Skip to content
My experiences as a chemist for installing and using deepchem
Branch: master
Clone or download
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
LICENSE Initial commit Jul 31, 2019
README.md Update README.md Jul 31, 2019
deepchem.yml conda environment file Aug 8, 2019

README.md

deepchem-for-dummies

My experiences as a chemist for installing and using deepchem

As a medicinal chemist interested in deep learning and trying to understand new tools to increase productivity I was very interested when I saw the blogpost by Derek Lowe on his in the pipeline blog about Deepchem. Since I am not a programmer I was a bit overwhelmed when I tried to use the tool and was originally unable to get any of the tutorials to work. After a little bit of experience I have been at least able to get the tutorials to work.

Here I plan on documenting first the installation of Deepchem and the required dependencies then as I get more familiar with the software I plan on documenting a how to use deepchem for dummies.

Installation

  • Install a working version of Linux
    • I used Linux Mint installed on Hyper-V on a Windows 10 computer at work. It would work even better on a native Linux box. Since Mint is a fork of Ubuntu/Debain I will use those commands
  • Install Miniconda - I used miniconda so I could control which packages/dependencies I install
    • download the installer, then navigate to the ~/Downloads folder in the terminal
    • bash Miniconda3-latest-Linux-x86_64.sh
  • Install git and download the deepchem repository - I built from the repository for 2 reasons. 1) it worked 2) so I would have the notebooks
  • Install Deepchem in a conda environment called deepchem
    • $ cd deepchem
    • $ bash scripts/install_deepchem_conda.sh deepchem
    • $ conda activate deepchem
    • $ python setup.py install
  • Install the required dependencies and Jupyter notebook - I used conda then updated/upgrades with pip. Make sure you are within your deepchem environment
    • $ conda install numpy, pandas, joblib, scikit-learn, tensorflow, matplotlib
    • $ conda install -c conda-forge rdkit
    • $ pip install --upgrade tensorflow
    • $ conda install jupyter
  • You should now have all of the required libraries to use deepchem - open the jupyter notebook and navigate to the deepchem notebooks
    • $ jupyter notebook
You can’t perform that action at this time.