Simulations of simple ODE models in biology

These Shiny apps were written with sole purpose of teaching modeling in Biology.

The models provided are:

1. Simple bistable system [Bistability.R]
2. Glycolysis model of Selkov (oscillations) [Selkov_Glycolysis.R]
3. The Goodwin oscillator [Goodwin.R]
4. Gene driven by oscillatory transcription factor [Clock_driven_gene.R]

Installation and execution

1. Install R from https://www.r-project.org

2. Install RStudio Desktop from www.rstudio.com

3. Download the model files using one of the following two options:

   a. In a terminal, if you have git installed, run git clone https://github.com/bharathananth/models_for_teaching.git

   b. Click on the green button marked Code on the github page and select Download ZIP. Then unzip it.

4. Run the commands below inside RStudio:

install.packages(c("deSolve","tidyverse","magrittr","gridExtra","shiny"))
setwd("<directory where files are located>") 
runApp('<Name of model .R file>') # i.e., to run first model use runApp('Bistability.R')
# It is often convenient to the click on 'Open in Browser' button in the new window to view the app in your browser.

License

This work is shared under a GPLv3 license.