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SPRFittingPaper2023.jl

SPRFittingPaper2023.jl provides a library of functions that were used in fitting the particle-based jump process model of [1] to SPR data. The library provides three main components:

  1. A forward solver for the particle-based jump process reaction model for bivalent antibody-antigen SPR interactions (in both two and three dimesions).
  2. Functionality for building the surrogate model approximation to the particle-based jump process model over a portion of parameter space.
  3. Functionality for fitting the surrogate model to SPR data sets to produce estimates for the biophysical parameters.

For each of these components we provide a tutorial on their use as part of this documentation. Readers interested in our general methodology should consult [1].

Installation

To install into your main Julia environment

using Pkg
Pkg.add(url="https://github.com/isaacsas/SPRFittingPaper2023.jl.git")

It is often better to first create a new, clean environment in the directory where you'll have your fitting script. Start Julia in that directory and then

using Pkg
Pkg.activate("Environment_Name")
Pkg.add(url="https://github.com/isaacsas/SPRFittingPaper2023.jl.git")

You can use the package manager or "Pkg.add" to add any other needed packages to that environment.

Bibliography

  1. A. Huhn, D. Nissley, ..., C. M. Deane, S. A. Isaacson, and O. Dushek, Analysis of emergent bivalent antibody binding identifies the molecular reach as a critical determinant of SARS-CoV-2 neutralisation potency, in review, available on bioRxiv (2024).