MCB 137 Exercises and Solutions

You will need Adobe Acrobat Reader 8 or later to read the exercises and solutions. You can download it here.

Guides

• Visual Madonna Guide

• Madonna Manual

References

• Reading List

Lesson 1: Learning Berkeley Madonna™

• Follow the Money

Lesson 2: Physiological models 1

• Pharmacology

• SA.txt

• ASA.txt

• SalicylicAcid.txt

• Benzene Example

• Steroid Example

• Homework solutions

Lesson 3: Chemical systems

• Chemistry

• Michaelis-Menten Kinetics

• Notes on numerical solution of differential equations

• Thyroid Diagram

• Life at low Reynolds number

Lesson 4 : Systems biochemistry

• Biochemical Control

• A Simple Hysteresis Switch

• Kinase Cascade Switches

• Tyson (2003)

Lesson 5 : Biological oscillations 1

• Excitable and Oscillatory Systems

• Tyson Chapter: Oscillations

• Somitogenesis Delay Model

• Cell Cycle

• Goldbeter Model for the mitotic oscillator

Lesson 6 : Neural systems

• The Passive Axon

• Voltage Activated Channels

• Voltage Clamp

• Complete Axon Chapter

Lesson 7: Biological Oscillations 2

• Calcium Oscillations

• Cell Cycle Oscillations

• Goldbeter Calcium Oscillation Paper

• Nullclines

Lesson 8: Epidemiology

• Virus Dynamics

• Perelson (1996)

• Bonhoffer (1997)

Lesson 9: Physiological models 2

• Thyroid

• Trouble Shooting

Lesson 10: Cellular regulation systems

• pH Regulation

• pH Data Sets

Lesson 10: Arrays

• Arrays

• Jin (1999)

• Delay model

Midterm Assignment

• Exercises due after mid-term break

Sample Models

Small Icons

PDF Files

Old Project Files

Home / Dr. Macey / Dr. Oster / Schedule / Exercises / Links & References