Course at EMBL-EBI
Bioinformatics resources for protein biology
Are you aware of the wide range of protein data resources that can easily be accessed and explored to enhance your research? Do you want to know more about the sequence of your protein and its functions? Wondered whether a structure of your protein exists and how to explore it? Want to know more about the potential complexes and reaction pathways your protein of interest is involved in, giving you a better overview of its biological context?
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.
Who is this course for?
This workshop is aimed at anyone interested in finding out more about protein biology. No prior experience of bioinformatics is required, but an undergraduate level understanding of biology would be of benefit.
What will I learn?
Learning outcomes
After this course 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
Course content
During this course you will learn about:
Day 1: UniProtKB, InterPro, HMMER
Day 2: PDBe, EMDB, EMPIAR
Day 3: IntAct, Complex Portal, Reactome
Trainers
David Armstrong
EMBL-EBI, UK Hema Bye-A-Jee
EMBL-EBI, UK Alexandra Holinski
EMBL-EBI, UK Birgit Meldal
EMBL-EBI, UK Osman Salih
EMBL-EBI, UK Thawfeek Mohamed Varusai
EMBL-EBI, UK Rossana Zaru
EMBL-EBI, UK Kalpana Paneerselvam
EMBL-EBI, UK
Programme
Day 1 – Tuesday 10 March 2020
Where can I find protein sequence, classification and comparison information?
08:00
Bus from Cambridge train station
09:00-09:15
Arrival and registration
09:15-10:00
Introduction to EMBL-EBI and overview of the course
Alex Holinski
10:00-11:00
UniProt
Rossana Zaru & Hema Bye-A-Jee
11:00-11:30
Coffee break
11:30-13:00
UniProt
Rossana Zaru & Hema Bye-A-Jee
13:00-14:00
Lunch
14:00-15:00
Sequence classification (InterPro, Pfam, HMMER)
Typhaine Paysan-Lafosse
15:00-15:30
Coffee break
15:30-16:30
Sequence classification (InterPro, Pfam, HMMER)
Typhaine Paysan-Lafosse
16:30-17:30
Explore and apply today's learning
18:00
Dinner at Hinxton Hall
19:45
Bus to Cambridge Station
Day 2 – Wednesday 11 March 2019
How do I choose a "good" protein structure and what can I learn from it?
08:00
Bus from Cambridge train station
09:00-10:30
PDBe
David Armstrong
10:30-11:00
Coffee break and group photo
11:00-12:30
PDBe
David Armstrong
12:30-13:30
Lunch
13:30-14:30
EMDB/EMPIAR
Osman Salih
14:30-15:00
Coffee break
15:00-15:45
EMDB/EMPIAR
Osman Salih
15:45-17:00
Explore and apply today's learning
17:15
Bus to Cambridge train station
Day 3 – Thursday 12 March 2020
What interactions, complexes and pathways is my protein involved in?
08:00
Bus from Cambridge train station
09:00-10:30
Molecular Interactions
Birgit Meldal
10:30-11:00
Coffee break
11:00-12:30
Molecular Interactions
Birgit Meldal
12:30-13:30
Lunch
13:30-14:30
Reactome
Thawfeek Mohamed Varusai
14:30-15:00
Coffee break
15:00-16:00
Reactome
Thawfeek Mohamed Varusai
16:00-16:40
Explore and apply today's learning
16:40-17:00
Wrap-up of "Explore and apply today's learning"
17:00-17:15
Feedback
Alex Holinski
17:30
Bus to Cambridge station
Attendance at this workshop is allocated on a first come, first served basis.
The registration fee covers your lunch, refreshments and a shuttle between Cambridge station, bus stop 5 and the Wellcome Genome Campus. Accommodation is not included and you will need to make your own arrangements.
Once you have registered and we have received payment we can provide a letter of support should you require a visa to travel to the UK. Applying for a visa can take several weeks, and it might not be possible to be granted a visa if you register just before the closing date. If you are unable to attend, then please notify us as quickly as possible so that we can offer your place to someone else.
EMBL-EBI, UK
EMBL-EBI, UK
EMBL-EBI, UK
EMBL-EBI, UK
EMBL-EBI, UK
EMBL-EBI, UK
EMBL-EBI, UK
EMBL-EBI, UK
Programme
Day 1 – Tuesday 10 March 2020 |
||
---|---|---|
Where can I find protein sequence, classification and comparison information? | ||
08:00 | Bus from Cambridge train station | |
09:00-09:15 | Arrival and registration | |
09:15-10:00 |
|
Alex Holinski |
10:00-11:00 |
UniProt |
Rossana Zaru & Hema Bye-A-Jee |
11:00-11:30 | Coffee break | |
11:30-13:00 |
UniProt |
Rossana Zaru & Hema Bye-A-Jee |
13:00-14:00 | Lunch | |
14:00-15:00 | Sequence classification (InterPro, Pfam, HMMER) | Typhaine Paysan-Lafosse |
15:00-15:30 | Coffee break | |
15:30-16:30 | Sequence classification (InterPro, Pfam, HMMER) | Typhaine Paysan-Lafosse |
16:30-17:30 | Explore and apply today's learning | |
18:00 | Dinner at Hinxton Hall | |
19:45 | Bus to Cambridge Station |
Day 2 – Wednesday 11 March 2019 |
||
---|---|---|
How do I choose a "good" protein structure and what can I learn from it? | ||
08:00 | Bus from Cambridge train station | |
09:00-10:30 | PDBe | David Armstrong |
10:30-11:00 | Coffee break and group photo | |
11:00-12:30 | PDBe | David Armstrong |
12:30-13:30 | Lunch | |
13:30-14:30 | EMDB/EMPIAR | Osman Salih |
14:30-15:00 | Coffee break | |
15:00-15:45 | EMDB/EMPIAR | Osman Salih |
15:45-17:00 | Explore and apply today's learning | |
17:15 | Bus to Cambridge train station |
Day 3 – Thursday 12 March 2020 |
||
---|---|---|
What interactions, complexes and pathways is my protein involved in? | ||
08:00 | Bus from Cambridge train station | |
09:00-10:30 | Molecular Interactions | Birgit Meldal |
10:30-11:00 | Coffee break | |
11:00-12:30 | Molecular Interactions | Birgit Meldal |
12:30-13:30 | Lunch | |
13:30-14:30 | Reactome | Thawfeek Mohamed Varusai |
14:30-15:00 | Coffee break | |
15:00-16:00 | Reactome | Thawfeek Mohamed Varusai |
16:00-16:40 | Explore and apply today's learning | |
16:40-17:00 | Wrap-up of "Explore and apply today's learning" | |
17:00-17:15 | Feedback | Alex Holinski |
17:30 | Bus to Cambridge station |
Attendance at this workshop is allocated on a first come, first served basis.
The registration fee covers your lunch, refreshments and a shuttle between Cambridge station, bus stop 5 and the Wellcome Genome Campus. Accommodation is not included and you will need to make your own arrangements.
Once you have registered and we have received payment we can provide a letter of support should you require a visa to travel to the UK. Applying for a visa can take several weeks, and it might not be possible to be granted a visa if you register just before the closing date. If you are unable to attend, then please notify us as quickly as possible so that we can offer your place to someone else.