Course at EMBL-EBI
Data-driven approaches to understanding dementia
This course provides individuals working in dementia research with the skills to access and analyse dementia data. Participants will learn to apply bioinformatics methodologies, combine different data types, and utilise relevant dementia data resources, enhancing their research capabilities in the field.
Who is this course for?
The course is aimed at individuals working in dementia research space who have minimal experience in bioinformatics. Applicants are expected to be at an early stage of using bioinformatics in their research with the need to develop their skills and knowledge further. Participants will need a basic knowledge of the Unix command line, and the R statistical package. We recommend these free tutorials:
- Introduction to the Unix environment – https://swcarpentry.github.io/shell-novice/index.html
- Basic R concepts – https://swcarpentry.github.io/r-novice-inflammation/
What will I learn?
Learning outcomes
- Locate and search publicly available bioinformatics data of interest, including dementia specific resources
- Use software and tools to manipulate and analyse data
- Apply appropriate bioinformatics methodologies to research projects
- Combine different types of data to gain further insights
Course content
- Bulk and Single-cell RNA sequencing and databases of regulatory information
- Tools to extract mechanism relevant for dementia from ‘omics’ data
- BioImaging in dementia
- Dementia data resources: ADDI, AD Atlas, DPUK, AD Knowledge portal
- EMBL-EBI data resources: Gene Expression Atlas, ChEMBL, PRIDE, Open Targets
Trainers
Matthias Arnold
Helmholtz Zentrum München, Germany Edward Avezov
UK Dementia Research Institute; University of Cambridge, UK Sarah Bauermeister
Dementia Platform UK Gabriel Mateus Bernardo-Harrington
Cardiff University, UK Annalisa Buniello
EMBL-EBI Charlotte Capitanchik
King's College London Sybilla Corbett
EMBL-EBI Helena Cornu
EMBL-EBI Valentina Escott-Price
UK Dementia Research Institute; Data Science Centre, UK Mark Fiers
Katholieke Universiteit Leuven, Nederlands Daria Gavriouchkina
UK Dementia Research Institute; Dementia Platforms UK Deepti Jaiswal Kundu
EMBL-EBI Aybuke Kupcu Yoldas
EMBL-EBI Pierre Parutto
UK Dementia Research Institute; University of Cambridge, UK Anita Scoones
Earlham Institute Emily Simmonds
UK Dementia Research Institute; Data Science Centre, UK Abby Vander Linden
Sage bionetworks, Seattle, US Maria Ulmer
Helmholtz Zentrum München Monica Scroggs
Alzheimer's Disease Data Initiative (ADDI) Graham Bearden
Alzheimer's Disease Data Initiative (ADDI) Emma Davis
The Francis Crick Institute Manuela Dorado
Alzheimer's Disease Data Initiative (ADDI)
Programme
Time
Topic
Trainer
Day one – Monday 8 April 2024
10:00 – 10:30
Registration and coffee
10:30 – 11:30
Course welcome and introduction to EMBL-EBI
Dayane Araujo
11:30 – 12:30
Introduction to single cell RNAs-seq analysis
Anita Scoones
12:30 – 13:30
Lunch with poster session
13:30– 15:30
Application of single cell analysis to dementia research: practical
Mark Fiers and Emma Davis
15:30 – 16:00
Break
16:00 – 17:00
Introduction to Expression Atlas and Single Cell Expression Atlas
Liora Vilmovsky 17:00 – 18:00
Accommodation check-in
19:00
Dinner
Day two – Tuesday 9 April 2024
09:30 – 11:30
Dementia Platform UK
Sarah Bauermeister
11:30 – 12:00
Break
12:00 – 13:00
Keynote: Application of machine learning in dementia research
Samaneh Kouchaki
13:00 – 14:00
Lunch with poster session
14:00 – 15:00
Extracting information from omics data: lecture
Mateus Bernardo-Harrington and Charlotte Capitanchik
15:00 – 15:30
Break
15:30 – 17:30
Extracting information from omics data: practical
Mateus Bernardo-Harrington and Charlotte Capitanchik
17:30
End of day
19:00
Dinner
Day three – Wednesday 10 April 2024
09:30 – 11:30
Biomarkers and polygenic risk score
Valentina Escott-Price and Emily Simmonds
11:30 – 12:00
Break
12:00 – 13:00
Dementia data resources: AD Atlas
Matthias Arnold and Maria Ulmer
13:00 – 14:00
Lunch
14:00 – 15:00
Dementia data resources: AD Atlas practical
Matthias Arnold and Maria Ulmer
15:00 – 15:30
Break
15:30 – 17:30
AD Knowledge Portal
Abby Vander Linden
17:30
End of day
19:00
Dinner
Day four – Thursday 11 April 2024
9:30 – 10:30
BioImaging in dementia
Edward Avezov and Pierre Parutto
10:30 – 11:00
Break
11:00 – 13:00
Imaging practical
Edward Avezov and Pierre Parutto
13:00 – 14:00
Lunch
14:00 – 15:00
Spatial transcriptomics
Daria Gavriouchkina
15:00 – 15:30
Break
15:30 – 17:30
Dementia data resources: ADDI
Graham Bearden and Monica Scroggs
17:30
End of day
18:30
Dinner at The Red Lion
Day five – Friday 12 April 2024
09:30 – 10:30
Open Targets
Helena Cornu and Annalisa Buniello
10:30 – 11:00
Break
11:00 – 12:00
PRIDE
Juan Antonio Vizcaino
12:00 – 13:00
Lunch
13:00 – 14:00
ChEMBL
Sybilla Corbett
14:00 – 15:00
Reactome
Krishna Tiwari 15:00 – 15:30
Break
15:30 – 16:00
BioImage Archive
Aybuke Kupcu Yoldas
16:00 – 16:15
Wrap up
Dayane Araujo
16:15
End of course
16:30
Coach to Cambridge
Please read our page on application support before starting your application. In order to be considered for a place on this course, you must do the following:
- Complete the online application form.
- Ensure you add relevant information to the ‘submission details’ section where you are asked to provide information on your:
- pre-requisite skills and knowledge
- current work and course expectations
- data availability
- Upload one letter of support from your supervisor or a senior colleague detailing reasons why you should be selected for the course.
Please submit all documents during the application process by 23:59 on Sunday 10 December 2023. Items marked * in the application are mandatory. Incomplete registrations will not be processed.
All applicants will be informed of the status of their application (successful, waiting list, unsuccessful) by 24 December 2023. If you have any questions regarding the application process please contact Juanita Riveros.
Accommodation
Hotel rooms will be provided onsite at Hinxton Hall Conference Centre. Please contact them directly if you wish to arrange to stay additional nights around the course dates.
Catering
The course includes catering as detailed on the programme tab. Successful applicants will be asked for any dietary requirements and allergies upon registration.
Posters
All participants are expected to present a poster. Successful applicants will be provided with further information and asked to submit this upon registration.
We expect the posters to act as a talking point between you, other participants and the trainers on the course. They should give the reader an idea of the work you are engaged in, what you are planning to do next, and anything of interest that might be useful for sharing with the gathered participants
COVID-related information
Please be aware that we are continually evaluating the ongoing pandemic situation and, as such, may need to change the format of courses at short notice. Your safety is paramount to us; you can read our COVID guidance policy for more information. All information is correct at time of publishing.
Please also note that there are delays in the issuing of visas from the UK Government. We encourage you to check if you need a visa and apply in plenty of time before travelling. Current waiting times are more than four weeks. For more information please visit the UK Government website.
Helmholtz Zentrum München, Germany
UK Dementia Research Institute; University of Cambridge, UK
Dementia Platform UK
Cardiff University, UK
EMBL-EBI
King's College London
EMBL-EBI
EMBL-EBI
UK Dementia Research Institute; Data Science Centre, UK
Katholieke Universiteit Leuven, Nederlands
UK Dementia Research Institute; Dementia Platforms UK
EMBL-EBI
EMBL-EBI
UK Dementia Research Institute; University of Cambridge, UK
Earlham Institute
UK Dementia Research Institute; Data Science Centre, UK
Sage bionetworks, Seattle, US
Helmholtz Zentrum München
Alzheimer's Disease Data Initiative (ADDI)
Alzheimer's Disease Data Initiative (ADDI)
The Francis Crick Institute
Alzheimer's Disease Data Initiative (ADDI)
Programme
Time | Topic | Trainer |
Day one – Monday 8 April 2024 | ||
10:00 – 10:30 | Registration and coffee | |
10:30 – 11:30 | Course welcome and introduction to EMBL-EBI | Dayane Araujo |
11:30 – 12:30 | Introduction to single cell RNAs-seq analysis | Anita Scoones |
12:30 – 13:30 | Lunch with poster session | |
13:30– 15:30 | Application of single cell analysis to dementia research: practical | Mark Fiers and Emma Davis |
15:30 – 16:00 | Break | |
16:00 – 17:00 | Introduction to Expression Atlas and Single Cell Expression Atlas | Liora Vilmovsky |
17:00 – 18:00 | Accommodation check-in | |
19:00 | Dinner | |
Day two – Tuesday 9 April 2024 | ||
09:30 – 11:30 | Dementia Platform UK | Sarah Bauermeister |
11:30 – 12:00 | Break | |
12:00 – 13:00 | Keynote: Application of machine learning in dementia research | Samaneh Kouchaki |
13:00 – 14:00 | Lunch with poster session | |
14:00 – 15:00 | Extracting information from omics data: lecture | Mateus Bernardo-Harrington and Charlotte Capitanchik |
15:00 – 15:30 | Break | |
15:30 – 17:30 | Extracting information from omics data: practical | Mateus Bernardo-Harrington and Charlotte Capitanchik |
17:30 | End of day | |
19:00 | Dinner | |
Day three – Wednesday 10 April 2024 | ||
09:30 – 11:30 | Biomarkers and polygenic risk score | Valentina Escott-Price and Emily Simmonds |
11:30 – 12:00 | Break | |
12:00 – 13:00 | Dementia data resources: AD Atlas | Matthias Arnold and Maria Ulmer |
13:00 – 14:00 | Lunch | |
14:00 – 15:00 | Dementia data resources: AD Atlas practical | Matthias Arnold and Maria Ulmer |
15:00 – 15:30 | Break | |
15:30 – 17:30 | AD Knowledge Portal | Abby Vander Linden |
17:30 | End of day | |
19:00 | Dinner | |
Day four – Thursday 11 April 2024 | ||
9:30 – 10:30 | BioImaging in dementia | Edward Avezov and Pierre Parutto |
10:30 – 11:00 | Break | |
11:00 – 13:00 | Imaging practical | Edward Avezov and Pierre Parutto |
13:00 – 14:00 | Lunch | |
14:00 – 15:00 | Spatial transcriptomics | Daria Gavriouchkina |
15:00 – 15:30 | Break | |
15:30 – 17:30 | Dementia data resources: ADDI | Graham Bearden and Monica Scroggs |
17:30 | End of day | |
18:30 | Dinner at The Red Lion | |
Day five – Friday 12 April 2024 | ||
09:30 – 10:30 | Open Targets | Helena Cornu and Annalisa Buniello |
10:30 – 11:00 | Break | |
11:00 – 12:00 | PRIDE | Juan Antonio Vizcaino |
12:00 – 13:00 | Lunch | |
13:00 – 14:00 | ChEMBL | Sybilla Corbett
|
14:00 – 15:00 | Reactome | Krishna Tiwari |
15:00 – 15:30 | Break | |
15:30 – 16:00 | BioImage Archive | Aybuke Kupcu Yoldas
|
16:00 – 16:15 | Wrap up | Dayane Araujo |
16:15 | End of course | |
16:30 | Coach to Cambridge | |
Please read our page on application support before starting your application. In order to be considered for a place on this course, you must do the following:
- Complete the online application form.
- Ensure you add relevant information to the ‘submission details’ section where you are asked to provide information on your:
- pre-requisite skills and knowledge
- current work and course expectations
- data availability
- Upload one letter of support from your supervisor or a senior colleague detailing reasons why you should be selected for the course.
Please submit all documents during the application process by 23:59 on Sunday 10 December 2023. Items marked * in the application are mandatory. Incomplete registrations will not be processed.
All applicants will be informed of the status of their application (successful, waiting list, unsuccessful) by 24 December 2023. If you have any questions regarding the application process please contact Juanita Riveros.
Accommodation
Hotel rooms will be provided onsite at Hinxton Hall Conference Centre. Please contact them directly if you wish to arrange to stay additional nights around the course dates.
Catering
The course includes catering as detailed on the programme tab. Successful applicants will be asked for any dietary requirements and allergies upon registration.
Posters
All participants are expected to present a poster. Successful applicants will be provided with further information and asked to submit this upon registration.
We expect the posters to act as a talking point between you, other participants and the trainers on the course. They should give the reader an idea of the work you are engaged in, what you are planning to do next, and anything of interest that might be useful for sharing with the gathered participants
COVID-related information
Please be aware that we are continually evaluating the ongoing pandemic situation and, as such, may need to change the format of courses at short notice. Your safety is paramount to us; you can read our COVID guidance policy for more information. All information is correct at time of publishing.
Please also note that there are delays in the issuing of visas from the UK Government. We encourage you to check if you need a visa and apply in plenty of time before travelling. Current waiting times are more than four weeks. For more information please visit the UK Government website.