BM 554 Modeling of Biological Systems – Instructor: Dr. Cengizhan Ozturk
(cozturk@boun.edu.tr)
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First Class (Feb 20, 06)
Introduction:
Have you ever build a model?
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Maybe not explicitly, but we all build models all the time.
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In his course, we will learn the art/science of modeling with a focus on biological
systems.
We will use an active learning environment in the classroom to think on some biological topics and learn
key concepts in modeling. We learn mathematics and software tools when needed.
Class Exercise:
You have 60 seconds.
Write your answer in this box in big letters
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BM 554 Modeling of Biological Systems – Instructor: Dr. Cengizhan Ozturk
(cozturk@boun.edu.tr)
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What is your answer?
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Did you notice the most important thing in modeling? Constraints (time was obvious here,
others are money, personal, resources)
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Another important property is its purpose (I did not tell you this in the previous question)
Most models are predictive. Some points when you do this type of class exercises:
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A rough answer is better than no answer
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A “ good “ model depends on circumstances
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A symbolic representation is powerful
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Equations (variables, parameters)
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Graphs
Most of the time is spend on cutting the details
William Ockham said: (commonly referred as Ockham’s razor)
(Non sunt multiplancanda entia praeter necessitatem)
Definition of a model: A partial representation of a real world problem. Kind of a caricature.
Certain heuristics (rule of thumbs) can be employed when building a model. We all do it implicitly; we
will learn how to do it explicitly.
We all make assumptions when building a model (Sometimes a chicken is just a sphere!)
We have to make a critique of our model. We should be able to learn what to improve in our model if we
have more time/resources.
Thinking of upper/lower bounds in predictive models is very helpful.
Homework 1:
How much do you think you will be spending for this class?
Go over the Matlab and Simulink tutorials below (or additional ones that you find at the web)
http://www.cyclismo.org/tutorial/matlab/
http://www.eng.fsu.edu/~cockburn/matlab/matlab_help.html
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BM 554 Modeling of Biological Systems – Instructor: Dr. Cengizhan Ozturk
(cozturk@boun.edu.tr)
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BM554 Modeling of Biological Systems - Second Class (Feb 20, 06)
Initial question:
A gas storage tank has volume of 3000 m3. It currently contains methane. The tank must be
emptied so it can be cleaned and inspected. Safety regulations require that it should contain no
more than 1 part in 100 of methane before work (which may include welding) can be started.
Nitrogen is available and can be pumped into an opening near one end of the tank. Another
opening (near the other end) will let gases escape. How much nitrogen will you need to dilute the
methane effectively?
Your first task:
Develop an approach to this problem, Make a plan.
Take about 10 minutes to prepare your plan, and come up with a representation that helps to
explain this problem to others. (diagram, algorithm, flow chart …etc) If too difficult make a list a
questions that you want to ask or assumptions that you will make.
Some other questions:
Is this really biology? What am I doing in this class?
Homework 2: Come up with a similar problem from a biological system
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BM 554 Modeling of Biological Systems – Instructor: Dr. Cengizhan Ozturk
(cozturk@boun.edu.tr)
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Heuristics that you might have used:
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Rephrasing the problem (did you understand it?)
Draw a simple diagram
Think what is going in and what is coming out?
Imagine yourself inside the tank.
Do you know any physical laws to consider? (Conservation of energy and matter)
Try to imagine the answer as number, graph, table
Try to identify the essential variables.
Choose a notation.
Look for a ready-made formula for the answer.
Look for simplifying assumption.
Try to find an easier version of the problem that you can solve.
Look for bounds (simple models that will definitely under or overestimate the answer)
Did you think what was the pressure in the tank? Is one atmospheric pressure a good assumption. Why?
Do they react? Do they mix (if yes, a thorough mixing or layering).
In-class discussion on several approaches
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A membrane model.
No air release model
Double the volume model
A ‘cognitive leap’ is sometimes needed. Most of the time you have to employ “Salami tactics”.
Write equations for two approaches below:
1. Let assume you are putting a small amount nitrogen x in a volume of V constantly, What will be the
concentration after N such step?
You answer:
2. Suppose we pump in p amount of nitrogen. Let the methane out. Mix the gases. What will be the
concentration after N such steps?
Your answer:
Mistake of jumping immediately into equations without understanding the problem.
What is the difference between an algorithm and a heuristic?
An algorithm guarantees an answer.
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