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Published on: December 4, 2021
Software applications toward quantitative metabolic flux analysis and modeling.
Thomas Dandekar1, Astrid Fieselmann, Saman Majeed
1Department of Bioinformatics, Biocenter, University of Wüerzburg, Am Hubland, 97074 Wuerzburg, Germany. Tel.: +49-931-318-4551; Fax: +49-931-318-4552; dandekar@biozentrum.uni-wuerzburg.de.
Metabolic modeling aids in understanding how organisms adapt by predicting metabolic fluxes. This review compares software tools for analyzing metabolic pathways and fluxes, aiding researchers in selecting appropriate methods.
Area of Science:
- Systems Biology
- Metabolic Engineering
Background:
- Metabolites and their pathways are crucial for organismal adaptation and survival.
- Metabolic modeling, including flux balance analysis (FBA), predicts metabolic fluxes in silico.
- Experimental isotopologue data can refine these predictive models.
Purpose of the Study:
- To review theoretical concepts and analysis steps in metabolic modeling.
- To compare various software programs for flux calculation and metabolite analysis.
- To discuss the strengths, limitations, and considerations for choosing specific software.
Main Methods:
- Introduction to theoretical concepts of metabolic modeling.
- Comparison of software tools: C13, BioOpt, COBRA toolbox, Metatool, efmtool, FiatFlux, ReMatch, VANTED, iMAT, and YANA.
- Discussion of strengths, limitations, and alternative software options.
Main Results:
- Metabolic modeling enables in silico elucidation of flux pathways and prediction of actual fluxes.
- Software comparison highlights differences in capabilities for metabolite analysis and flux calculation.
- Considerations for selecting software based on specific research needs are provided.
Conclusions:
- Metabolic modeling is a powerful tool for understanding metabolic networks.
- The choice of software depends on the specific analysis requirements and scale of the network.
- Future directions include addressing challenges in large-scale network computation and incorporating regulatory interactions.
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