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.
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.
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/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 .
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.
You can download all course notebooks at once here.