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References

RAVEN

Wang H, Marcišauskas S, Sánchez BJ, Domenzain I, Hermansson D, Agren R, Nielsen J, Kerkhoven EJ (2018). RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor. PLoS Computational Biology 14(10): e1006541. https://doi.org/10.1371/journal.pcbi.1006541

Agren R, Liu L, Shoaie S, Vongsangnak W, Nookaew I, Nielsen J (2013). The RAVEN toolbox and its use for generating a genome-scale metabolic model for Penicillium chrysogenum. PLoS Computational Biology 9(3): e1002980. https://doi.org/10.1371/journal.pcbi.1002980

GEM reconstruction protocol

Zorrilla F, Kerkhoven EJ (2022). Reconstruction of Genome-Scale Metabolic Model for Hansenula polymorpha Using RAVEN. In: Mapelli V, Bettiga M (eds), Yeast Metabolic Engineering: Methods and Protocols, Methods in Molecular Biology, vol. 2513. Humana, New York, NY, pp. 271–290. https://doi.org/10.1007/978-1-0716-2399-2_16

Methods cited in the protocol

  1. Orth JD, Thiele I, Palsson BØ (2010). What is flux balance analysis? Nat Biotechnol 28:245–248. https://doi.org/10.1038/nbt.1614
  2. Lewis NE, Nagarajan H, Palsson BO (2012). Constraining the metabolic genotype–phenotype relationship using a phylogeny of in silico methods. Nat Rev Microbiol 10:291–305. https://doi.org/10.1038/nrmicro2737
  3. Thiele I, Palsson BØ (2010). A protocol for generating a high-quality genome-scale metabolic reconstruction. Nat Protoc 5:93–121. https://doi.org/10.1038/nprot.2009.203
  4. Heirendt L, Arreckx S, Pfau T, et al. (2019). Creation and analysis of biochemical constraint-based models: the COBRA Toolbox v3.0. Nat Protoc 14:639–702. https://doi.org/10.1038/s41596-018-0098-2
  5. Sánchez BJ, Li F, Kerkhoven EJ, Nielsen J (2019). SLIMEr: probing flexibility of lipid metabolism in yeast with an improved constraint-based modeling framework. BMC Syst Biol 13:4. https://doi.org/10.1186/s12918-018-0673-8
  6. Kerkhoven EJ (2019). Modeling lipid metabolism in yeast. In: Geiger O (ed), Biogenesis of Fatty Acids, Lipids and Membranes. Springer, pp. 375–388.
  7. Moretti S, Martin O, Van Du TT, et al. (2016). MetaNetX/MNXref — reconciliation of metabolites and biochemical reactions to bring together genome-scale metabolic networks. Nucleic Acids Res 44:D523–D526. https://doi.org/10.1093/nar/gkv1117