Joint EBI-Wellcome Trust Proteomics workshop
This joint EMBL-EBI/Wellcome Trust workshop provides an introduction to bioinformatics tools provided by the European Bioinformatics Institute and freely available on the internet. Students will be given hands-on training in the use of public sequence databases for peptide analysis, annotation of subsequent proteins lists using these resources and information from molecular interaction and pathway databases. The use of PRIDE – a public repository of protein and peptide identifications from multiple species, tissues and sub-cellular locations – will be examined, both as a source of additional information and with a view to eventual data deposition. The workshop is aimed at research scientists with a minimum of a degree in a biological discipline, including laboratory and clinical staff as well as specialists in related fields. Acceptance will be subject to a selection process.
Topics include
- Sequence databases and their uses
- Gene Ontology as a data classification tool
- Using ontologies to annotate data
- Standardising proteomics data
- PRIDE - The Proteomics Identification Database
- IntAct Molecular Interaction database
- Reactome - placing proteins in pathways
| Time | Topic | Length |
|---|---|---|
| Sunday 18 November | ||
| 17:00-18:00 | Registration – Conference Centre Foyer | 1 hour |
| 18:00-19:00 | Welcome Drinks, Hall Bar | 1 hour |
| 19:00-20:00 | Dinner, Hall Restaurant | 1 hour |
| Monday 19 November | ||
| 09:00-10:20 | EBI Overview-EB-eye glimpse tutorial (Vicky Schneider) | 30 minutes |
| Lecture: UniProt and the International Protein Index (Sandra Orchard) | 1 hour | |
| 10:20-10:35 | Morning Tea | 15 minutes |
| 10:35-12:15 | UniProt Tutorial | 1 hour 30 minutes |
| 12:15-13:15 | Lunch | 1 hour |
| 13:15-15:00 | Lecture: First Choose Your Database (Lennart Martens) | 35 minutes |
| Lecture Gene Ontology – classifying your protein list (Emily Dimmer) | 40 minutes | |
| Tutorial: Gene Ontology | 45 minutes | |
| 15:15-15:35 | Afternoon Tea | 20 minutes |
| 15:35- 16:15 | Lecture: HUPO and the Proteomics Standards Initiative (Sandra Orchard) | 40 minutes |
| 16.15-16.45 | Lecture: OLS and PICR – Using Ontologies in Proteomics and accession number remapping (Richard Cote) | 30 minutes |
| 16.45-17.15 | Completion of tutorials and Q&A | 30 minutes |
| 18.00197.00 | Dinner | 1 hour |
| 19.00-20.00 | Invited Speaker | 1 hour |
| Tuesday 20 November | ||
| 9:00-10:30 | Lecture: PRIDE – The Proteomics Identification Database (Phil Jones) | 1 hour |
| Tutorial: PRIDE | 30 minutes | |
| 10:30-10:50 | Morning Tea | 20 minutes |
| 10:50-12:00 | Tutorial: PRIDE | 1 hour 10 minutes |
| 12:00-13:00 | Lunch | 1 hour |
| 13:00-14:00 | Tutorial: OLS and PRIDE Submission: The Proteome Harvest Data Submission Spreadsheet | 1 hour |
| Lecture: IntAct Molecular Interaction database – from protein lists to complexes (Sam Kerrien) | 40 minutes | |
| 14:40-15:00 | Afternoon Tea | 20 minutes |
| 15:30-17:00 | Lecture: Reactome – placing proteins in pathways (David Croft) | 30 minutes |
| Tutorial: IntAct + Reactome | 1 hour | |
Applicants should be research scientists with a minimum of a degree in a biological discipline, including laboratory and clinical staff as well as specialists in related fields.
The course tuition fees are subsidised by the Wellcome Trust for scientists based in academic institutions anywhere in the world. This is a residential course, without exception, and there is a fee of £260 for academic applicants, which includes all accommodation and food for the duration of the course. The fee for commercial (non-academic) applicants is £1000.
Registration Closed.