Complex Systems in Biology

Welcome to the website of the module Complex Systems in Biology that is being taught in the summer semester 2015 at the Institute of Biology at Humboldt University. On this site you will find specific information about all the components of this module, the Lectures, the Seminar and the Practical Course (Fachkurs). Announcements will be made on this site and all the resources, e.g. papers for the seminar, code that is being used in the lectures and lecture notes will be made available for download in the respective sections. If you have further questions please see the contact page.

General Information about this Module

The module Complex Systems in Biology consists of the Lecture Introduction to Complex Systems, the Seminar Complex Systems in Biology and the Practical Course Computer Simulations and Modeling of Complex Systems. Information on each of these is available in the respective sections.

The module will provide an interdisciplinary perspective on complex dynamical phenomena in biological systems. A solid theoretical/modeling foundation will be provided as well as a number of applications to biological systems.
The module Complex Systems in Biology is part of the Masters Biophysics program and can count as a mandatory module (Pflichtmodul) in theoretical biophysics II or alternatively as an elective module (Wahlpflichtmodul) for the program.


The course will cover various topics in complex systems research, ranging from self-organization, pattern formation, critical phenomena, growth processes, nonlinear phenomena, chaotic behavior, synchronization and much more. You’ll find an overview here.


For further information contact me (Dirk Brockmann) by email or make an appointment. See contact page for getting in touch.


The basic requirements for the successful completion of the course is the basic knowledge of calculus and very basic knowledge of differential equations. Programming skills are not required but helpful.

If you are uncertain whether you meet the requirements, contact me.


The lecture will provide an introduction to the theoretical foundation for modelling and analysing complex biological systems.
The theoretic foundation will focus on dynamical systems theory, basic stochastic processes and complex network theory.
The lecture will also introduce all applied topics covered in the module and discuss their properties and dynamic aspects.

Practical Course (Fachkurs)

Computer Simulations are a central analysis tool for understanding complex dynamic phenomena in biology. In the practical course the student will learn how to model complex systems with netlogo, a free programming environment for agent based simulations. Netlogo is easy to learn also for students who have never been exposed to computer programming. Examples of netlogo programs and simulations can be found in the resources section.


The seminar is designed for students to focus more deeply and individually on a specific research project from the range of topics discussed in the lecture. Each student can pick a recent paper, the contents of which he/she will present in class. A pool of possible papers will be provided on the Seminar page.

Date and Time

Lectures will be between 8-10am on Wednesdays.
The Seminar will take place between 8-10am on Fridays.
The practical course will take place in the weeks of 26.6.-3.7.2015. This time slot may be subject to change.

More information is provided in the side bar.


The module will provide 10 credits.

Exams / Evaluation

A written exam will be given at the end of the semester on the theoretical foundation covered in the lecture.

The students will also be evaluated according to their oral presentation in the Seminar
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