spacer
spacer

Hands-on training at EBI - Joint EBI-Wellcome Trust Proteomics workshop

Course Summary
Course DetailsTitle: Joint EBI-Wellcome Trust Proteomics workshop
Date: 08-12 December 2008
Venue: Hinxton, Cambridge, UK
EBI Organisers: Vicky Schneider and James Watson
WTAC Organisers: Rebecca Twells and Darren Hughes
Admin Support: Yvonne Hitching and Julie Ormond
Extended Registration Deadline: 10th October 2008

About this Course

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

Course requirements

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.

Register >>>

Trainers


trans.gif
Vicky Schneider
Vicky
Schneider

trans.gif
trans.gif
Jennifer MacDowall
Phil
Jones

trans.gif
trans.gif
James Watson
James
Watson

trans.gif
trans.gif
Rachael Huntley
Rachael
Huntley

trans.gif
trans.gif
Lennart Martens
Lennart
Martens

trans.gif

Bijay Jassal
Bijay
Jassal

trans.gif
trans.gif
Sandra Orchard
Sandra
Orchard

trans.gif
trans.gif
Bruno Aranda
Bruno
Aranda

trans.gif
trans.gif
Florian Reisinger
Florian
Reisinger

trans.gif
trans.gif
John S. Garavelli
John S.
Garavelli

trans.gif
trans.gif

trans.gif
trans.gif

trans.gif


Program Contents



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








spacer
spacer