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memote tested DOI

iRhto_memote

Memote-created repository for Rhodotorula toruloides (organism previously called Rhodosporidium toruloides) genome-scale metabolic model iRhto1108 (strain IFO0880)

Current version

Release 2: version 2023-03-01

Usage

Please use the latest model version if possible since the model is constantly updated based on new knowledge on the organism from the literature.

Hoang Dinh, 2023-03-01
Update release 2 model files, see changes in iRhto_memote/model_files

Hoang Dinh, 2020-06-30
Update to release 2, curation of beta-oxidation

Multiple formats of the model (JSON, SBML, MATLAB, YAML, and Excel) are in model_files. Escher pathway visualization maps are available at escher_maps. Supplementary files including details on biomass reaction and memote report are in supplementary_files.

Please let us know if you have any issues about or suggestions for the model by using the repository issues system.
KBase model at https://narrative.kbase.us/narrative/ws.42217.obj.1 is not functional and longer supported due to technical issues.

Reference

If you used this model or associated results, please cite and reference the following article:
A comprehensive genome-scale model for Rhodosporidium toruloides IFO0880 accounting for functional genomics and phenotypic data. Hoang V Dinh, Patrick F Suthers, Siu Hung Joshua Chan, Yihui Shen, Tianxia Xiao, Anshu Deewan, Sujit S Jagtap, Joshua D Rabinowitz, Christopher V Rao, Huimin Zhao, Costas D Maranas. Met Eng Comm. e00101. doi: https://doi.org/10.1016/j.mec.2019.e00101