Graduate School of health and Medical Sciences

Bioinformatics for Microbiology
Provider: Faculty of Health and Medical Sciences

Activity no.: 3122-19-00-01	There are no available seats
	Enrollment deadline: 21/10/2019

Date and time	18.11.2019, at: 08:30 - 29.11.2019, at: 17:00
Regular seats	12
Course fee	12,480.00 kr.
Lecturers	Henrik Christensen
ECTS credits	8.50

Contact person	Henrik Christensen E-mail address: hech@sund.ku.dk

Enrolment Handling/Course Organiser	PhD administration E-mail address: phdkursus@sund.ku.dk

Aim and content This course is free of charge for PhD students at Danish universities (except Copenhagen Business School), and for PhD students at graduate schools in the other Nordic countries. All other participants must pay the course fee. Anyone can apply for the course, but if you are not a PhD student at a Danish university, you will be placed on the waiting list until enrollment deadline. This also applies to PhD students from Nordic countries. After the enrollment deadline, available seats will be allocated to applicants on the waiting list. Learning objectives A student who has met the objectives of the course will be able to: 1. To be able to understand and discuss the advantages and disadvantages of the methods, analyze data in a bioinformatics context using the procedures described below and draw valid conclusions based on the results obtained. 2. To assemble Illumina reads, to do simple prediction of open reading frames from DNA sequences and to deposit sequences with NCBI. 3. To download DNA sequences from DNA databases, to understand the detailed information of proteins in Uniprot, to view 3D structures, to predict the function of unknown proteins by database comparison. 4. To know the differences between local compared to global pair-wise and multiple alignments, to perform more complicated alignment of proteins, to perform BLAST searches and to obtain precise data of similarity and identity. 5. To construct a phylogenetic tree by neighbour joining including the bootstrap as well as to use maximum likelihood and Baysian inference and to select the most appropriate phylogenetic method for the situation. 6. To design PCR primers to target a single DNA sequence and to design PCR primers to separate a target group of sequences from a non-target. 7. To gain access to prokaryotic genomes and compare organization of prokaryotic genomes and perform SNP analysis including phylogenetic trees based on whole genomic sequences. 8. To perform sequence based identification of prokaryotes based on 16S rRNA sequences including high throughput 16S rRNA amplicon reads (metagenomics) and to use computer programs to infer population structures. To perform simple sequence based identification of virus, fungi and parasites. 9. To use the tools introduced for independent work on their own project related to their PhD study. Content Bioinformatics for Microbiology first introduces the basic bioinformatics tools including sequence assembly, annotation, databases, pair wise and multiple alignmends, protein structure prediction and primer design. More in depth treatments of phylogeny, comparative genonomics and sequences based identification then follows. The bioinformatical programs will both be introduced with Windows or Apple based operating systems as well as on Linux. To allow easy access to installation of Linux pipelines, VirtualBox can be installed on the participants computers. The Linux pipelines are suited for large scale genomic investigations. The first week will provide hands on experience with the most common diciplines and computer programs. In the second week the participants will work in groups on a project they formulate on their own combining a problem from microbiology which can be from their PhD project with the bioinformatics toolbox. The participation of the course will be evaluted by activities, persentation of the project and a written report after the course. Participants The course is relevant to Ph. D. students with a very limited background in bioinformatics as well as participants who received some training in bioinformatics during their candidate study. The course is mainly relevant for participants that work with prokaryotes, although topics in relation to virus, fungi and parasites are covered as well. The participants need to have basic knowledge about biochemistry and genetics at BSc level. The participants need to bring at least one updated labtop computer with one of the major operating systems (Windows, Apple, Linux), some extra space on the hard disk drive best with 8 or more Gbyte RAM and which can access wireless networks. To coordinate teaching in relation to participants backgrounds, applications including CV with full contact address including Email address and a 1/2-1 page justification of educational qualifications can be submitted to Email: hech@sund.ku.dk when participants have got the message that they are enrolled on the course. Relevance to graduate programmes The course is relevant to PhD students from the following graduate programmes at the Graduate School of Health and Medical Sciences, UCPH: Molecular Bacteriology and Infection Biostatistics and Bioinformatics Veterinary Clinical Sciences Language English Form The course is theoretical and practical. During the first week, theory will be introduced by lectures where the participants are encouraged to contribute to some of the theoretical presentations. Practical computer exercises will have the main focus and the outcome of the exercises will be discussed between teacher and participants. The exercises allow training in relation to the theory introduced and will be solved in groups of 1-3 persons per computer with help from the teachers. The book "Introduction to Bioinformatics in Microbiology" edited by Henrik Christensen, Springer will be used to provide the theoretical background. A preliminary outline of the course can be found at www.bioinformatics.es. The second week will be devoted to project work that will involve groups of 1-3 students and be related to cases with microorganisms of environmental, food, veterinary and human health importance if possible based on data from the participants own PhD project. The participants will give a presentation of their project work the last day of the course and deliver a short report after the course. The outline of the report will have to be like a short scientific paper. Course director Henrik Christensen, associate professor, Department of Veterinary Animal Sciences, University of Copenhagen, hech@sund.ku.dk Teachers Egle Kudirkiene, assistant professor, Department of Veterinary and Animal Sciences, University of Copenhagen, Dates 18 - 22 and 25 - 29 November 2019 Time: 8:30 - 12:00 and 13:00 - 17:00 Course location SUND / SCIENCE Campus, Frederiksberg Registration Please register before 21 October 2019 Seats to PhD students from other Danish universities will be allocated on a first-come, first-served basis and according to the applicable rules. Applications from other participants will be considered after the last day of enrolment. Note: All applicants are asked to submit invoice details in case of no-show, late cancellation or obligation to pay the course fee (typically non-PhD students). If you are a PhD student, your participation in the course must be in agreement with your principal supervisor.

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