Graduate School of health and Medical Sciences

Computational Phage Genomics
Provider: Faculty of Health and Medical Sciences

Activity no.: 3432-23-00-00
	Enrollment deadline: 01/05/2024

Date and time	01.06.2024, at: 10:00 - 07.06.2024, at: 16:00
Regular seats	25
Course fee	10,560.00 kr.
Lecturers	Bent Petersen
ECTS credits	3.90

Contact person	Bent Petersen E-mail address: bent.petersen@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 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 Knowledge: 1. Understand the basic insights into phage therapy and put into perspective how bioinformatics can support the acceleration of the therapeutic use of phages 2. Understand the concept of phage taxonomy 3. Understand the context and implications of lack of sequence similarity Skills: 1. Install and use programs in Unix for analysis of phage genomics data 2. Critically assess the quality of Next Generation Sequencing data 3. Be able to perform the most basic NGS analysis (de-novo assembly, gene finding, gene and genome annotation) 4. Preparing a phage genome for submission to ENA and NCBI Participants The target group is PhD students at Danish Universities and anybody interested from outside of Denmark as well: Requirements: - Understanding of basic phage biology - Basic understanding of genome sequencing - Participants should bring their own laptops. Software requirements will be communicated before the course and help with software installation will be done online Friday, October 27th. - A basic understanding of working with the command line on UNIX-based systems like Linux, Mac, or Windows Subsystem for Linux (WSL). If you do not feel comfortable with UNIX commands, please take our UNIX fundamentals pre-workshop module Saturday, October 28th. - Throughout the course, participants will retrieve newly sequenced phage genomes, collected in the Malaysian rainforests (https://www.combio-aimst.my). If possible, participants are encouraged to bring their own phage genome sequencing data (Illumina, PE). 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: All graduate programmes Language English Form Lectures and computer exercises Course director Bent Petersen: Senior Researcher, Globe institute, University of Copenhagen, bent.petersen@sund.ku.dk Teachers Thomas Sicheritz-Pontén: Professor, Globe Institute, University of Copenhagen (DK) Bent Petersen: Senior Researcher, Globe Institute, University of Copenhagen (DK) Martha Clokie: Professor, University of Leicester (UK) Andrew Millard: Associate Professor, University of Leicester (UK) Heera Rajandas Associate Professor, AIMST University, (MY) Gemma Atkinson Associate Professor, Lund University, (SE) Dates Pre-workshop Zoom sessions 1 and 2 June 2024 3 to 7 June 2024 Course location The Globe Institute Section for Evolutionary Genomics, Faculty of Health and Medical Sciences, University of Copenhagen Øster Farimagsgade 5, 1353 Copenhagen K, Denmark Registration Please register before 1 May 2024 Expected frequency Twice per year 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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