Date: 5-7 July 2022 in Maastricht (details location)
Organizers: Nhung Pham, Susan Steinbusch-Coort, Martina Summer-Kutmon
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.
- Follow the instructions to install all required software for the tutorial.
| Date | Time | Title | Presenter | Link |
|---|---|---|---|---|
| 5 July 2022 | 10:00-10:15 | Welcome | Nhung Pham | slides |
| 10:15-11:00 | Pathway Resources | Susan Coort | slides | |
| 11:00-12:00 | Hands-on pathway curation | Nhung Pham | slides | |
| 12:00-13:00 | Lunch | |||
| 13:00-16:00 | Draw your own pathway | Nhung Pham | pathway list | |
| 16:00-17:00 | Discussion: Importance of curation | Martina Kutmon | ||
| 17:30-22:30 | Social Event & Dinner | |||
| 6 July 2022 | 10:00-12:00 | Introduction to Cytoscape | Martina Kutmon | Info/Material |
| 12:00-13:00 | Lunch | |||
| 13:00-14:30 | Pathway analysis | Martina Kutmon | Info/Material | |
| 14:30-14:45 | Break | |||
| 14:45-16:30 | Network analysis | Martina Kutmon | Info/Material | |
| 16:30-17:00 | Q&A | |||
| 7 July 2022 | 10:00-12:00 | Automation in R | Martina Kutmon | Info/Material |
| 12:00-13:00 | Lunch | |||
| 13:00-16:00 | Bring your own data / Practice | Example Dataset | ||
| 16:00-17:00 | Q&A - evaluation - closing |
On day 2 and 3 of the workshop, we will use a transcriptomics dataset as an example. More information about the dataset can be found here.
- Friederike Ehrhart
- Egon Willighagen
- Finterly Hu
- John Figueira Hasbun
- Duygu Dede Sener
- Michiel Adriaens
If you have any questions, send us an email or submit an issue in the issue tracker and we will get back to you as soon as possible.
- WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research paper
- Ten simple rules for creating reusable pathway models for computational analysis and visualization paper
- COVID-19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms paper
The workshop is sponsored by the ZonMW COVID-19 grant (#10430012010015).