BioModMe is an application that is meant to streamline building biological computational models. It is an all-in-one tool that allows the user to build a model, solve for its mathematical equations, and plot all relevant features.
The application can be accessed online at https://biomodme.ctsi.mcw.edu.
Step 1: Install R and RStudio
Before running the app you will need to have R and RStudio installed (tested with R 4.1.1 and RStudio 1.4.1717).
Please check CRAN (https://cran.r-project.org/) for the installation of R.
Please check https://www.rstudio.com/ for the installation of RStudio.
Step 2: Install the R Shiny package and other packages
Start an R session using RStudio and run these lines:
load.lib<-c("shinydashboard", "bs4Dash", "shiny","ggplot2","gridExtra","shinythemes",
"shinyWidgets","shinyjs","DT","tidyverse","dplyr","rhandsontable","data.table","ggpmisc",
"colourpicker","shinyBS","shinyjqui", "bsplus", "plotly", "deSolve", "waiter", "ggpubr",
"viridis", "Deriv", "shinycssloaders")
install.lib <- load.lib[!load.lib %in% installed.packages()]
for (lib in install.lib) install.packages(lib, dependencies = TRUE)
sapply(load.lib, require, character = TRUE)
Step 3: Start the app
Download the zip file of code for this application from Github. Start an R session using RStudio, navigate to the downloaded unziped folder and run these lines:
shiny::runApp()
If you open the "ui.R" or "server.R" scripts in Rstudio, you will notice a "Run App" button at the top right of the script screen that can also be used to run the application.