EMBL-EBI Bioinformatics resources for exploring functional genomics data
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Date:
Thursday 9 - Friday 10 November 2017Venue:
Deutsches Krebsforschungszentrum (DKFZ) - German Cancer Research Centre (GCRC) - Deutsches Krebsforschungszentrum (DKFZ)Im Neuenheimer Feld 280, 69120, Heidelberg, GermanyParticipation:
By invitationContact:
Monika Kulka-SchuhRegistration closed
Course Overview
This course will provide participants with an introduction to functional genomics resources at EMBL-EBI, in particular to ArrayExpress (one of the ELIXIR core data resources) and Expression Atlas.
The course will focus on accessing data relevant to their areas of interests and on visualizing gene expression analysis results with Expression Atlas. It will also explain how to submit functional genomics data (e.g. microarray expression profiling, RNA-seq, ChIP-seq) to a public repository such as ArrayExpress and the importance of data standards for functional genomics.
Activities will include interactive presentations by the trainer and practical exercises to give the trainees hands on experiences.
Audience
This course is for wet-lab researchers at any career stage at the German Cancer research Centre, Heidelberg, interested in exploring functional genomic data and applying EMBL-EBI resources in their research.
No prior knowledge of programming is required, however an undergraduate level knowledge of biology and/or biochemistry is essential.
Modules
- arrayexpress-public-database-functional-genomics
- expression-atlas-gene-expression-across-species-and-biological-conditions
Learning outcomes
After this course you should be able to:
- Submit data to ArrayExpress through Annotare, and search for data of interest effectively.
- Relate microarrays and RNA-seq data analysis in Expression Atlas to your work
- Use Expression Atlas to answer expression related questions on genes and proteins of interest.
Programme
|
Time |
Topic |
|
Day 1 – Thursday 9th November 2017 |
|
|
09:30 - 10:00 |
Welcome and Introduction to EMBL-EBI resources |
|
10:00 – 11:00 |
Data quality: standards, curation and ontologies |
|
11:00 – 11:30 |
Tea/coffee break |
|
11:30 - 12:30 |
Discover functional genomics data with ArrayExpress |
|
12:30 - 13:30 |
Lunch |
|
13:30 – 15:00 |
Practical session: ArrayExpress |
|
15:00 – 15:30 |
Tea/coffee break |
|
15:30 - 16:30 |
Annotare: ‘your’ web-form submission tool |
|
16:30 - 17:30 |
Hands-on session: data submission with Annotare |
|
17:30 |
End of Day 1 |
|
Day 2 – Friday 10th November 2017 |
|
|
09:00-10:30 |
Expression Atlas: gene expression results across species and biological conditions |
|
10:30-11:00 |
Tea/coffee break |
|
11:00-12:30 |
Practical session I: Expression Atlas |
|
12:30-13:30 |
Lunch |
|
13:30-14:30 |
Expression Atlas behind the scenes |
|
14:30-15:30 |
Practical session II: Expression Atlas |
|
15:30-16:00 |
Expression Atlas data integrated in other resources: Open Targets |
|
16:00-16:30 |
RNASeq-er API: accessing RNA-seq analysis results |
|
16:30-17:00 |
Course wrap-up and feedback |
|
17:30 |
End of course |
In association with
How to apply
Registration is run by the German Cancer Research Centre (DKFZ). This course is available to staff and students within the DKFZ only.
Number of places
10 places
Organisers
Piraveen Gopalasingam - EMBL-EBI, UK
Trainers
Laura Huerta Martinez - EMBL-EBI, UK