Chemical Dataset Exploration Tool Built on Plotly Dash

The chemdash app is a simple analysis application built upon the plotly dash framework. As input the application takes a csv file requiring both smiles and Compound_id fields, other fields will be retained and displayed in the data table portion of the application. A UMAP (similar to t-SNE/PCA) plot will be generated as well as a Molecular Grid Map (MGM). Depending on the column selection in the data table, a distribution plot for the given column will also be displayed. Selection of data points in either the UMAP or MGM plot will result in filtering of the data table and highlighting within the distribution plot. For more information on this demo app please check out my blog post.

The included yml file should allow you to get started quite easily if you have anaconda installed.

conda env create -f environment.yml

Download or clone the repository locally, make sure your new environment is active and navigate to the directory containing chemdash.py and run:

python chemdash.py

Takes about 30 seconds to load the application

Takes ~20 minutes to load the application. If you refer to the blog post above you will see that this is due to the Molecular Grid Map, if you alter the code slightly you should be able to turn that feature off and 10k compounds will likely load in a few minutes.