agilebiofoundry / lstarkeyigsm

Lipomyces starkeyi GSM Development

LstarkeyiGSM (iLst996)

Lipomyces starkeyi code for developing GSM iLst996 based on strain NRRL Y-11557 genome and NRRL Y-11558 phenotypic data.

• Setup
• Summary of files
• Reference
• License

Setup

Model development utilizes the cobra toolbox to perform simulations and has the following dependences:

• cobra
• scipy
• pandas
• numpy
• matplotlib
• scikit-learn
• seaborn

If the required packages are not installed, you can use the following line from the command prompt to install:

pip install cobra scipy pandas numpy matplotlib seaborn scikit-learn

Summary of files

• BiologData_experimental - Biolog phenotypic plates experimental data and analysis files.
• Notebooks - notebooks used to build the GSM, with seven seperate steps (labeled step1-step7). Also includes notebooks for simulating GSM fluxes and for essential gene examinations.
• blastp - results from using ncbi protein blast of the L. starkeyi NRRL Y-11557 and R. sporidium IFO0880_4.
• data - Omic data, lipidData, biolog summary data, and Lipst1_1genome used for building and refining the GSM.
• finalGSM - iLst996 in various formats.
• memoteReport - memoteReport for iLst996.
• models - GSMs used and generated in this work.
• orthoMCL - load and read the orthoMCL results performed on L. starkeyi NRRL Y-11557, R. sporidium IFO0880_4, S. cerevisiae, and Y. lipolytica.
• orthoMCL_multispecies - orthoMCL results and analysis for Lipomyces clade and outlying species (26 species).

Reference

This project has been published in Genome-scale model development and genomic sequencing of the oleaginous clade Lipomyces. Frontiers in Bioenergy and Biotechnology, Volume 12. DOI: 10.3389/fbioe.2024.1356551. Link to online article.