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Analyzing and Designing Cell Factories with OptFlux

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Metabolic Network Reconstruction and Modeling

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1716))

Abstract

OptFlux was launched in 2010 as the first open-source and user-friendly platform containing all the major methods for performing metabolic engineering tasks in silico. Main features included the possibility of performing microbial strain simulations with widely used methods such as Flux Balance Analysis and strain design using Evolutionary Algorithms. Since then, OptFlux suffered a major re-factoring to improve its efficiency and reliability, while many features were added in the form of novel plug-ins, such as the BioVisualizer and the over/under expression plug-ins. The current chapter described the main mathematical formulations of the major methods implemented within OptFlux, also providing a detailed guide on the usage of those functionalities.

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Notes

  1. 1.

    https://projects.coin-or.org/Clp

  2. 2.

    https://www.gnu.org/software/glpk/

  3. 3.

    https://www-01.ibm.com/software/commerce/optimization/cplex-optimizer/

  4. 4.

    https://sourceforge.net/projects/optflux/

  5. 5.

    http://pinguin.biologie.uni-jena.de/bioinformatik/networks/metatool/metatool5.0/ecoli_networks.html

  6. 6.

    http://bigg1.ucsd.edu

  7. 7.

    https://escher.github.io/

  8. 8.

    http://bigg.ucsd.edu/

  9. 9.

    http://www.genome.jp/kegg/pathway.html

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Author notes

  1. Isabel Rocha and Miguel Rocha contributed equally to this work.

Authors and Affiliations

  1. SilicoLife Lda., Braga, Portugal

    Paulo Vilaça, Paulo Maia, Hugo Giesteira, Isabel Rocha & Miguel Rocha

Authors
  1. Paulo Vilaça
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  2. Paulo Maia
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  3. Hugo Giesteira
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  4. Isabel Rocha
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  5. Miguel Rocha
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Corresponding author

Correspondence to Paulo Vilaça .

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Editors and Affiliations

  1. Department of Biology, University of Florence, Sesto Fiorentino, Florence, Italy

    Marco Fondi

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Vilaça, P., Maia, P., Giesteira, H., Rocha, I., Rocha, M. (2018). Analyzing and Designing Cell Factories with OptFlux. In: Fondi, M. (eds) Metabolic Network Reconstruction and Modeling. Methods in Molecular Biology, vol 1716. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7528-0_2

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  • DOI: https://doi.org/10.1007/978-1-4939-7528-0_2

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7527-3

  • Online ISBN: 978-1-4939-7528-0

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