You will need:
- Cytoscape 3.8
- The clustermaker2 plug-in for Cytoscape
- Python 3.8 or higher.
- You can use the Anaconda package manager.
- Several Python packages
- Jupyter Notebooks.
- Follow these instructions.
Practice sessions are conducted with a computer.
There are 09 practice sessions in this course. The first two sessions have handouts that are documents, the remaining sessions have handouts that are Python notebooks. Download the notebooks, open them, and follow the instructions there (some instructions are in color and are not visible in the preview shown on the GitHub website). Each session starts with psNN and describe the activities that the students must perform during the practice session.
💡 Read the practice descriptions before the session, as they can be sometimes long. You can start working on these at any point, but they are not definitive until the end of the session; details may change.
At the end of each handout there is a description of what you should deliver. Please ask in the course forum or to your practice instructor ("profesor/a de prácticas") any questions you may have.
| # | Handouts | Contents | Deadline 101 | Deadline 102 |
|---|---|---|---|---|
| 1 | PS01 | Cytoscape: editing and visualizing networks | 2021-10-06 18:30 | 2021-10-06 16:30 |
| 2 | PS02 | Cytoscape: importing, creating, and editing networks | 2021-10-08 20:30 | 2021-10-11 18:30 |
| 3 | PS03 | Python: data management of networks data | 2021-10-29 20:30 | 2021-11-02 18:30 |
| 4 | PS04 | Python and Cytoscape: creating a network using textual data | 2021-10-29 20:30 | 2021-11-02 18:30 |
| 5 | PS03+PS04 | Wrap-up | ||
| 6 | PS05 | NetworkX: network models | 2021-11-04 18:30 (was: 3rd) | 2021-11-04 16:30 (was: 3rd) |
| 7 | PS06 | NetworkX: PageRank | 2021-11-24 18:30 | 2021-11-24 16:30 |
| 8 | PS07 | NetworkX: hubs and authorities | 2021-11-24 18:30 | 2021-11-24 16:30 |
| 9 | PS06+PS07 | Wrap-up | ||
| 10 | PS08 | NetworkX: connected components and k-cores | 2021-12-03 20:30 | 2021-12-07 18:30 |
| 11 | PS09 | NetworkX: simulating the spread of a virus | 2021-12-03 20:30 | 2021-12-07 18:30 |
| 12 | PS08+PS09 | Wrap-up |
- Complex Network Analysis in Python (2018) by Dmitry Zinoviev. Also available as an e-book for UPF students.
- NetworkX documentation
- Social network analysis with NetworkX by Manojit Nandi
- NetworkX: Network analysis with Python by Salvatore Scellato