ecBSU1

The process for enzyme-constrained model construction.

About

The pipeline was written and tested on Linux. The core libraries essential for the pipeline including: cobra, plotly (draw figures), and related packages.

Installation

1. create ECMpy environment using conda:

$ conda create -n ECMpy python=3.6.5

2. install related packages using pip:

$ conda activate ECMpy
$ pip install cobra==0.13.3
$ pip install plotly
$ pip install -U kaleido
$ pip install nbformat
$ pip install requests
$ pip install Bio
$ pip install scipy
$ pip install pylab
$ pip install ipykernel
$ python -m ipykernel install --user --name ECMpy --display-name "ECMpy"

Steps to reproduce the analysis in the publication

Download all data and analysis code from github (directlt download or use git clone).

$ cd /file path/project save path/
$ git clone https://github.com/tibbdc/ecBSU1.git

All results can be reproduced by executing the Jupyter Python notebooks:

• 01_model_calibration.ipynb

  • Model Calibration.

• 02_construct_ecBSU1.ipynb

  • Construction of ecBSU1.

• 03_CDF_kcat_and_mw.ipynb

  • Cumulative distribution of kcat and molecular weights.

• 04_PhPP_analysis.ipynb

  • Phenotype phase plane (PhPP) analysis.

• 05_trade_off.ipynb

  • Overflow metabolism simulation.

• 06_growth_rate_diff_carbon.ipynb

  • Predict growth rates on different carbon sources.

• 07_target_predict.ipynb

  • Predict target genes for the production of chemicals.

How to cite:

Ke Wu, Zhitao Mao, Yufeng Mao, Jinhui Niu, Jingyi Cai, Qianqian Yuan, Lili Yun, Xiaoping Liao, Zhiwen Wang and Hongwu Ma, ecBSU1: A Genome-Scale Enzyme-Constrained Model of Bacillus subtilis Based on the ECMpy Workflow, Microorganisms, 2023; https://doi.org/10.3390/microorganisms11010178