The Metano Modeling Toolbox MMTB: An Intuitive, Web-Based Toolbox Introduced by Two Use Cases
| Autor: | S Alexander Riemer, Dietmar Schomburg, Julia Koblitz, Meina Neumann-Schaal, Thomas Ulas, Sabine Eva Will |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2021 |
| Předmět: |
0301 basic medicine
Computer science Interface (Java) Endocrinology Diabetes and Metabolism Systems biology 030106 microbiology lcsh:QR1-502 flux balance analysis computer.software_genre Biochemistry lcsh:Microbiology Article tropodithietic acid Phaeobacter inhibens 03 medical and health sciences Upload metabolic modeling Web application Use case Veröffentlichung der TU Braunschweig Molecular Biology ddc:5 business.industry systems biology Toolbox Flux balance analysis ddc:57 030104 developmental biology Minification Data mining Publikationsfonds der TU Braunschweig business computer |
| Zdroj: | Metabolites Volume 11 Issue 2 Metabolites, 2021, 11(2), 113; https://doi.org/10.3390/metabo11020113--http://www.bibliothek.uni-regensburg.de/ezeit/?2662251--http://www.mdpi.com/journal/metabolites--https://www.ncbi.nlm.nih.gov/pmc/journals/2273/--2218-1989 Metabolites, Vol 11, Iss 113, p 113 (2021) |
| ISSN: | 2218-1989 |
| DOI: | 10.3390/metabo11020113 |
| Popis: | 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 (mmtb.brenda-enzymes.org (accessed on 9 Febraury 2021)), 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. |
| Databáze: | OpenAIRE |
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