| Responsible Department | Department of Veterinary Disease Biology | ||||||||||||
| Course Dates | 5 - 9 November, 12 - 16 November - 2012 (8.30-17.00) | ||||||||||||
| Course Abstract | The course introduces areas of bioinformatics relevant to microbial research within natural, agricultural, veterinary, and human health sciences at Ph. D. course level. The first week introductory course is intended for students without previous background in bioinformatics. The second week is for students who have attended the first week or with bioinformatical skills achieved elsewhere. | ||||||||||||
| Course Home Page | http://www.staff.kvl.dk/~hech/ | ||||||||||||
| Course Registration | Applications including CV with full contact address including Email address and a 1/2-1 page justification of educational qualifications should be submitted to Email: hech@life.ku.dk not later than 15 October (first come, first in). | ||||||||||||
| Deadline for Registration | 15 October (first come, first in). | ||||||||||||
| Credits | 6 (ECTS) | ||||||||||||
| Level of Course | PhD course | ||||||||||||
| Organisation of Teaching | Theoretical and practical course with one week introduction course and a second week research project. | ||||||||||||
| Language of Instruction | English | ||||||||||||
| Restrictions | 20 | ||||||||||||
| Course Content | |||||||||||||
| Week 1: Theory will be introduced by lectures in 35 % of the course time. Practical computer exercises will cover another 50 % of the course and 15 % of course time will be used to discuss exercises. The exercises allow training in relation to the theory introduced and will be solved in groups of 1-3 persons per computer with extensive help from the teachers. Day 1: DNA sequencing, databases, search functions and sequence exchange. Day 2: Pairwise -, multiple alignment, Day 3: Primer-design and phylogeny. Day 4: Genomics including metagenomics. Day 5: Sequence based typing (MLST etc) and identification of microorganisms. Week 2: The project work will involve groups of 1-3 students and be related to cases with microorganisms of environmental, food, veterinary and human health importance. This part of the course is planned for students who want to work with their own projects related to their Ph.D. study in more detail. The week can be used directly to produce material for a scientific paper in relation to investigations in progress or the participant can do pilot investigations relevant to coming activities. Students cannot retrospectively hand in material for the report that was done before the course and included in manuscripts. The project will be extensively supervised and will aim at writing up a project report. The outline of the report should be like a short scientific paper (Introduction, Material & methods, Results, Discussion, References). For students without a project it will be possible to select from predefined projects. | |||||||||||||
| Teaching and learning Methods | |||||||||||||
| Theoretical and practical course with one week introduction course and a second week research project. Each participant can choose to give a presentation (30 min) of theory from the course book (week 1) or from the project (week 2). E-learning will be used for some parts of week 2. | |||||||||||||
| Learning Outcome | |||||||||||||
| The aim is to teach applied bioinformatics to the level that allows independent investigations and reporting in scientific papers relevant for the Ph. D. thesis. The course introduces areas of bioinformatics relevant to microbial research within natural, agricultural, veterinary, and human health sciences at Ph. D. course level. The first week introductory couse is intended for students without previous background in bioinformatics. The second week is for students who have attended the first week or with bioinformatical skills achieved elsewhere. | |||||||||||||
| Course Literature | |||||||||||||
| Textbook for week 1 (obligatory): Zvelebil, M. & Baum, J. O. 2008. Understanding Bioinformatics. Garland Science, New York. Supplementary course books especially for week 2 (not obligatory): Felsenstein, J. 2004. Inferring phylogenies. Sinauer, Sunderland. Nei, M. and Kumar, S. 2000. Molecular evolution and phylogenetics. Oxford Univ. Press. Petsko, G. A. and Ringe, D. 2004. Protein structure and function. New Science Press, London. | |||||||||||||
| Course Material | |||||||||||||
| You need to buy the book: Zvelebil, M. & Baum, J. O. 2008, listed above. Before the course you will have to read chapters 1-5 (background, protein structure, databases and alignments), 7 (evolution), 11 (secondary structure) and 16 (clustering and statistics) (320 pages). If you have a similar bioinformatics book already you can use it if the same topics are included. You will also have to read a compendium (35 pages) provided online before course start. | |||||||||||||
| Course Coordinator | |||||||||||||
| Henrik Christensen, hech@life.ku.dk, Department of Veterinary Disease Biology/Section for Microbiology, Phone: 353-32783 | |||||||||||||
| Course Fee | |||||||||||||
| According to KU rules. | |||||||||||||
| Course Costs | |||||||||||||
| According to KU rules. | |||||||||||||
| Type of Evaluation | |||||||||||||
| Week 1. Evaluation based on answers to the first week exercises. Week 2. Evaluation of project report of second weeks work. | |||||||||||||
| Work Load | |||||||||||||
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