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
- Protein 3D-structure data and proteomics
- Proteomics data and services integration
| Time | Topic |
|---|---|
| Day 1 - Mon 08 Dec 2008 | |
| 15:00 - 15:10 | Rebecca Twells- Welcome |
| 15:10 - 16:00 | EBI Overview-EB-eye glimpse tutorial (Vicky Schneider & James Watson) |
| 16:00 - 16:20 | Afternoon Tea |
| 16:20 - 17:30 | Lecture: First Choose Your Database & Proteomics identification algorithms (Lennart Martens) |
| Day 2 - Tue 09 Dec 2008 | |
| 09:30 - 10:15 | Lecture: UniProt and the International Protein Index (Sandra Orchard) |
| 10:15 - 11:15 | UniProt Tutorial (Sandra Orchard) |
| 11:15 - 11:30 | Morning Tea |
| 11:30 - 12:15 | Lecture: HUPO and the Proteomics Standards Initiative (Sandra Orchard) |
| 12:15 - 13:15 | Lunch |
| 13:15 - 14:00 | Lecture Gene Ontology – classifying your protein list (Rachael Huntley) |
| 14:00 - 15:15 | Tutorial: Gene Ontology (Rachael Huntley) |
| 15:15 - 15:35 | Afternoon Tea |
| 15:35 - 16:15 | Lecture: PTMs (John Garavelli) |
| 16:15 - 17:00 | PTMs Hands On (John Garavelli) |
| Day 3 - Wed 10 Dec 2008 | |
| 09:30 - 11:15 | Lecture & Tutorial: PRIDE – The Proteomics Identification Database (Phil Jones) |
| 11:15 - 11:30 | Morning Tea |
| 11:30 - 12:15 | Lecture and Hands On PICR and OLS (Phil Jones) |
| 12:15 - 13:15 | Lunch |
| 13:15 - 14:30 | Lecture on InterPro (Jennifer McDowall) |
| 15:15 - 15:35 | Afternoon Tea |
| 15:35 - 17:00 | Hands On InterPro (Jennifer McDowall) |
| 18:00 - 19:00 | Dr Kathryn Lilley |
| Day 4 - Thu 11 Dec 2008 | |
| 09:30 - 10:15 | Lecture: IntAct Molecular Interaction database – from protein lists to complexes (Sam Kerrien) |
| 10:15 - 11:15 | Tutorial: IntAct (Bruno Aranda) |
| 11:15 - 11:30 | Morning Tea |
| 11:30 - 12:15 | Tutorial: IntAct (Bruno Aranda) |
| 12:15 - 13:15 | Lunch |
| 13:15 - 15:15 | Tutorial: Reactome (Bijay Jassal) |
| 15:15 - 15:35 | Afternoon Tea |
| 15:35 - 16:00 | Lecture: Data Integration: ENFIN & EnVision (Florian Reisenger) |
| 16:00 - 17:00 | Hands On: Data Integration (Florian Reisenger and James Watson) |
| Day 5 - Fri 12 Dec 2008 | |
| 09:30 - 10:15 | Lecture: Proteomics and 3D-structures (James Watson) |
| 10:15 - 11:15 | Hands On: Protein structures (James Watson) |
| 11:15 - 11:30 | Morning Tea |
| 11:30 - 12:15 |
Hands On: Protein structures continued (James Watson) OR Hands On: Additional Data Integration (James Watson and Florian Reisenger) |
| 12:15 - 13:15 | Lunch |
| 13:15 - 17:00 | Your own data |
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 £500 for academic applicants, which includes all accommodation and food for the duration of the course. The fee for commercial (non-academic) applicants is £1250.
Registration Closed.