Introduction to Biological Modeling

The modeling of real biological systems can aid greatly in the understanding of the behavior of such systems, and in predicting how they will behave under all kinds of circumstances. In this course, we will study how to build models using differential equations, and how to analyze their behavior.
We will use a context of diverse examples from biology, including ecological growth, predator-prey systems, enzyme reactions, genetic regulation, animal coat patterns, and firing neurons.
Models are built from the ground up, using biological knowledge and mathematical tools, enabling the students to gain the experience necessary to build their own models, analyze them, and valuate their worth.
The course runs for 5-6 weeks in period 1, and is a combination of lectures, tutorials, and computer practicals on your own laptop using Mathematica. No previous experience with Mathematicais required (we will start practicals with a *Mathematcia-*tutorial). The practicals account for 20% of your grade. A final written test at the end of the course accounts for 80%.

Understanding of the behavior of biological systems by means of mathematical modeling.
The ability to construct ODE-based mathematical models of biological systems.
To develop mathematical skills for analyzing such models.
To learn to approximate solutions and study model behavior using software.
To have specific knowledge of growth models, modeling of population interactions, separation of time scales, enzyme kinetics, genetic regulation, excitable systems, and spatial models.

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High-school level biology and mathematics, most notably elementary functions (including lines, parabolas, fractional functions, exponentials, and logarithms), elementary algebra (arithmetic skills, including manipulation of fractions, and solving equations involving elementary functions), and functional analysis (including finding zero crossings and asymptotes, and computing and analyzing derivatives).

• Book Reader ‘Introduction to Biological Modeling’ – will be made available in pdf.
• Software A laptop with Mathematica installed – see https://students.uu.nl/gratis-software Always bring your laptop to the computer practicals! Mathematica is available for free for UU students. It can be run without installation from your own laptop using MyWorkplace, but we strongly recommend you install it fully on your laptop before the start of the course. See the link above for installation instructions.