- REGISTRATION TO JOURNAL CLUB OR WORKSHOPS IS NOT ANYMORE POSSIBLE!
- Symposia and journal club may include preliminary tasks (e.g. reading) and an on-line exam after the course. Both parts are required in addition to the presence at the course in order to receive the credits.
- The workshops have traditionally been oversubscribed and we may not be able to accept all registered students to each workshop. Please indicate in the registration form which workshops (if any) you would like to attend and rank your choices (1=most interested, 3=least interested).
- Please also note that Workshops I and II are relatively advanced and may require special computational skills. Workshop III is suitable to everyone.
Pre-Symposium Journal Club (ILS-104, 1 cr)
Monday 15.10. at 10-12 (Biocenter 2, room 2012)
and Monday 22.10.2018 at 10-16 (Biocenter 2, room 1015)
Workshop I, Computational methods to analyze human genetic variation, Stephan Schiffels (ILS-106, 2 cr)
Thu – Fri 25.-26.10.2018, 9:15-17:00
Room: B-building (Metsätieteiden talo), hall 106
Instructor: Stephan Schiffels
Course description: This course will consist of lectures and practical sessions on how to analyze genomic data to infer a population's history. The course is targeted at students of all disciplines who are interested in human population structure and demographic history. Basic experience with command line tools and a Unix environment are necessary. The course covers several software packages, including MSMC (Schiffels and Durbin, 2014), Eigensoft and Admixtools (Patterson et al. 2012), and python's matplotlib plotting framework. Participants are required to bring their own laptop. Software and Data will be provided through a virtual machine that is used through a web browser. No special software is needed.
Four articles suggested by Stephan Schiffels can be found in
Workshop II, RNAseq data analysis (ILS-107, 2 cr)
Mon – Wed 29.-31.10.2018, 9:15-17:00
Room: C-building, hall K110
Instructor: Nicolas DelHomme, Umeå University, Sweden
Target audience: This course is aimed at MSc students with suitable background studies as well as PhD students and post-doctoral researchers who are applying or planning to apply high throughput sequencing technologies and bioinformatics methods in their research.
Course content: Lectures will give insight into how biological knowledge can be generated from RNA seq experiments and illustrate different ways of analyzing such data. Practicals will consist of computer exercises that will enable the participants to apply statistical methods to the analysis of RNA-seq data under the guidance of the lecturers and teaching assistants. Familiarity with the technology and biological use cases of high throughput sequencing is required, as is some experience with R/Bioconductor. Participants can bring along and analyze their own RNA-seq data on the course.
Software and Data will be provided through a virtual machine that is used through a web browser. No special software is needed.
Please note! The workshop is intensive and it is recommended that all participants get familiar with central concepts before the course. Please read the seven articles (LINK) covering the different stages of RNAseq analysis. Material from these articles will be included in the exam that students need to pass to obtain the study credits.
Workshop III, ENSEMBL genome browser (ILS-120, 1 cr)
Thu 1.11.2018, 9:15-17:00
Room: Infocenter Korona, room 511
Instructor: Erin Haskell, EBI
This one-day browser workshop offers participants the possibility of gaining lots of hands-on experience in the use of the Ensembl genome browser, but also provides them with the necessary background information. The workshop is primarily targeted at wetlab researchers.
Content: The workshop consists of a series of modules (announced later). Most modules consist of a presentation and a demonstration of the tools, followed by the opportunity to do exercises. Participants are encouraged to bring problems/questions about their research and we will try to tackle these during the workshop using Ensembl.
Feedback from previous courses:
“There are probably quite few people out there who all assume that Ensembl today is the same as it was years ago. It is not. With many new features and datasets incorporated/interlinked, it offers data exploration like never before. This course was a very useful update on what Ensembl has become” Browser workshop, CRUK, April 2016
“Very useful workshop, certainly one of the most informative and useful I have attended. Delivered by someone who was extremely familiar with the website and its capabilities, not someone who had used it a couple of times and proclaimed themselves to be an expert.” Browser workshop, Cardiff, March 2014
At the end of this course participants should be able to:
- view genomic regions and manipulate the view to add features they are interested in.
- explore information about genes and their sequences, and gene data in bulk using BioMart.
- analyse genomic variants and associated phenotypes and their own variation data using the VEP.
- view homologous genes and genomic regions, functional elements involved in gene regulation and their activity in different cell types.