Metabolic modeling for cell factory engineering: Setup

Option 1: Launch Binder

For a zero installation option, launch the cell factory design course by clicking on the Binder button:

Option 2: Install on your own machine

Below are the steps to install the cell factory design course on your own machine

Prerequisites

Before installing any of the course-specific packages below, please head over to https://pnnl-compbio.github.io/2019-03.14-15-PNNL-SWC/#python and follow the installation instructions for Python.

Create the cell-factory-design-course conda environment

Please open a shell (terminal) and create a conda environment for the course using the following command.

conda env create  -f environment.yml

If you’re on Linux or OS X or are using the git-bash shell on Windows run

source activate cell-factory-design-course

to activate the environment. If you’re on Windows using the default terminal (cmd) run the following command instead.

activate cell-factory-design-course

If you successfully activated you’re environment, your command prompt will look similar to this.

(cell-factory-design-course)$

Run the following command to check that the installation was successful (this can take a few seconds).

python -c "from cameo import models;print(models.bigg.e_coli_core.optimize().objective_value)"

The output should be approximately 0.8739.

Lastly, you need to add this virtual environment to the Jupyter notebook kernel

python -m ipykernel install --user --name cell-factory-design-course --display-name "cell factory design course"

You also have received an email with with a download link for CPLEX (only intended for academic use). Download the respective installer for your platform and install CPLEX. After you succeeded follow the respective instructions for your platform.

OS X and Linux

On Linux or OS X, run the following in your terminal (make sure you activated the cell-factory-course environment first) to install CPLEX for Python.

pip install <path-to-your-cplex-installation>/CPLEX_Studio128/cplex/python/3.6/<platform>/

For OS X, this should look like

Windows

If you installed CPLEX on Windows, cd into the following directory first

cd "C:\Program Files\IBM\ILOG\CPLEX_Studio128\cplex\python\3.6\<platform>"

and then run (make sure you activated the cell-factory-design-course environment first)

pip install .

Download course materials

You can download all course notebooks at once here.