Metabolic modeling for cell factory engineering: Setup

Prerequisites

Before installing any of the course-specific packages below, please head over to https://biosustain.github.io/2016-09-05-software-carpentry/ and follow the installation instructions for Python.

Installing cameo

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

conda create -y --name cell-factory-course python=3.6

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

source activate cell-factory-course

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

activate cell-factory-course

Maybe

conda activate cell-factory-course

works now in a platform independent fashion too (not tested).

If you successfully activated you’re environment, your command prompt will look similar to this (maybe not true anymore in 2019).

(cell-factory-course)$

Then use pip to install cameo and a few other handy things.

pip install cameo memote ipykernel pandas escher==1.6.0 plotly matplotlib --upgrade

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.

Finally run

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

to make this environment available in Jupyter notebook.

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

pip install /Applications/CPLEX_Studio128/cplex/python/3.6/x86-64_osx/

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-course environment first)

pip install .

Fallback solution

Please create a GitHub account if you don’t already own one at https://github.com/join?source=header-home. That way we’ll be able to provide you with access to a Jupyterhub notebook server that already contains all necessary software pre-installed as a fallback solution in case you run into troubles during the course.

Download course materials

You can download all course notebooks at once here.