volkamerlab / teachopencadd

TeachOpenCADD: a teaching platform for computer-aided drug design (CADD) using open source packages and data
https://projects.volkamerlab.org/teachopencadd
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Add support for Google Colab #149

Open dominiquesydow opened 3 years ago

dominiquesydow commented 3 years ago

We currently offer running the notebooks


In the future, add support for Google Colab.

Per notebook add cells at the beginning of the notebook to install the dependencies from our teachopencadd environment, e.g. like this (see discussion https://github.com/volkamerlab/teachopencadd/issues/129#issuecomment-913715209):

!pip install condacolab
import condacolab
condacolab.install()
!wget https://raw.githubusercontent.com/volkamerlab/TeachOpenCADD/master/devtools/other-conda-envs/users_env.yml
!mamba env update -n base -f users_env.yml 

However, some dependencies seem to cause problems:

schallerdavid commented 3 years ago

I found a workaround for colab and MDAnalysis (#148). However, google colab does not support nglview. So, there is no way we can make all talktorials properly work out on colab (#816).

hainm commented 3 years ago

FYI: https://github.com/googlecolab/colab-cdn-widget-manager/pull/14

dominiquesydow commented 3 years ago

Linking https://github.com/volkamerlab/teachopencadd/pull/151 because the MDAnalysis problem (for Colab or not) may get resolved there.