Bioinformatics for Microbiology

Aim and content

This course is free of charge for PhD students at Danish universities (except Copenhagen Business School), and for PhD Students from NorDoc member faculties. 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 NorDoc member faculties. 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. 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. Assemble Illumina reads, predict open reading frames from DNA sequences, annotate genomes and to deposit sequences at NCBI.

3. Be introduced to Nanopore sequencing and analysis.

4. Have an overview of the bioinformatics toolbox including databases, dataformats, accession numbers, download of DNA and protein sequences, proteins in Uniprot, 3D structures of proteins, predict the function of proteins, know differences between local compared to global pair-wise alignments, obtain precise results of similarity and identity, make multiple alignments, perform BLAST searches and to construct phylogenetic trees including the bootstrap as well as to use maximum likelihood.

5. Gain access to prokaryotic genomes and compare prokaryotic genomes with respect to core and accessory elements and perform SNP analysis including phylogenetic trees based on whole genomic sequences. To have a basic understanding of full DNA metagenomics.

6. Perform sequence based identification of prokaryotes including high throughput 16S rRNA amplicon reads (metagenomics). To perform simple sequence based identification of virus, fungi and parasites.

7. To use the tools introduced for independent work on their own bioinformatics 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 alignments. More in depth treatments of phylogeny, comparative genonomics, sequences based identification and 16S rRNA amplicon analysis (metagenomcis) 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 disciplines and computer programs. In the second week the participants will work more in depth on a bioinformatics project they formulate on their own combining a problem from microbiology with the bioinformatics toolbox.

The participation of the course will be evaluted by activities, an oral presentation of the project and a written report after the course. Homepage: www.bioinformatics.es

Participants
The course is relevant to PhD-students with a very limited background in bioinformatics as well as to 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), extra space on the hard disk drive (more than 100 Mbyte free) and with 8 or more Gbyte RAM. It is important that the computer is set up with permissions to allow the participant to install programs on the computer including access to edit the Bios.
The partipants are encouraged to bring their own data for the 2nd week of the course dedicated to the independent bioinformatics project.

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 teachers and participants. The exercises allow training in relation to the theory introduced and will be solved in groups of 1-3 persons with help from the teachers. The book “Introduction to Bioinformatics in Microbiology 2nd ed,” from 2023 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 the participants own PhD project and own data. The participants will give an oral 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. Homepage: www.bioinformatics.es

Course director
Henrik Christensen, associate professor, Department of Veterinary Animal Sciences, University of Copenhagen, hech@sund.ku.dk

Teachers
Henrik Christensen, associate professor, Department of Veterinary Animal Sciences, University of Copenhagen;
Xiao Fei, PhD, post. doc.
Yufei Zhao, PhD student

Dates
10 – 21 June 2024 (weekend excluded)
All days 8:30 – 17:00

Course location
TBD

Registration
Please register before 13 May 2024

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.

Disclaimer:
DDSA has explicit permission from Arcanic and the owners of the https://phdcourses.dk/ website to display the courses on ddsa.dk.