTB: An Intuitive, Web-Based Toolbox Introduced by Two Use Cases

1
Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7 B, 38124 Braunschweig, Germany
2
Department of Bioinformatics and Biochemistry and Braunschweig Integrated Center of Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106 Braunschweig, Germany
*
Authors to whom correspondence should be addressed.
Academic Editors: Dario Pescini and Marzia Di Filippo
Metabolites 2021, 11(2), 113; https://doi.org/10.3390/metabo11020113
Received: 20 January 2021 / Revised: 12 February 2021 / Accepted: 15 February 2021 / Published: 17 February 2021
(This article belongs to the Special Issue Computational Biology for Metabolic Modelling)
Genome-scale metabolic models are of high interest in a number of different research fields. Flux balance analysis (FBA) and other mathematical methods allow the prediction of the steady-state behavior of metabolic networks under different environmental conditions. However, many existing applications for flux optimizations do not provide a metabolite-centric view on fluxes. Metano is a standalone, open-source toolbox for the analysis and refinement of metabolic models. While flux distributions in metabolic networks are predominantly analyzed from a reaction-centric point of view, the Metano methods of split-ratio analysis and metabolite flux minimization also allow a metabolite-centric view on flux distributions. In addition, we present MMTB (Metano Modeling Toolbox), a web-based toolbox for metabolic modeling including a user-friendly interface to Metano methods. MMTB assists during bottom-up construction of metabolic models by integrating reaction and enzymatic annotation data from different databases. Furthermore, MMTB is especially designed for non-experienced users by providing an intuitive interface to the most commonly used modeling methods and offering novel visualizations. Additionally, MMTB allows users to upload their models, which can in turn be explored and analyzed by the community. We introduce MMTB by two use cases, involving a published model of Corynebacterium glutamicum and a newly created model of Phaeobacter inhibens. View Full-Text
Keywords: systems biology; metabolic modeling; flux balance analysis; Phaeobacter inhibens; tropodithietic acid systems biology; metabolic modeling; flux balance analysis; Phaeobacter inhibens; tropodithietic acid
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MDPI and ACS Style

Koblitz, J.; Will, S.E.; Riemer, S.A.; Ulas, T.; Neumann-Schaal, M.; Schomburg, D. The Metano Modeling Toolbox MMTB: An Intuitive, Web-Based Toolbox Introduced by Two Use Cases. Metabolites 2021, 11, 113. https://doi.org/10.3390/metabo11020113

AMA Style

Koblitz J, Will SE, Riemer SA, Ulas T, Neumann-Schaal M, Schomburg D. The Metano Modeling Toolbox MMTB: An Intuitive, Web-Based Toolbox Introduced by Two Use Cases. Metabolites. 2021; 11(2):113. https://doi.org/10.3390/metabo11020113

Chicago/Turabian Style

Koblitz, Julia; Will, Sabine E.; Riemer, S. A.; Ulas, Thomas; Neumann-Schaal, Meina; Schomburg, Dietmar. 2021. "The Metano Modeling Toolbox MMTB: An Intuitive, Web-Based Toolbox Introduced by Two Use Cases" Metabolites 11, no. 2: 113. https://doi.org/10.3390/metabo11020113

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