Quantitative analysis by Jesse Bloom of virus neutralization by IgG versus Fab antibody forms accounting for IgG avidity and the possibility of ligand depletion for potent antibodies.
The marimo notebook notebook.py contains a detailed description of the model.
The conda environment for running this notebook is in environment.yml.
To export the notebook to a standalone HTML notebook file run:
marimo export html notebook.py -o notebook.html
This will create the HTML rendering of the notebook notebook.html as well as the standalone interactive chart chart.html created by the notebook. It also creates plots of model-simulated and real RSV F neutralization data in simulated_vs_actual_curves.pdf and simulated_vs_actual_curves.svg.
To view the notebook and interactive chart directly, go to the GitHub Pages rendering at https://jbloomlab.github.io/IgG-vs-Fab-neutralization.
The file actual_RSV-F_data.csv has some actual data for RSV F that is plotted by the notebook.
A schematic conceptually illustrating the the principle created with BioRender is in ./biorender/.
The fonts directory contains font files used for plotting:
- Comic Neue (
ComicNeue-Regular.ttf,ComicNeue-Bold.ttf): Used for the simulated data panels which are rendered in matplotlib's xkcd (hand-drawn) style. Comic Neue is a more legible alternative to Humor Sans that properly supports the minus sign glyph. - Open Sans (
OpenSans-Regular.ttf,OpenSans-SemiBold.ttf,OpenSans-Bold.ttf): Used for the actual data panels. Open Sans provides semibold weight support for intermediate emphasis between regular and bold text.
These fonts are registered at runtime by the notebook and do not require system-wide installation.