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Optimizing Thermodynamic Bindings Parameters (in algebraic systems)

This repository contains tools for optimizing unknown parameters in algebraic systems that describe thermodynamic bindings of dyes and guests to a host. The package includes a script interface and a Shiny app for convenient usage.

Documentation

Documentation

Features

  • Identification of specific parameters (kHD or kGuest, I0, IHD, and ID) of different algebraic systems using the R package tsf.
  • Preliminary work involves defining systems in Maxima, and subsequent elimination of specific variables, yielding two polynomials. More details can be found in documentation and maxima code.
  • Each polynomial includes known variables (e.g., concentration of the host), variables to be optimized (e.g., kGuest), and an unknown variable (either d or hd).
  • For each algebraic system, a loss function is defined in R, taking the four parameters to be optimized as arguments and returning an error for the received parameter set.
  • The parameterset consists of kHD or kGuest, I0, IHD, and ID, along with constant parameters such as the concentration of the host and a data.frame containing the independent variable (dye or guest) and the corresponding signal.
  • Roots are calculated for each polynomial at each concentration of the independent variable, defining the concentration of either d or hd to the independent variable.
  • In silico signal calculation based on the formula: SignalInSilico = I0 + IHD[hd] + ID[d].
  • Comparison of the in silico signal to the measured signal, with the error returned by the loss function indicating the match quality.

Installation

Install R, RStudio, and a GitHub Package

Step 1: Install R

Linux (Ubuntu)
sudo apt update
sudo apt install -y r-base

Verify installation:

R --version
Windows/Mac
  • Download R from CRAN.
  • Follow the installer instructions.

Step 2: Install RStudio

  1. Download RStudio Desktop (free version) from RStudio's website.
  2. Install it by following the installation steps for your operating system.

Step 3: Install remotes for GitHub Packages

  1. Open R or RStudio.
  2. Install the remotes package:
install.packages("remotes")

Step 4: Install a Package from GitHub

  1. Load the remotes library:
library(remotes)
  1. Use the install_github function to install the package "tsf".
remotes::install_github("ComPlat/Thermosimfit", subdir = "tsf", ref = "v1.1") # Stable version
# remotes::install_github("ComPlat/Thermosimfit", subdir = "tsf") # Development version