Summer School on Microbial Community Modeling

The summer school consists of research talk and teaching (hands-on) sessions. Each day is focused on a particular topic, which is introduced by an overview talk on the morning of that day. The afternoons are dedicated to hands-on sessions on the computer.

The summer school will take place in a class-room style lecture hall. Participants are required to bring their own laptop. To be able to follow the hands-on sessions, participants should install the following software beforehand:

1. R with package microPop
   For the installation of an R package, you can use this R command:
   install.packages("microPop", dependencies=TRUE)
   or in RStudio, you can click "Packages" and then "Install" with "Install dependencies" enabled
2. Daphne, a Python tool available through Github
   Please install anaconda and carry out installation by following Daphne's installation instructions for anaconda. For copying the moma file, you first need to download Daphne via "clone or download" in Github and then copy your local daphne_ecoli-diauxie/filescobra/moma.py to ANACONDAPATH/envs/daphnePy2/lib/python2.7/site-packages/cobra/flux_analysis/
   You can find your ANACONDAPATH by typing "which conda" on command line. The path up to and including anaconda is the required ANACONDAPATH, so for instance if "which conda" gives: /anaconda3/bin/conda the ANACONDAPATH is /anaconda3/
3. NetLogo
4. Jupyter notebooks
5. ffmpeg via "conda install ffmpeg". Windows users: please try instructions here.