Within the bachelor program of the Department of Biology we teach eightcourses introducing modeling and bioinformatics to students in biology andthe sciences in general. These courses run for 10 weeks, half-time, and eachcourse is 7.5 EC-points. A subset of these courses can be attended bystudents from all over the world and will be given in English wheneverrequired. Students preparing for the master Bioinformatics and Biocomplexityare advised to attend the bachelor courses listed below and supplementthat with biological courses in their field of interest.
Level 1 courses:
Modern biology is accumulating enormous amounts of information resultingin very rich data bases. Additionally, modern biology increasingly involvesa systems approach, aiming to understand biological processes from theinteractions of its constituent parts Therefore, we aim to introduce at leastthe basics of bioinformatic pattern recognition, essential to deal withbiology’s big data, and the basics of mathematical modeling, crucial for asystems approach, to all students in biology. These topics will be coveredas part of the courses Quantitative Biology and Genomics, respectively.These level-1 courses are given to a large (>200) group of students.
Quantitative Biology (Kwantitatieve Biologie)
In the first half of this course, you will be introduced to the programminglanguage R and learn the basics of statistics. The second part of the coursestarts with an introduction to mathematics of non-linear differentialequations (ODEs). Students learn to analyze models by phase plane methods(i.e., nullclines and local stability analysis). After mastering thesemathematical skills, the remainder of the course focuses on interpretingresults from mathematical models in biological terms. Reviewing classicalmodeling examples from a variety of biological disciplines, students learnto translate between mathematical models and biological insight.
For this course basic knowledge of working with fractions, logarithms,exponentials, differentiation, drawing of functions, solving equations, etc.is essential. Students will brush up their knowledge of these mathematicalsubjects during the first part of the course using the electronicmathematics environment DWO. For students wanting to further brush upthese we have compiled the following site(in Dutch).
Genomics (Genomica)
In the first part of the course, you will gain insight into theprinciples and concepts of classical and systems genetics,genetic techniques, genotype-phenotype interactions and how genes can beidentified and investigated. The second part of the course gives anintroduction in bioinformatics methods (like clustering, building phylogenies,sequence alignment and blast). We aim to explain how these methods work andhow they have contributed to biological research.
Level 2 courses:
Biological modeling (Biologische modellering)
Mathematical modeling plays an important role in biological research.This course covers modeling biological populations, e.g., populations ofbacteria and phages, cells, epidemics, and ecological populations.We derive these models from biological principles, such that students learnhow to develop models themselves. In the first part of the course, we devisemodels for population growth, consumption of resources, and competition.This leads to models resembling the Lotka-Volterra model, predator-prey modelswith various functional responses, and various models for competitiveexclusion and co-existence. Students learn to compute steady states andperform phase plane analysis to study the properties of their models,and to interpret these mathematical properties biologically.We work with paper-and-pencil exercises and a R-script called Grind toperform phase plane analysis, stability analysis, and simulation.In the second part of the course, we read several papers, and students workon their own research project that typically starts with a recent paper.Results are reported in a symposium and a written report.This is a level-2 course for motivated groups of 30-40 students.We require participants to have a basic knowledge of differentialequations (i.e., the material taught in our level-1 Quantitative biologycourse), and/or have a sufficient background in math or modeling such thatthey can catch up. The home page providesgeneral information about the course content (in English).
Data science and biology (Data science en biologie)
This time is characterized by the enormous amount of available data.These so-called ‘big data’ are especially abundant in biology since affordablehigh-throughput DNA sequencing technologies exist, by which an enormous numberof genomes, metagenomes, transcriptomes, epigenomes, and variations thereofare generated. Also in other biological disciplines big data files are nolonger rare. In this course you learn the theory and skills to obtain novelbiological insights from big data files. In the Quantitive Biology and Genomicscourses, you have already become familiar with programming and these skillswill be sharpened in this course. You will learn to use the Unix terminaland to write scripts in Python. The focus will be on how to go from a bigtable with numbers to a visualization that gets the data structure clearlyacross. Moreover, an introduction to machine learning will be given: how tocluster or classify data and how to make predictions for new data points basedon existing data?
Level 3 courses:
Computational Biology (Computationele Biologie)
The emphasis of this course is on composing exact models, based onspecific hypotheses, in different formalisms (ODEs, cellular automata,agent based models). The models are analyzed, the results yieldinginsights in the original biological system. The models that arestudied address fundamental questions from a variety of biologicalfields like evolution, development, and behavior. This is a level-3course given at two levels for bachelor and master students. Forpractical information please read more.
ImmunoBiology (Immunobiologie)
The immune system comprises innate and acquired defense mechanismsagainst (pathogenic) microorganisms. Immunology has traditionallybeen a qualitative science describing the cellular and molecularcomponents of the immune system and their functions.In the last twenty years this traditional approach is beingreplaced by a systems biology approach, where theoretical studies helpsto interpret experimental data, to resolve controversies,and --most importantly-- to suggest novel experiments allowingfor more conclusive and more quantitative interpretations.This course is planned to give an overview of wet and theoreticalimmunological research.We aim to provide insight into the function of the immune system inhealth and disease and to give an introduction to the use ofmathematical models and bioinformatics in immunological research.For practical information please read more.
Genome Biology (Genoombiologie)
Biology is increasingly being performed at the genome-wide level andthis level 3 course deals with various aspects of this research. Thefirst three weeks of this course are focusing on genome-organisation,the second three weeks centre around genome evolution, and the thirdweek deals with the steps from the genome to the phenotype. Altoughthis course is coordinated by Guido van den Ackerveken, our departmentis heavily involved in this course because of the importance ofbioinformatics in genome-wide analyses and our knowledge of genomeevolution.
