Chlamydomonas reinhardtii metabolic model
Sara Calhoun
Generated August 4, 2020

Chlamydomonas reinhardtii metabolic modeling and genome analysis

Here, we've imported a metabolic model and the genome for Chlamydomonas reinhardtii to enable analyses in KBase narratives. The published metabolic model was built, manually curated, and validated by Imam et al. The genome annotation v5.5 by Merchant et al. was imported from Phytozome. Furthermore, additional genome analysis tools and datasets can be accessed at the PhycoCosm portal page: https://phycocosm.jgi.doe.gov/Chlre5_6

image

References:

  • Merchant SS, et al. The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science. 2007 Oct 12;318(5848):245-50. doi:10.1126/science.1143609
  • Imam S, Schäuble S, Valenzuela J, et al. A refined genome-scale reconstruction of Chlamydomonas metabolism provides a platform for systems-level analyses. Plant J. 2015;84(6):1239-1256. doi:10.1111/tpj.13059
iCre1355_KBase
v1 - KBaseFBA.FBAModel-11.0
The viewer for the data in this Cell is available at the original Narrative here: https://narrative.kbase.us/narrative/67576
Creinhardtii_v5.5
v11 - KBaseGenomes.Genome-8.2
The viewer for the data in this Cell is available at the original Narrative here: https://narrative.kbase.us/narrative/67576
Insert Genome Into SpeciesTree - v2.2.0
Add one or more Genomes to a KBase SpeciesTree.
This app completed without errors in 3m 30s.
Report
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/67576
  • Creinhardtii_Tree.newick
  • Creinhardtii_Tree-labels.newick
  • Creinhardtii_Tree.png
  • Creinhardtii_Tree.pdf
Run Flux Balance Analysis
Predict metabolite fluxes in a metabolic model of an organism grown on a given media using flux balance analysis (FBA).
This app completed without errors in 2m 17s.
Objects
Created Object Name Type Description
iCre1355_KBase_FBA FBA FBA-13 iCre1355_KBase_FBA
Report
Summary
A flux balance analysis (FBA) was performed on the metabolic model 67576/26/1 growing in 67576/27/1 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/67576

Released 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

Apps in Beta

  1. 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