20.109(F13): Mod 2 Day 1 System Design

Introduction

Today we will begin our journey through Systems Biology and the careful consideration of experimental and computational design that is required for large-scale biological engineering studies. At the end of lab today, you will choose two chemical inhibitors that target the Epidermal Growth Factor Receptor (EGFR) signaling network with the goal of overcoming a growing common problem in the treatment of disease -- drug resistance.

Part 1: Simulation of the EGFR network

There are many approaches to computational modeling that each aim to understand how information travels through a signaling network and ultimately produces a cell phenotype.

1. Open CellDesigner
2. Under Database choose "Import model from BioModels.net..."
   • A large list of models opens in a subwindow.
   • Scroll all the way down to the bottom and choose BIOMD0000000452 Bidkhori2012 - normal EGFR signaling
     • Note: only models that have been curated (or ...) by an SBML expert are shown in the list
   • Click Description to go to the BioModels database and read the abstract that describes the model.
   • Click Reference to see the official paper reference -- notice how computational modeling of biological systems is happening all around the world!
   • Finally, click Import to load the model into CellDesigner. (You may ignore the two errors at this point.)