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Metabolic Modeling with MetaFlux

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Microbial Systems Biology

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2349))

Abstract

The MetaFlux software supports creating, executing, and solving quantitative metabolic flux models using flux balance analysis (FBA). MetaFlux offers four modes of operation: (1) solving mode executes an FBA model for an individual organism or for an organism community, (2) gene knockout mode executes an FBA model with one or many gene knockouts, (3) development mode assists the user in creating and improving FBA models, and (4) flux variability analysis mode generates a report of the robustness of an FBA model. MetaFlux also solves dynamic FBA (dFBA) for both individual organisms and communities of organisms. MetaFlux can be used in two different environments: on your local computer, which requires the installation of the Pathway Tools software, or through the web, which does not require installation of Pathway Tools. On your local computer, MetaFlux offers all four modes of operation, whereas the web environment provides only the solving mode.

Several visualization tools are available to analyze model solutions. The Cellular Overview tool graphically shows the reaction fluxes on an organism’s metabolic map once a model is solved. The Omics Dashboard provides a hierarchical approach to visualizing reaction fluxes, organized by metabolic subsystems. For a community of organisms, plotting of accumulated biomasses and metabolites can be performed using the Gnuplot tool.

In this chapter, we present eight methods using MetaFlux. Five solving mode methods illustrate execution of models for individual organisms and for organism communities. One method illustrates the gene knockout mode. Two methods for the development mode illustrate steps for developing new metabolic models.

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References

  1. Karp PD, Latendresse M, Paley SM, Krummenacker M, Ong QD, Billington R, Kothari A, Weaver D, Lee T, Subhraveti P, Spaulding A, Fulcher C, Keseler IM, Caspi R (2016) Pathway tools version 19.0 update: software for pathway/genome informatics and systems biology. Brief Bioinform 17:877–890

    Article  CAS  Google Scholar 

  2. Mahadevan R, Edwards JS, Doyle FJ (2002) Dynamic flux balance analysis of diauxic growth in Escherichia coli. Biophys J 83:1331–1340

    Article  CAS  Google Scholar 

  3. Mahadevan R, Schilling CH (2003) The effects of alternate optimal solutions in constraint-based genome-scale metabolic models. Metab Eng 5:264–276

    Article  CAS  Google Scholar 

  4. Dandekar T, Fieselmann A, Majeed S, Ahmed Z (2014) Software applications toward quantitative metabolic flux analysis and modeling. Brief Bioinform 15:91–107

    Article  Google Scholar 

  5. Lakshmanan M, Koh G, Chung BK, Lee DY (2014) Software applications for flux balance analysis. Brief Bioinform 15:108–122

    Article  Google Scholar 

  6. Heirendt L, Arreckx S, Pfau T, Mendoza SN, Richelle A, Heinken A, Haraldsdóttir HS, Wachowiak J, Keating SM, Vlasov V, Magnusdóttir S, Ng CY, Preciat G, Žagare A, Chan SHJ, Aurich MK, Clancy CM, Modamio J, Sauls JT, Noronha A, Bordbar A, Cousins B, Assal DCE, Valcarcel LV, Apaolaza I, Ghaderi S, Ahookhosh M, Guebila MB, Kostromins A, Sompairac N, Le HM, Ma D, Sun Y, Wang L, Yurkovich JT, Oliveira MAP, Vuong PT, Assal LPE, Kuperstein I, Zinovyev A, Hinton HS, Bryant WA, Artacho FJA, Planes FJ, Stalidzans E, Maass A, Vempala S, Hucka M, Saunders MA, Maranas CD, Lewis NE, Sauter T, Palsson BØ, Thiele I, Fleming RMT (2019) Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0. Nat Protoc 14:639

    Article  CAS  Google Scholar 

  7. Latendresse M, Karp P (2018) Evaluation of reaction gap-filling accuracy by randomization. BMC Bioinformatics 19:53

    Article  Google Scholar 

  8. Karp PD, Weaver D, Latendresse M (2018) How accurate is automated gap filling of metabolic models? BMC Syst Biol 12:93

    Article  Google Scholar 

  9. Caspi R, Billington R, Fulcher CA, Keseler IM, Kothari A, Krummenacker M, Latendresse M, Midford PE, Ong Q, Ong WK, Paley S, Subhraveti P, Karp PD (2018) The MetaCyc database of metabolic pathways and enzymes. Nucleic Acids Res 46:D633–D639

    Article  CAS  Google Scholar 

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Acknowledgments

We would like to thank Markus Krummenacker for the template biomass generation procedure.

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Correspondence to Peter D. Karp .

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Latendresse, M., Ong, W.K., Karp, P.D. (2022). Metabolic Modeling with MetaFlux. In: Navid, A. (eds) Microbial Systems Biology. Methods in Molecular Biology, vol 2349. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1585-0_12

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  • DOI: https://doi.org/10.1007/978-1-0716-1585-0_12

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1584-3

  • Online ISBN: 978-1-0716-1585-0

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