NCCR / SIB Summer School: Computational RNA Biology

The course is full with a waiting list. Registration is closed.

This course will be in a face-to-face format complying with the rules associated with the current COVID-19 situation (distance and hygiene). In the event of new restrictions from the Swiss Government, this course will be cancelled, the participants will be informed, and the registration fee will be reimbursed in full.

This School is co-organized by the SIB PhD Training Network and the NCCR RNA & Disease program. Priority is given to their members, but seats will be available for external participants.

Overview

Bioinformatics has always been a foundation for understanding RNA. This importance has only grown with the advent of next generation sequencing (NGS), as rapidly diversifying methods have been developed to study virtually all aspects of RNA, including expression, processing, structure and translation. While these techniques are based on a common foundation of NGS, each has unique aspects that remain within the realm of specialists. This presents a challenge for young researchers wishing to add these techniques to their skills toolkit.

The aim of this School is to broaden early-stage researchers’ expertise in RNA bioinformatics, with a particular focus on NGS-based analyses. Participants will gain an overview of the state-of-the-art in RNA bioinformatics, before embarking on a challenging, hands-on training project in a chosen area. Learning will be guided by experts from fields including:

1. single cell RNA analysis,

2. long-read RNA sequencing,

3. ribosome-profiling,

4. UV cross-linking immunoprecipitation (CLIP-seq).

There will be a focus on team-work and many opportunities for networking with trainers and other participants.

Audience

This course is aimed at early-stage researchers (PhD students, postdocs) in the RNA field. Given the course subject matter, only participants with working knowledge of scientific computing can be considered (see Prerequisites for further details).

Learning objectives

At the end of the course, the participants are expected to:

• have a good understanding of the most common methods of RNA-seq analysis,
• repeat the same type of analysis achieved during the mini-project,
• present the mini-project and more globally disseminate their experience to the members of their group.

Prerequisites

Knowledge / competencies

This course is designed for intermediate user and the followings are required:

• previous experience with RNA-seq analysis
• Familiar with command line and UNIX language (link to a UNIX tutorial)
• Basic usage of R

Technical

You are required to bring your own laptop (meaning you have installation permission). A list of software to be installed in advance will be communicated on due time.

Application

The registration fees are 800 CHF for academics, with a special price of 400 CHF for SIB PhD students or NCCR members. This includes participation to the school and full board accommodation in double rooms (5 nights). Participants from non-academic institutions should contact us before application.

Deadline for free-of-charge cancellation is set is set to [24/07/2020]. Cancellation after this date will not be reimbursed. Please note that participation to SIB courses is subject to our general conditions.

You will be informed by email of your registration confirmation.

IMPORTANT: Participant's selection will be based on several criteria, and we ask you to fill the Comments field of the application form with:

• your experience with RNA-seq analysis
• your skills with UNIX and R
• the order of preference for the projects topics (see list below), e.g. 4, 1, 3, 2. We will try to take your preferences into account, but keep in mind that we need to build homogeneous groups with the same number of people.

Projects: 1) single cell RNA analysis, 2) long-read RNA sequencing, 3) ribosome-profiling, 4) UV cross-linking immunoprecipitation (CLIP-seq).

Your application will not be taken into consideration if you leave this field empty.

Venue and Time

Hotel & Bildungszentrum Matt, Schwarzenberg, Switzerland.

The School will start on Sunday around 6PM and finishes on Friday around 2PM.

The hotel and the organization will adapt so that measures related to COVID can be applied.

Preliminary Program

Sunday 23.08: Arrival and welcome

Monday 24.08: RNA-seq (lectures and hands-on)

Tuesday 25.08: lectures for the 4 Project topics & projects in groups

Wednesday 26.08: Project in groups (morning), social activity (afternoon)

Thursday 27.08: Projects in groups + results exchange between groups of the same topic

Friday 28.08: Presentation of the projects

Additional information

Coordination: Norbert Polacek & Dominik Theler (NCCR), Gregoire Rossier (SIB)

Trainers: Sarah Djebali (INSERM), Sebastian Leidel (University of Bern), Kathi Zarnack (BMLS), Melina Klostermann (BMLS), Paulo Czarnewski (NBIS), Erik Fasterius (NBIS), Geert van Geest (IBU/SIB), others to be announced.

We will recommend 2 ECTS credits for this course.

You are welcome to register to the SIB courses mailing list to be informed of all future courses and workshops, as well as all important deadlines using the form here.

For more information, please contact training@sib.swiss.