Hi!

⊕ A rolling die: A complex system.

Welcome to the website of the course Complex Systems in Biology that I teach every winter term at the Institute of Biology, at Humboldt University of Berlin. On this site you will find specific information about all components of this course, the Lectures, the Seminar and the Lab Course (Fachkurs).

All resources, e.g. papers for the seminar or information mentioned in class, suggested reading material, code that is being used in the lectures, lecture notes and presentation slides will be made available here for download in the respective sections.

The Posts

The most important section on this site is the Post Section. It’s like the blog section of the course. Every time there’s a new piece of information, it goes into a new blog post, some blog posts are updated regularly.

General information for the particular semester are also found in the corresponding blog posts for that semester. Everything is neatly ordered there.

Announcements will be made in the Posts Section, too.

What is this course about?

The aims of this course are… ⊕ A growing sandpile: An example of self-organized criticality.

providing a solid theoretical foundation…

… for understanding complex dynamic phenomena in biological, physical and social systems. The lecture will cover a number of basic theoretical modeling methods, analysis tools and techniques that are required to understand and appreciate the richness and beauty of complex systems,

giving a broad overview of various dynamical phenomena…

… in biological systems that are considered keystone complex systems, learning how to extract the key and often hidden features and mechanisms that generate complex behavior, and …

learning techniques …

… for constructing and designing models that capture observed phenomena and specific example systems. ⊕ Complex Networks: A topic we will discuss in class.

Complexity Explorables

A while back I launched the Complexity Explorables website. It contains a collection of models that exhibit complex behavior and help explaining complex systems observed in natural and social systems. The Complexity Explorables will play a prominent role in the course.

Take a quit break and explore some here.

In the seminar, every student will give a presentation on one of the explorables.

Topics:

The course will cover various topics that play an essential role in complex systems. Most of these topics are concepts and phenomena that occur across a broad range of fields. We will be discussing the topics listed below. When you click on a topic, you’ll be directed to a collection of Complexity Explorables that illustrates one of more of the topics. ⊕ Five metronomes on a board on two cans: A simple experiment for spontaneous synchronization.

• Chaotic Systems
• Synchronization
• Pattern formation
• Critical phenomena & Tipping points
• Growth processes
• Collective behavior
• Complex networks
• Fractals & Self-similarity
• Cooperative Systems

General Information

Language

The course language is English. This means the lectures will be given in English and the students given there seminar talk in English, too. ⊕ Tipping points: Irreversible processes occur frequently in complex systems.

The Lecture

The lecture will provide an introduction to the theoretical foundation for modelling and analysing complex biological systems. The lecture will also introduce all applied topics covered in the module and discuss their properties and dynamic aspects. Lot’s of keystone models will be discussed.

The Seminar

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 will pick a Complexity Explorable and study the system it describes and related papers in more detail.

Each student will have to give a presentation of the explorable. The presentations will be collected on the Seminar page.

Explorables are picked on a first come first serve basis.

The Lab Course

Computer simulations are a central analysis tool for understanding complex dynamic phenomena in biology. In the lab course the students will learn how to model complex systems with netlogo, a free programming environment for agent based simulations. Netlogo is easy to learn also useful for students who have never been exposed to computer programming.

Don’t worry, you are going to have a blast. ⊕ Collective Behavior: How do birds flock? We will discuss it in this course.

Requirements

The basic requirements for the successful completion of the course is a 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.

Every student requires a laptop computer. Most students have a laptop, for those of you who do not have a laptop I can provide one.

Contact

All the details are given in the contact section.