57 Jul 2022

Workshop on COVID-19 pathways and omics data analysis with WikiPathways and Cytoscape

In this 3-day workshop, you will learn about molecular pathway curation, pathway and network analysis, and how to automate such an analysis in R to increase reproducibility. We would like to bring together researchers in the COVID-19 field to learn together, exchange ideas and discuss results. The course is a continuous program and builds on each other but it is possible to join only on specific days if needed.

Where: Maastricht, the Netherlands (hybrid setup but limited seats onsite and online).
Location: MECC Maastricht, Forum 100, 6229 GV Maastricht.

Description: The workshop focuses on pathway-based analysis of COVID-19 related omics data.

  • Day 1: Pathway curation
    • You will learn how to design and curate biological pathways for the online pathway repository, WikiPathways. 
  • Day 2: Pathway and network analysis
    • The hands-on practicals will give instruction on how to conduct pathway enrichment analysis, analyze protein-protein interaction, and data visualization using COVID-19 pathways as pathway models. You will learn to do it manually using tools such as g:Profiler and Cytoscape. 
  • Day 3: Automated pathway and network analysis with R
    • You will learn to conduct the same analysis as day 2 but in an automated manner using R. In the bring-your-own data session, you can apply the obtained knowledge and skills to analyse your own data. 

Registration: Please register before June 20, 2022, via this link

Costs: The workshop is sponsored by the ZonMW COVID-19 grant (#10430012010015) so there will be no registration fee. However, for on-site participants, there is a 50 euros cancellation/no-show fee if you cannot attend without informing us by the latest on 27 June 2022. 



Day 1:  Pathway curation

Time Description
10:00-12:00 Introduction and basics of pathway curation
12:00-13:00 Lunch
13:00-16:00 Draw your own pathway
16:00-17:00 Discussion: Importance of curation
17:00-21:00 Social event & dinner

Day 2: Pathway and network analysis

Time Description
10:00-12:00 Cytoscape
12:00-13:00 Lunch
13:00-14:30 Pathway analysis                                              
14:30-14:45 Break  
14:45-16:30 Network analysis
16:30-17:00 Q&A

Day 3: Automated pathway and network analysis in R

Time Description
10:00-12:00 Automated analysis in R
12:00-13:00 Lunch
13:00-16:00 Bring your own data or practice with our dataset
16:00-17:00 Q&A - evaluation - closing