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SciLifeLab workshops, hosted by WABI

SciLifeLab will organize two bioinformatics workshops hosted by WABI (Wallenberg Advanced Bioinformatics Infrastructure), and with extensive help from other SciLifeLab facilities, SNIC (Uppmax) and BILS. The workshops will contain both lectures and hands-on training. Participants are welcome to apply one or both of the workshops. During the workshops there will be ample time to discuss and interact with the WABI team and other SciLifeLab staff.

You will leave the workshops with:

– Enhanced understanding of current state-of-the-art analysis methods, and interesting cutting edge research questions.
– Hands-on experience of handling real datasets.

A course fee of 1000 SEK for one workshop (1800 SEK for both) will be invoiced to accepted participants (includes the study material, coffee, lunches and course dinners).

23-24 September 2013
RNA-seq workshop (1 hp)

In this workshop, you will get both theoretical and hands-on exposure to current topics in RNA-seq analysis. Lectures from experts in RNA-seq, proteomics and biostatistics will cover a range of cutting-edge issues in different RNA-seq applications. An extensive case study in the computer lab will familiarize you with concepts of mapping, de novo assembly, isoform quantification, multivariate data analysis, genome annotation and comparisons between RNA and protein data. There is also a possibility to bring your own data and get help with analyzing those during the workshop.


25-26 September 2013
Human genetic variation workshop (1 hp)

The two-day workshop will cover state-of-the-art practices in variation discovery and analysis using 2nd generation sequence data. The workshop includes both morning lectures and hands-on sessions in the afternoons. Invited speakers are leading scientists in the field of disease variation and cancer genomics. The first day will focus on SNP and indel calling from short read data, discussing read mapping, data processing and variant calling, including SV and CNV. The second day will focus more on somatic variation in cancer, especially structural variation and functional analysis thereof.


Entry requirements (both workshops):

– Basic knowledge in linux is a requirement! We will not teach Linux at the workshops and you will have considerable trouble to follow the practical sessions if you are not reasonably used to work in a linux environment.

– Some programming/scripting experience is desirable, but not required.
– Experience working on the SNIC center Uppmax is desirable, but not required.
– A background in genetics, cell biology, biomedicine, biochemistry, bioinformatics or comparable is desirable.
– Participants of the SciLifeLab Course “Next generation sequencing / genome analysis” and “Computational Methods for Massively Parallel Sequencing” are most welcome to apply, but this course is not required. Some overlap with this course is expected, but the workshops will be considerably more detailed on the covered topics.

To get the maximum benefit from the course we would like you to have
– Relevant previous experience in sequencing or analysis
– A current research project where you are currently using next generation sequencing or are planning to use next generation sequencing.
– It is beneficial if you are directly performing analyses or if you have a support role and will be able to participate in a wide range of projects and transfer your knowledge to others.

Selction criteria include correct entry requirements, motivation to attend the course as well as gender and geographical balance.

General information

Application form

National Course

The course is open for PhD students, postdocs, researchers, and other employees in need of bioinformatic skills within all Swedish universities

Responsible teacher: Björn Nystedt

Important dates:

Application open: June 27th
Application deadline: August 19th
Confirmation to accepted students: August 26th
If you don’t receive information according to the dates above, contact:

Course fee

A course fee of 1000 SEK for one workshop (1800 SEK for both) will be invoiced to accepted participants (includes the study material, coffee, lunches and course dinners).

 Organizer: SciLifeLab