Basic Tutorial

This tutorial covers basics features of BioModME by building a simplified, single compartment model. In this example, we focus on a set of reactions occurring in a cell. Compound “A” is synthesized by “Prot” at a constant rate and reacts with a limited supply of compound “B” found in the cell to make an intermediate “C1”. C1 undergoes an enzymatic conversion to “C2” and this new intermediate undergoes self-cleavage to the desired end product, “P”, and an inhibitor, “I”, of Prot. This inhibitor feedback binding to Prot stopping the synthesis of A, and thereby the entire reaction scheme.

../_images/cell_model.png

In the following sections of this tutorial, we will design the above system and look at how this program can be used to visualize and modify the data. The contents include the following:

  1. Creating model variables

  2. Building a system of equations

  3. Entering the inputs and outputs of the system

  4. Inputting numerical parameter values

  5. Solving and plotting the differential model

  6. Exploring the different types of plotting features

  7. Exporting the model and its features in meaningful ways

To use the online version of this application visit https://biomodme.ctsi.mcw.edu/. Note this app is stored on an Rshiny server that close unused applications after 15 minutes of inactivity. Your current model can be downloaded in the “Export” tab as an .RDS file and can be loaded in by opening the right sidebar of the application. The application can also be directly downloaded at https://github.com/MCWComputationalBiologyLab/BioModME and opened using the R programming language using stand shiny app protocol.