EBI resources introductory course - Zaragoza, Spain
This two-day course aims both to give a general overview about the resources hosted at EBI and to go in depth into selected resources and tools.
During the first day a general overview of the EBI, its mission and its resources will be given, in order to provide the audience with an idea as to which type of information they can access, analyse and submit to the different databases hosted in our institute. Introductory talks to resources such as Ensembl, UniProt, InterPro, Chebi or Array Express will be given (see complete list below).
The second day will host the two following hands-on sessions:
Session 1: Browsing Genomes with Ensembl and Ensembl Genomes: The Ensembl (http://www.ensembl.org) and Ensembl Genomes (http://www.ensemblgenomes.org) projects provide a comprehensive and integrated source of annotation of genomes from across the taxonomy (ranging from vertebrates to bacteria). All supported species include evidence-based gene annotations and a selected set of genomes includes additional data focused on variation, comparative and regulatory annotation. In this session a general overview of the Ensembl and Ensembl genomes browsers as well as the data retrieval tool BioMart will be given.
Session 2: Interactions and pathways analysis tutorial: In this tutorial you will learn how to browse and use the molecular interactions database IntAct (http://www.ebi.ac.uk/intact/) and which are the possibilities and pitfalls of working with molecular interactions data. We will also work with the pathways database Reactome (http://www.reactome.org/), exploring its data structure and the depth of the information hosted there and learn how to perform basic pathway analysis and how to use BioMart to access Reactome information.
Audience
This course is aimed to every biological sciences researcher with an interest in the resources hosted at EBI. No previous bioinformatics knowledge or programming skills are required.
Tools and Resources
During this course you will learn about…
- DNA & RNA: Ensembl and Ensembl Genomes, ENA.
- Gene expression: Array Express and Expression Atlas.
- Proteins and proteomics: UniProt, InterPro, PDBe and PRIDE.
- Systems: IntAct, Reactome, BioModels and GO.
- Chemical biology: ChEMBL, ChEBI and MetaboLights
| Time | Topic | Trainer |
|---|---|---|
| Day 1 - 17 September 2013 | ||
| 08:30 | Introduction to EMBL-EBI | Pablo Porras |
| 09:30 | Expectations assessment | Pablo Porras/Bert Overduin |
| 10:00 | Browsing the genome and exploring sequences: DNA & RNA services Ensembl, Ensembl Genomes, ENA | Bert Overduin |
| 11:30 | Break | |
| 12:00 | Studying expression profiles: Gene expression services Array Express and Expression Atlas | Pablo Porras |
| 12:30 | Understanding proteins: resources for identification and annotation GO, UniProt & InterPro | Pablo Porras |
| 13:30 | Lunch | |
| 14:30 | Proteomics and systems: From mass spectrometry data to models PRIDE, IntAct, Reactome & BioModels | Pablo Porras |
| 15:30 | Break | |
| 16:00 | Small molecules bioinformatics ChEMBL, ChEBI, Metabolights | Pablo Porras |
| 16:30 | Expectations re-assessments, Q&A | Pablo Porras/Bert Overduin |
| 17:30 | Bus | |
| Day 2 - 18 September 2013 | ||
| 08:30 | Browsing Genomes with Ensembl and Ensembl Genomes: The Ensembl (http://www.ensembl.org) and Ensembl Genomes (http://www.ensemblgenomes.org) projects provide a comprehensive and integrated source of annotation of genomes from across the taxonomy (ranging from vertebrates to bacteria). All supported species include evidence-based gene annotations and a selected set of genomes includes additional data focused on variation, comparative and regulatory annotation. In this session a general overview of the Ensembl and Ensembl genomes browsers as well as the data retrieval tool BioMart will be given. Tutorial Tutorial - answers |
Bert Overduin |
| Approx 13:00 | Lunch | |
| Approx 14:00 | Interactions and pathways analysis tutorial: In this tutorial you will learn how to browse and use the molecular interactions database IntAct (http://www.ebi.ac.uk/intact/) and which are the possibilities and pitfalls of working with molecular interactions data. We will also work with the pathways database Reactome (http://www.reactome.org/), exploring its data structure and the depth of the information hosted there and learn how to perform basic pathway analysis and how to use BioMart to access Reactome information. Presentation Tutorial - A tour of the IntAct Portal Tutorial - Reactome |
Pablo Porras |
| 17:00 | Wrap up and feedback | |
The format of both sessions will be a mix of short presentations, demos and hands-on exercises.
The course is free. Places will be filled on a first-come-first-served basis.
To register for the course, please send an email to "Virginia Peribáñez" <vperibannez@cita-aragon.es>.
Please state if you are interested in coming on the first day only or in coming to both sessions. Include a brief summary of your research and a short text explaining your interest in your research (maximum 150 words).
NOTE: Participants for the hands-on session on day two need to bring their own laptops to the course.
Number of places available: Day one: 56, Day two (hands-on): approximately 20.