Virtual course

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 short virtual course will introduce you to data resources and tools developed by EMBL-EBI that can help you in your protein studies.

This course will take place from 21 to 23 February and on 2 March. During the first three days you will learn about how to browse, retrieve and use EMBL-EBI protein data in theory. Those who are interested in learning more about programmatic access to EMBL-EBI protein resources can attend an optional section on this topic on the afternoon of 22 February. For an introduction to the concept of web services and how you can use them to access the tools and data available programmatically, please watch this EMBL-EBI, programatically webinar.

You will be provided exercises for each resource that you will work through on your own in the following week, with remote trainer support available if needed. We will then meet again on 2 March to discuss issues that occurred while working through the material in more detail.

All participants will be asked to pre-record a short presentation (three minutes) about their research work as part of the course. These will provide an opportunity to share your research with the other participants and provide a forum for discussion. Further details will be provided to participants once registrations have closed.

This course will be run virtually and delivered over Zoom, with additional text communication over Slack.  In order to make the most out of the course, you should make sure to have a stable internet connection throughout the course.

 

Who is this course for?

This course 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 sessions on programmatic access, 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 programmatically, please watch this EMBL-EBI, programatically webinar.

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:

Trainers

Aurélien Luciani
EMBL-EBI
David Armstrong
EMBL-EBI
Hema Bye-A-Jee
EMBL-EBI
Alexandra Holinski
EMBL-EBI
Typhaine Paysan-Lafosse
EMBL-EBI
Nandana Madhusoodanan
EMBL-EBI
Kalpana Panneerselvam
EMBL-EBI
Eliot Ragueneau
EMBL-EBI
Sara Rocio Chuguransky
EMBL-EBI
Osman Salih
EMBL-EBI
Krishna Kumar Tiwari
EMBL-EBI
Rossana Zaru
EMBL-EBI

Programme

All times in GMT

Time Subject Trainer
Day one - 21 February 2022
10:00 - 10:30 Welcome Alexandra Holinski
10:30 - 11:30 Icebreaker Alexandra Holinski
11:30 - 12:30 UniProt Hema Bye-A-Jee, Rossana Zaru
12:30 - 13:30 Break  
13:30 - 15:00 Sequence classification (Pfam, InterPro) Sara Chuguransky, Typhaine Paysan-Lafosse
Day two - 22 February 2022
9:45 - 10:00 Start the course day - activity Alexandra Holinski
10:00 - 11:30 PDBe David Armstrong
11:30 - 11:45 Break  
11:45 - 12:15 AlphaFold DB TBC
12:15 - 13:15 EMDB and EMPIAR Osman Salih
13:15 - 14:00 Break  
The following part is optional.  

In the following part we will provide an introduction to programmatic access to selected protein resources of EMBL-EBI.
14:00 - 14:30 A general introduction to programmatic access Nandana Madhusoodanan
14:30 - 15:00 UniProt Aurélien Luciani
15:00 - 15:30 Break  
15:30 - 16:00 InterPro Sara Chuguransky, Typhaine Paysan-Lafosse
16:00 - 16:30 PDBe David Armstrong
Day three - 23 February 2022
9:45 - 10:00 Start the course day - activity  
10:00 - 11:00 Molecular interactions Kalpana Panneerselvam
11:00 - 11:15 Break  
11:15 - 12:00 Molecular interactions continued Kalpana Panneerselvam
12:00 - 13:00 Break  
13:00 - 14:30 Reactome Eliot Ragueneau
14:30 - 15:00 Wrap-up and feedback Alexandra Holinski
Day four - questions, answers, and reflection - 2 March 2022
10:00 - 10:15 Welcome Alexandra Holinski
10:15 - 10:45 Q&A - UniProt Hema Bye-A-Jee, Rossana Zaru
10:45 - 11:00 Break  
11:00 - 11:30 Q&A - Sequence classification Sara Chuguransky, Typhaine Paysan-Lafosse
11:30 - 12:30 Q&A - Protein structures David Armstrong, Osman Salih
12:30 - 13:30 Break  
13:30 - 14:00 Q&A - Molecular interactions Kalpana Panneerselvam
14:00 - 14:30 Q&A - Reactome Eliot Raguenau
14:30 - 14:45 Course wrap-up and feedback Alexandra Holinski
14:45 - 15:00 Break  
15:00 - 16:00 Optional roundtable session - join any of the trainers to ask more questions All

Attendance at this course is allocated on a first come, first served basis. Please complete the online application form to register.

You should indicate whether you wish to attend the optional sessions on the afternoon of 22 February.

Registration will close on 7 January, so please register as soon as you can.  After you have registered, you will be able to update your registration with your flash talk recording and slides until 4 February.

This course has ended

21 February - 02 March 2022
£120
Contact
Jane Reynolds

Organisers
  • Alexandra Holinski
    EMBL-EBI

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