Saccharomyces cerevisiae metabolic model
Sara Calhoun
Generated September 9, 2020

Saccharomyces cerevisiae metabolic modeling and genome analysis

Here, we share imported datasets to enable analyses in KBase narratives. We've imported the published metabolic model of Saccharomyces cerevisiae strain S288C, which was built, manually curated, and validated by Mo et al. (2009). The Saccharomyces cerevisiae strain S288C genome was retrieved from NCBI RefSeq (GCF_000146045.2) and is described in the publication by Goffeau et al. (1996).

Furthermore, genome analysis tools and datasets can be accessed at the MycoCosm portal page: https://mycocosm.jgi.doe.gov/Sacce1

References:

  • Mo ML, Palsson BO, Herrgård MJ. Connecting extracellular metabolomic measurements to intracellular flux states in yeast. BMC Syst Biol. Mar 25 2009;3:37. doi:10.1186/1752-0509-3-37
  • Goffeau A, Barrell BG, Bussey H, et al. Life with 6000 genes. Science. 1996;274(5287):546-567. doi:10.1126/science.274.5287.546

Metabolic model of Saccharomyces cerevisiae

iMM904_KBase3
v2 - KBaseFBA.FBAModel-11.0
The viewer for the data in this Cell is available at the original Narrative here: https://narrative.kbase.us/narrative/70457

Flux balance analysis run on the Saccharomyces cerevisiae metabolic model

Run Flux Balance Analysis
Use flux balance analysis to predict metabolic fluxes in a metabolic model of an organism grown on a given media.
This app completed without errors in 1m 25s.
Objects
Created Object Name Type Description
iMM904_FBA FBA FBA-13 iMM904_FBA
Report
Summary
A flux balance analysis (FBA) was performed on the metabolic model 70457/28/2 growing in 70457/4/1 media.
Output from Run Flux Balance Analysis
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/70457

Saccharomyces cerevisiae genome imported into KBase

GCF_000146045.2
v1 - KBaseGenomes.Genome-8.2
The viewer for the data in this Cell is available at the original Narrative here: https://narrative.kbase.us/narrative/70457

Species tree

Insert Genome Into SpeciesTree - v2.2.0
Add one or more Genomes to a KBase SpeciesTree.
This app completed without errors in 4m 5s.
Report
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/70457
  • Sacce1_SpeciesTree.newick
  • Sacce1_SpeciesTree-labels.newick
  • Sacce1_SpeciesTree.png
  • Sacce1_SpeciesTree.pdf

Apps

  1. Insert Genome Into SpeciesTree - v2.2.0
    • Price MN, Dehal PS, Arkin AP. FastTree 2 Approximately Maximum-Likelihood Trees for Large Alignments. PLoS One. 2010;5. doi:10.1371/journal.pone.0009490
  2. Run Flux Balance Analysis
    • Henry CS, DeJongh M, Best AA, Frybarger PM, Linsay B, Stevens RL. High-throughput generation, optimization and analysis of genome-scale metabolic models. Nat Biotechnol. 2010;28: 977 982. doi:10.1038/nbt.1672
    • Orth JD, Thiele I, Palsson B . What is flux balance analysis? Nature Biotechnology. 2010;28: 245 248. doi:10.1038/nbt.1614