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.
Organisation:
- Nhung Pham, PhD (n.pham@maastrichtuniversity.nl)
- Susan Steinbusch-Coort, PhD (susan.coort@maastrichtuniversity.nl)
- Martina Summer-Kutmon, PhD (martina.kutmon@maastrichtuniversity.nl)
Program
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 |
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