COURSE COMPUTATIONAL BIOLOGY
Coordinator: Prof. dr. Paulien Hogeweg
Theoretical Biology and
Kruytgebouw, Padualaan 8
3584 CH Utrecht
Time & Place:14 November 2016- 3 Februari 2017
On Monday 13:15-17:00; Tuesday and Thursday
The course will be held in various lecture rooms in the Uithof.
(changed nov 8 2016)
SYMPOSIUM Januari 6th 2017 (10-15hr).
This course is for bachelors and master students, as well as PhD
students. Please consult to Prof.
Anybody who has successfully completed the Theoretical Ecology
course can participate. The 3rd year
bachelors students who have completed the Systems Biology course
can also participate. Others please consult Prof.
dr. P. Hogeweg
Computational Biology uses computer modeling to investigate
biological problems. The course teaches a variety of modeling
techniques and techniques to analyse the model behaviour. Moreover
biological theory obtained by computational modeling is examined.
During the course, the emphasis will be on composing exact models,
based on specific hypotheses. The models are analyzed, the results
yielding insights in the original biological system. The models that
are studied address fundamental questions from a variety of biological
fields, among which:
- Evolutionary dynamics
- eco-evolutionary dynamics and spatial pattern
- host-pathogen co-evolution
- genome evolution, e.g. interaction between gene regulation
- evolution of complexity, robustness and evolvability
- Developmental dynamics (from genes to organisms) (plant and animal models will be used)
- pattern formation
- cell differentiation
- morphogenesis and mechanical interactions between cells
- EVO-DEVO (evolution of development).
- Network dynamics
- gene regulation and metabolic networks
- RNA interference
- behavioral self-structuring through local interactions
- interface between learning and evolution
(Spatial) pattern formation and emergent properties are
common themes emphasised in all these areas
and the related general theory is introduced as a separate module.
A number of different model formalisms are used, namely:
- Non-linear differential/difference equations (ODE
- Reaction Diffusion Systems (PDE)
- Cellular automata machines
- Event based models
- Individually oriented models
- Evolutionary computation
- Hybrid models using several combinatiions of the above formalisms
Analysis tools include
bifurcation analysis, sensitivity analysis, and various pattern
The course is given on tuesdays and thursday. A typical day
starts with lectures from 10:00 to 13:00, followed by computational
until about 17:00. Literature will be handed out related to the
computer excercises , and at the end of the course, litterature
seminars are given by the students.
The student's final mark is primarily based on the exam;
a miniproject and litterature seminar for rounding the grade
Course materials :
Before you run anything, make sure to run "/clz/bio-binf/setup-binf", and follow instructions :)