Date:Wednesday 11 - Thursday 12 September 2019
Venue:European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
Application opens:Thursday 18 April 2019
Application deadline:Friday 30 August 2019
Participation:First come, first served
This workshop, organised in conjunction with the RNA Informatics conference, provides an overview of RNAcentral and Rfam, two databases for non-coding RNA analysis.
Non-coding RNAs (ncRNAs) are RNA molecules that are not translated into proteins and are found in every living organism. Many ncRNAs are responsible for important biological functions. For example, rRNA is a key component of the ribosome, and microRNAs regulate gene expression. Researchers from different fields of biology may need to find what is known about specific ncRNA or identify ncRNA in their data, but may not have the required expertise.
The workshop is aimed at a general audience of biologists and bioinformaticians working with non-coding RNA who are interested in using RNAcentral and Rfam, or for users who would like to bring their projects and discuss them with the RNAcentral and Rfam teams. A basic familiarity with web browsing and an undergraduate level knowledge of molecular biology is recommended for this course. Familiarity with Unix/Linux command line is desirable for part of the course. We recommend these free tutorials:
- Basic introduction to the Unix environment: www.ee.surrey.ac.uk/Teaching/Unix
- Introduction and exercises for Linux: https://training.linuxfoundation.org/resources/free-courses/introduction...
Syllabus, tools and resources
This workshop provides an overview of two RNA databases developed at EMBL-EBI. RNAcentral is a database of ncRNA sequences that provides a single entry point for accessing all types of ncRNA from a broad range of organisms. RNAcentral provides unified access to ncRNAs data from >30 specialised databases. Rfam is a database of >3,000 RNA families that can be used to identify RNA families in DNA or RNA sequences. Together these resources provide the tools for ncRNA sequence analysis. The goal of the course is to familiarise the audience with the RNAcentral and Rfam websites and demonstrate relevant software, including Infernal and Galaxy.
After this workshop you should be able to:
- Know when and how to use the RNAcentral and Rfam databases
- Apply this knowledge to a real-world problem relating to ncRNAs
The workshop includes an evening meal at the Hinxton Hall Restaurant on campus, and breaks and lunch outside the EMBL-EBI training rooms.
Day 1 – Wednesday 11 September 2019
|Part 1: Overview of RNAcentral and Rfam|
|13:30-14:00||Arrival and registration|
Introduction to RNAcentral and Rfam
Overview of the websites and data contents
|Anton Petrov & Blake Sweeney|
Exploring ncRNAs in RNAcentral and Rfam practical
Learn how to search for different types of ncRNA data and export information for further processing
|Anton Petrov & Blake Sweeney|
How to use RNAcentral and Rfam with RNA-Seq data practical
Learn how to analyse RNA-Seq datasets using RNAcentral, Rfam, and Galaxy
|Blake Sweeney & Ioanna Kalvari|
|18:00||End of day|
|19:00-20:30||Evening meal||Hinxton Hall Restaurant|
|20:30||Panther Taxi to Whittlesford Parkway Station and then Cambridge Station (outside ibis hotel)|
Day 2 – Thursday 12 September 2019
|Part 2: Problem solving session|
|08:00||Panther Taxi from Cambridge Station (outside ibis hotel), then Whittlesford Parkway Station to campus|
|08:45-09:00||Arrival and registration|
How to use Rfam for genome annotation practical
Learn how to use Infernal with Rfam covariance models
Discuss your research with trainers and other participants. Examples might include:
|Anton Petrov, Blake Sweeney & Ioanna Kalvari|
|13:30||Panther Taxi to Whittlesford Parkway Station and then Cambridge Station (outside ibis hotel)|