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Pharmacodynamic Function

blevin@emory.edu

Emory University
Dept. of Biology
1510 Clifton Road
Atlanta, GA 30322

Office: 404-727-2826
Lab: 404-727-2956
Fax: 404-727-2880

Programs

The following "programs" are written for Berkeley Madonna™, a mathematical modelling and differential equation solving software package developed by George Oster and Robert Macey at the University of California Berkeley and programmed by Tim Zahnley. You can use it with either a Windows or Mac operating system.

You can download Berkeley Madonna™ and try it out for no charge. This software is fully functional with the following exceptions:

• Models cannot be saved
• Graphs and tables cannot be saved or copied
• A "watermark" appears in all printouts (people will know you didn't buy it)
• The Register dialog appears each time the program is started

To run the programs below in Berkeley Madonna™,

1. Download and install Berkeley Madonna™ on your computer
2. Run Berkeley Madonna™
3. Copy and paste the programs below into Madonna (one at a time)
4. Run the program
5. Click on the Graph menu in the header and select "Choose Variables...". Remove those that you don't want and add those you do.
6. Click on the Graph menu in the header and select "Axis Settings...". In the "Scales" window, remove the "Automatic" scaling and click on Log for the Left and Right Y axes. You can then set the scale to that you desire, for example, a minimum of 1, a maximum of 1E10, with 10 divisions.
7. The Help menu is indeed helpful if you have problems (with the program, that is).
8. The names of the parameters and variables noted in the programs. You can change their values them as you like. Some values may be off a realistic scale and give you weird behavior. I don't offer any guarantees.

Although I have no financial interest in Berkeley Madonna™, it is not clear how ethical it would be for me to endorse this commercial product or encourage its purchase. Were it ethical, I would say something like, "It's super: a great way to program even relatively complex differential and difference equation models for theoretical studies, or to use as a tool for teaching students mathematical modeling or quantitative subjects that use differential and difference equations."

If you don't already know, running computer simulations is fun and a lot easier than doing real experiments. If you are of the right mindset, you can even feel like you are working.

Enjoy,

Bruce
 

Note: These programs are currently being modified and more programs are being added. If you want any specific programs or have trouble running any of these, write to Bruce Levin

Lytic phage model: batch culture with time delays

Model of host defense and phage and bacterial control of an acute infection

Simulation of a fluctuation test experiment

Simulation of cycling three antibiotics in hospitals

Phenotypic-Switch Model for Antibiotic Tolerance

SOS-Induction Model for Antibiotic Tolerance