Time: Friday, July 16, 9:00 am - noon
Place: Bioinformatics Computer Core Lab (Rm 104), Life Sciences Bldg
Organizers: Tarynn M. Witten
Audience: Primarily 1st year students

Topics of session

• Understand the underlying concepts of the five scenarios motivating this research simulation.
• Continue to develop the basic ideas behind mathematical modeling/computer simulation and to move to more complex models of biological systems.
• Continue to understand the basics of the Maple programming language for solving differential equations (Maple4Students) and extend that knowledge into systems of differential equations.
• Understand modeling basics behind some multivariate differential equations models such as the autocatalytic oscillator, the Hopf BZ-CSTR chaos model, the Rossler Chaotic Oscillator, and the cyclical neutropenia model.
• Be introduced to some of the more sophisticated modeling concepts such as chaos, attractors, and stochasticity.
• Be introduced to high performance computing models through a discussion of modeling the T. cruzi parasite (causal agent of Chagas disease) and a cat brain column.

Resources of session

• Notes: None. You will get them as we go in class.
  
• Papers: Look through the papers. Do not let the mathematics scare you. Just get a sense of what the papers are attempting to address.
• CyclicalNeutropeniaModeling.pdf – Examines the problem of modeling the production and regulation of circulating blood neutrophil numbers.
• CellularAutomataArticleWithKier.pdf – Examines the role of cellular automata in biological modeling.
• ModelingTheHeart.pdf – Looks at high performance computer modeling of the heart.
• Programs:
• There are a number of programs we will use today. When you get into class, download the file Day3Programs.zip. Save it to the desktop folder you created on Day 1.
• Open up Maple so that it is ready to be used.
• Links:
• Maple – Maplesoft Home Page
• Maple4Students – More on Maple for students
• Mathematica – Steve Wolfram’s Home Page for Mathematica

Before coming to the session

• Review the scenarios. Make sure to read Scenario5.
• Read the Cyclical Neutropenia Modeling article from the Day 3 article list and be prepared to discuss it in class. Also sketch out, using what you have learned about Maple, a system of differential equations to model the cyclic neutropenia. Use what the article tells you. Obtain all necessary parameter and initial condition values to make a Maple run in class.
• Download the programs for today.

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