Bioinformatics Resources for Protein Biology

Date:

 Tuesday 26 Thursday 28 February 2019

Venue: 

European Bioinformatics Institute (EMBL-EBI) - Training Room 1 - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom

Application opens: 

Thursday August 30 2018

Application deadline: 

Friday January 04 2019

Participation: 

First come, first served

Contact: 

Marina Pujol

Registration fee: 

£130

Overview

This three day workshop will introduce you to data resources and tools developed by EMBL-EBI that can help you in your protein studies. Each day will focus on a particular protein topic, with the aim of helping you get more from your data and also to explore publically-available data that can further support your research. On the last day you will have the opportunity to either explore the data resources presented in the course further, tackling a biologically relevant problem, or to learn how to access some of the EMBL-EBI resources and tools programmatically.

Workshop topics

Day 1 (26 February): Where can I find protein sequence, classification and comparison information?

Day 2 (27 February): How do I choose a “good” protein structure and what can I learn from it?

Day 3 (28 February): What interactions, complexes and pathways is my protein involved in?

Audience

This workshop is aimed at anyone interested in finding out more about protein biology. No prior experience of bioinformatics is required, but participants should have an undergraduate level understanding of biology.

For those who wish to attend the session on programmatic access a prior knowledge of coding/programming would be of benefit. For an introduction to the concept of web services and how you can use them to access the tools and data available at EMBL-EBI please watch our webinar.

 

Syllabus, tools and resources

Day 1: UniProtKB, InterPro, HMMER

Day 2: PDBe, EMDB

Day 3: IntAct, Complex Portal, Reactome

Outcomes

At the end of the workshop you should be able to:

•Access and explore a range of appropriate protein resources

•Use these resources to retrieve relevant protein information

•Apply the information you have discovered in your research

Programme

Time Topic Trainer
Day 1 - Where can I find protein sequence, classification and comparison information?
9:00 - 9:15 Registration  
9:15 - 9:30 Welcome and course introduction Alexandra Holinski
9:30 - 11:00 UniProt Rossana Zaru, Hema Bye-A-Jee
11:00 - 11:15 Tea/coffee break  
11:15 - 12:45 UniProt Rossana Zaru, Hema Bye-A-Jee
12:45 - 13:30 Lunch  
13:30 - 15:15 HMMER Sara El-Gebali
15:15 - 15:30 Tea/coffee break  
15:30 - 17:00 InterPro Lorna Richardson
17:15 Bus to Cambridge Train Station  
Day 2 - How do I choose a "good" protein structure and what can I learn from it?
09:00 - 10:30 PDBe: Introduction and search David Armstrong
10:30 - 11:00 Tea/coffee break  
11:00 - 12:15 PDBe: Entry pages and validation David Armstrong
12:15 - 13:15 Lunch  
13:15 - 14:30 PDBe tools David Armstrong
14:30 - 15:00 Tea/coffee break  
15:00 - 17:00 Electron Microscopy DataBank (EMDB) Osman Salih
17:15 Bus to Cambridge Train Station  
Day 3 - What interactions, complexes and pathways is my protein involved in?
09:00 - 10:30 Molecular Interactions Birgit Meldal
10:30 - 10:45 Tea/coffee break  
10:45 - 12:15 Molecular Interactions Birgit Meldal
12:15 - 12:45 Lunch  
12:45 - 14:15 Reactome Thawfeek Mohamed Varusai
14:15 - 14:30 Tea/coffee break  
14:30 - 16:00 Reactome Thawfeek Mohamed Varusai
16:00 - 17:00 Exploring EMBL-EBI data resources (additional hands-on session) All
17:00 - 17:15 Wrap up and feedback Alexandra Holinski
17:30 End of course; bus to Cambridge Train Station