Generated September 9, 2020

Penicillium chrysogenum metabolic modeling and genome analysis

Here, we share imported datasets to enable analyses in KBase narratives. We've imported the published metabolic model of Penicillium chrysogenum Wisconsin 54-1255, which was built, manually curated, and validated by Agren et al. (2013). The Penicillium chrysogenum Wisconsin 54-1255 genome was retrieved from NCBI RefSeq (GCF_000226395.1) and is described in the publication by ven den Berg et al. (2008).

Furthermore, genome analysis tools and datasets can be accessed at the MycoCosm portal page:


  • Agren R, Liu L, Shoaie S, Vongsangnak W, Nookaew I, Nielsen J. The RAVEN toolbox and its use for generating a genome-scale metabolic model for Penicillium chrysogenum. PLoS Comput Biol. 2013;9(3):e1002980. doi:10.1371/journal.pcbi.1002980
  • van den Berg MA, et al. Genome sequencing and analysis of the filamentous fungus Penicillium chrysogenum. Nat Biotechnol. 2008 Oct;26(10):1161-8. doi: 10.1038/nbt.1498

Metabolic model of Penicillium chrysogenum

v3 - KBaseFBA.FBAModel-11.0
The viewer for the data in this Cell is available at the original Narrative here:

Flux balance analysis run on the Penicillium chrysogenum metabolic model

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 44s.
Created Object Name Type Description
iAL1006_FBA FBA FBA-13 iAL1006_FBA
A flux balance analysis (FBA) was performed on the metabolic model 70449/16/3 growing in 70449/4/1 media.
Output from Run Flux Balance Analysis
The viewer for the output created by this App is available at the original Narrative here:

Species tree

v1 - KBaseGenomes.Genome-8.2
The viewer for the data in this Cell is available at the original Narrative here:

Penicillium chrysogenum genome imported into KBase

Add one or more Genomes to a KBase SpeciesTree.
This app is still in progress.
No output found.


  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