Overview of the major building plans: animals

Academic year: 2010-2011 Course code module 1BBIO-024 Semester: 1st semester Credits: 6 Study load (hours) 168 Theory (hours): 35,00 Practice/Exercises(hours): 40,00 Other (hours): Part-time program: 1/2 Instructor(s) Stefan Van Dongen Language of instruction: Dutch Semester exam information: exam in the 1st semester Contract restriction information: 1. Prerequisites *Algemene competenties General preriquisites: Specific competences are not required. Knowledge of English is important as most textbooks to be used are in English. Practical courses requires working with animals, slides and from time to time dissection of animals. *Sequentiality None 2. Objectives (expected learning outcomes) The student knows the most recent theories on the emergence and the body plan of the most important recent animal groups. This insight is essential for courses given in later years (fi. Form and function, Diversity ..). The student learns critical thinking on these issues and how the differentiation of the animal kingdom has originated and evolved. He/she can recongnize the major building plans within the animal kingdom on the basis microscopic and macroscopic observations including dissections. He/she is able to use English written textbooks for additional information.   3. Course content Overview of the builing plans of all major animal groups and the most important evolutionary transitions in the animal kingdom. This will be illustrated during the practical courses, some examples are: from colony to multicellular organisms (Protista - Porifera) emergence and complexity of body cavities (Nemathelminthes - Molluca) vetebrate animals: their basic body structure 4. Teaching method Direct contact: Lectures Practical sessions Personal work: Assignments - individual Assignments - in group Excursion(s) Portfolio 5. Assessment method Exam: Written, with oral presentation Closed book Multiple choice Open questions Practical exam Continuous assessment: Assignments Written assignment: Without oral presentation Portfolio: Without oral presentation 6. Compulsory reading – study material A syllabus will be available as well as a CD-rom with texts, pictures, movie fragments etc.. All these items will also be available on blackboard. 7. Recommended reading - study material Hickman, Roberts, Larson & I'Anson, 2004. Integrated principles of Zoology. Mc Graw Hill. 2nd edition or higher. 8. Tutoring At all times students are allowed to ask questions via blackboard or can visit the teachers personally laatste aanpassing: last update: 03/02/2009 11:02 ron.verhagen

Zoology

Academic year: 2010-2011 Course code module 1BBIR-11 Semester: 2nd semester Credits: 6 Study load (hours) 168 Theory (hours): 30,00 Practice/Exercises(hours): 45,00 Other (hours): Part-time program: 1 Instructor(s) Stefan Van Dongen Language of instruction: Dutch Semester exam information: exam in the 2nd semester Contract restriction information: exam contract not possible 1. Prerequisites *Algemene competenties Students have the required competencies to start education at the bachelor level *Sequentiality None 2. Objectives (expected learning outcomes) Students acquire a well founded basic knowledge of diversity in the animal kingdom and the general morphological patterns across the different animal groups. Students have gained general and basic insights in evolutionary and ecological principles, and how different life forms interact with their environment (biotic and abiotic). Students have acquired pratical skills to work independently with a microscope and have explored aspects of animal morphology with it through the observation and reporting of morphologies. They have a basic knowledge of using determination keys. 3. Course content The zoology course starts with a basic overview of principles of evolution and ecology and how an individual is made up out of cells, tissues and organs. An overview of diversity of the animal kingdom then follows, with the fylogenetic relationsships among the different groups as a common factor. For each animal group, special attention is paid to their importance for humans. Aspects of animal welfare are briefly toughed. In paralell to these theoretical courses, a number of basic skills are being addressed during lab-sessions. Students will learn how to use a microscope as a way to acquire knowledge about morphological diversity. Students are trained and coached on a continuous basis to be able to independently acquire and report on morphological patterns. The use of determination keys is thought. 4. Teaching method Direct contact: Lectures Skills training Personal work: Assignments - individual Supervised self-study 5. Assessment method Exam: Oral, with written preparation Closed book 6. Compulsory reading – study material Course notes are made available and additional information can be found in the lecture presentations made available through blackboard. 7. Recommended reading - study material consulting additional reading material is voluntary 8. Tutoring You can ask questions during and after the courses or make an appointment (preferably by email) laatste aanpassing: last update: 26/11/2008 17:20 stefan.vandongen

Probability Calculus and Statistics

Academic year: 2010-2011 Course code module 2BBIR-01 Semester: 1st semester Credits: 5 Study load (hours) 140 Theory (hours): 25,00 Practice/Exercises(hours): 25,00 Other (hours): Part-time program: 2 Instructor(s) Sandra Van Aert Stefan Van Dongen Language of instruction: Dutch Semester exam information: exam in the 1st semester Contract restriction information: 1. Prerequisites *Algemene competenties The students need basic knowledge of mathematics (linear algebra, integration, differentiation) such as taught in the first year bachelor in (Bio-Engineering) Sciences. *Sequentiality [Applied Mathematics I (BWET-001) OR Linear algebra and calculus (1BBIR-32)] AND [Applied Mathematics II (BWET-002) OR Applied Analysis (1BBIR-012)] 2. Objectives (expected learning outcomes) The general objective of this course is to familiarise students with the basic principles of probability theory and with the statistical methods used to support the analysis of scientific research questions. The 'Probability calculus and statistics' course contributes to the following competences : acquiring a basic understanding of relevant scientific methods and techniques, developing problem-solving skills and powers of analysis, synthesising and integrating different perceptions, learning to apply and assess methods in a critical way. More specifically, students will be able to justify, explain and apply statistical methods with regard to concrete research questions; they will acquire an understanding of statistical methods and will be able to construct accurate reasoning (from analysis to solution and conclusion). The course makes intensive use of the statistical package R. 3. Course content The course-content has the following chapters: General introduction : purpose of statistics Descriptive statistics : graphical and numerical representation to summarize the data Probability theory Univariate random variables : discrete and continuous random variables, probability distributions Multivariate random variables : joint probability distributions, covariance, correlation and variance Estimation of parameters : random sample averages, random sample proportions, random sample variance Interval estimation : setting up of reliability intervals Hypothesis testing : after a general introduction on testing, we deal with the most important tests for location, dispersion and distribution for different measurement scales and for 1, 2 or more than 2 populations respectively. Linear regression The course is entirely based on scientific and technological applications. 4. Teaching method Direct contact: Lectures Exercise sessions Personal work: Exercises 5. Assessment method Exam: Written, without oral presentation Closed book Multiple choice Open questions Practical exam Continuous assessment: Exercises Assignments (Interim) tests 6. Compulsory reading – study material Printed lecture notes available at the "cursusdienst". Additional examples, slides, exercises are provided via Blackboard. 7. Recommended reading - study material There is no additional literature that the students should read. 8. Tutoring Lecturers are available during and after the courses to answer questions. Students facing problems with the theoretical concepts and/or exercises are encouraged to contact the lecturers by email to make an appointment. laatste aanpassing: last update: 17/09/2010 12:05 sandra.vanaert

Statistics

Academic year: 2010-2011 Course code module 3BBIO-A-07 Semester: 2nd semester Credits: 6 Study load (hours) 168 Theory (hours): 30,00 Practice/Exercises(hours): 30,00 Other (hours): Part-time program: 1/2 Instructor(s) Stefan Van Dongen Language of instruction: Dutch Semester exam information: exam in the 2nd semester Contract restriction information: 1. Prerequisites *Algemene competenties Students have the required mathematical background to start bachelor studies *Sequentiality None 2. Objectives (expected learning outcomes) Students have gained insights in the basic principles of (bio)statistics. Biological problems can be translated into statistical hypotheses and appropriate tests can be selected and performed. Output from the package R can be interpreted. 3. Course content We start by providing an overview of the basic principles of statistics and the properties of a random sample. Then, we proceed by giving an overview of univariate statistical tests (t-test, ANOVA, regression, correlation, comparing distributions). The course is example-based and the software package R will be used to perform analyses. 4. Teaching method Direct contact: Lectures Exercise sessions Personal work: Exercises 5. Assessment method Exam: Written, without oral presentation Closed book Open book 6. Compulsory reading – study material Course notes will be made available 7. Recommended reading - study material Consultation of additional material is optional 8. Tutoring The teacher is available for further questions laatste aanpassing: last update: 08/02/2010 14:25 stefan.vandongen

Applied Statistics and Dataprocessing

Academic year: 2010-2011 Course code module 3BBIR-A-03 Semester: 1st semester Credits: 3 Study load (hours) 84 Theory (hours): 15,00 Practice/Exercises(hours): 15,00 Other (hours): Part-time program: 2 Instructor(s) Stefan Van Dongen Sandra Van Aert Language of instruction: Dutch Semester exam information: exam in the 1st semester Contract restriction information: exam contract not possible 1. Prerequisites *Algemene competenties A basic knowledge of probability theory and elementary statistics (including the inverse probability model) is assumed. These topics are shortly reviewed as a start. Furthermore a working knowledge of the following topics is assumed: mathematical techniques based on linear algebra and of the computational techniques necessary to write code in R. *Sequentiality Probability Calculus and Statistics (2BBIR-01) 2. Objectives (expected learning outcomes) Studenst will be able to us graphical representation of data as an exploratory tool for model selection. They wiil be able to select among different techniques to analyze data adequately (linear model with continuous, discrete or a mixture of both and the generalized linear model). Attention to reporting statistical investigations will be emphasized. 3. Course content The basic principles of data analysis, a survey of graphical techniques will be studied, starting from box-plots and going to scatter plot matrices. The linear model and the generalized linear model will be reviewed or introduced in an example driven approach. Computational techniques such as clustering an principal component analysis are exemplified. Some attention will be given to simulation of statistical models. 4. Teaching method Direct contact: Lectures Exercise sessions Personal work: Exercises Assignments - in group 5. Assessment method Exam: Written, without oral presentation Closed book Open book 6. Compulsory reading – study material Notes by the instructor are available on Bb 7. Recommended reading - study material A list of freely available material will be published on Bb 8. Tutoring Students can ask questions during or after the lectures or make an appointment by email laatste aanpassing: last update: 11/01/2011 09:55 stefan.vandongen

Biostatistics

Academic year: 2010-2011 Course code module MBIO1031 Semester: 1st semester Credits: 7 Study load (hours) 196 Theory (hours): 30,00 Practice/Exercises(hours): 45,00 Other (hours): Part-time program: 1+2 Instructor(s) Stefan Van Dongen Language of instruction: English Semester exam information: exam in the 1st semester Contract restriction information: 1. Prerequisites *Algemene competenties A solid understanding of basic statistical concepts, analysis of variance and regression. *Sequentiality Undefined 2. Objectives (expected learning outcomes) You are able to translate a biological question into a statistical hypothesis. You can select the appropriate technique to test this hypothesis. You can perform this technique in the programme R. You can interpret and present the outcome to a wide audience. 3. Course content The following topics are covered: ANOVA, two-way ANOVA, mixed models, regression, multiple regression, ANCOVA, generalized mixed models (binomial and poisson), experimental design (including simulation techniques), multivariate statistics (PCA, factor analysis, ordination, manova, discriminant analysis, canonical correlation). 4. Teaching method Direct contact: Lectures Personal work: Exercises Assignments - individual Project-based work - individual 5. Assessment method Exam: Written, without oral presentation Continuous assessment: Exercises 6. Compulsory reading – study material The R book (Crawley) 7. Recommended reading - study material Selected literature for each lecture 8. Tutoring Teachers are available after class for questions and individual counselling. laatste aanpassing: last update: 12/05/2010 11:44 pascale.claes

Conservation genetics

Academic year: 2010-2011 Course code module MBIO1043 Semester: 2nd semester Credits: 6 Study load (hours) 168 Theory (hours): 30,00 Practice/Exercises(hours): 30,00 Other (hours): Part-time program: Instructor(s) Zjef Pereboom Stefan Van Dongen Language of instruction: English Semester exam information: exam in the 2nd semester Contract restriction information: 1. Prerequisites *Algemene competenties A basic knowledge of molecular genetics, statistics and evolutionary biology at Bachelor level. Students are able to read and understand scientific literature *Sequentiality Undefined 2. Objectives (expected learning outcomes) You can apply the basic principles of genetics to a conservation context. You can explain the role of gene flow in maintaining genetic diversity, and the loss of genetic diversity in fragmented populations. You can define effective population size, extinctions, genetic drift, inbreeding, inbreeding depression and purging. You can perform a population viability analysis. You can analyze the results of molecular methods to estimate genetic diversity and population genetic structure (allozymes, RAPD, ISSR, AFLP, microsats), You can make a management plan for small populations, captive breeding and reintroduction. 3. Course content Biological diversity decreases worldwide at an increasing speed as a consequence of human activities. Conservation genetics studies the processes in small and isolated populations affecting genetic diversity, its fitness consequences and approaches to minimize fitness loss. Loss of genetic diversity not only induces problems of inbreeding, but also compromises the ability to adapt to changing environmental conditions. In this course, students will be introduced to the basic concepts of this relatively young discipline and will acquire basic skills to perform population genetic analyses and critically evaluate scientific literature. 4. Teaching method Direct contact: Seminars (possible question and answer sessions) Skills training Personal work: Exercises Assignments - individual Assignments - in group 5. Assessment method Exam: Written, with oral presentation Continuous assessment: Assignments Portfolio: With oral presentation 6. Compulsory reading – study material Frankham et al (2002) Introduction to conservation genetics. Cambridge UP ISBN 0-521-63985-9 7. Recommended reading - study material Selected literature for each lecture 8. Tutoring Teachers are available after class for questions and individual counselling. laatste aanpassing: last update: 12/05/2010 14:39 pascale.claes

Advanced biostatistics

Academic year: 2010-2011 Course code module MBIO20481 Semester: 2nd semester Credits: 6 Study load (hours) 168 Theory (hours): 30,00 Practice/Exercises(hours): 30,00 Other (hours): Part-time program: Instructor(s) Stefan Van Dongen Language of instruction: English Semester exam information: exam in the 2nd semester Contract restriction information: 1. Prerequisites *Algemene competenties A solid understanding of linear and generalised linear models. Sequentiality: Biostatistics (MA1) *Sequentiality Undefined 2. Objectives (expected learning outcomes) You can translate a complex biological question into an advanced statistical hypothesis. You can select the appropriate advanced technique to test this statistical hypothesis. You can perform this advanced technique in the programme R or Winbugs. You can interpret and present the outcome to a wide audience. 3. Course content The following topics will be covered in order to broaden and deepen the previoulsy acquired statistical knowledge and skills: model selection, mixtures, time series, robust statistics, survival analysis and Bayesian statistics. 4. Teaching method Direct contact: Seminars (possible question and answer sessions) Personal work: Exercises 5. Assessment method Exam: Written, with oral presentation Presentation 6. Compulsory reading – study material The R book (Crawley) 7. Recommended reading - study material Selected literature for each lecture 8. Tutoring Teachers are available after class for questions and individual counselling. laatste aanpassing: last update: 12/05/2010 14:33 pascale.claes

Experimental design

Academic year: 2010-2011 Course code module MBIO3002 Semester: 1st semester Credits: 4 Study load (hours) 112 Theory (hours): 20,00 Practice/Exercises(hours): 20,00 Other (hours): Part-time program: 1+2 Instructor(s) Stefan Van Dongen Language of instruction: Dutch Semester exam information: exam in the 1st semester Contract restriction information: 1. Prerequisites *Algemene competenties Students have insights in basic statistical modelling (statistics BA2 BIO) and have followed, or follow in parallel, the course on univariate techniques (MA1 BIO) *Sequentiality None 2. Objectives (expected learning outcomes) Students have aquired insights in different experimental designs and are able to select the best design for a particular problem. They are also able to critically evaluate the experimental design used in scientific papers and have aquired skills in programming in R to determine the power of a test. 3. Course content Basic principles about type I and I error rates will be reiterated. Next the use of simulation methods to determine power is applied to different tests including t-test, regression, ANOVA and more complex designs (block, split-plot, latin square). Finally, the use of longitudinal data and the problem of missing data is presented. 4. Teaching method Direct contact: Lectures Personal work: Assignments - in group 5. Assessment method Exam: Oral, with written preparation Closed book Open book 6. Compulsory reading – study material Not required 7. Recommended reading - study material Course notes and papers will be made available through blackboard 8. Tutoring NA laatste aanpassing: last update: 16/12/2009 11:09 jan.vos