EMBL-EBI: Network Analysis with Cytoscape
23, 24 January 2024 | 09:30 - 13:00 GMT | Check Your Timezone
Embedded Files
Instructors: Kalpana Paneerselvam, Eliot Ragueneau, Juan Jose Medina Reyes, Sucharitha Balu (All from European Bioinformatics Institute)
UTBS event page: https://training.cam.ac.uk/bioinformatics/event/4877402
Welcome to the wonderful world of Cytoscape! This course provides an introduction to the basic theory and concepts of network analysis. Attendees will learn how to construct protein-protein interaction networks and subsequently use these to overlay large-scale data such as that obtained through RNA-Seq or mass-spec proteomics. The course will focus on giving attendees hands-on experience in the use of one of the most commonly used open source Network Visualisation Platforms, Cytoscape. The course will also access and analyse the data through Cytoscape apps, including IntAct app.
Before the course
Please introduce yourself in the 'Introductions' document linked above before the course so that the tutors may understand your background.
Software
We will be using an online training environment for this module and you will receive a separate email with login details. Please use this environment as it makes it easier for the tutors to assist with any coding errors. Please install the Google Chrome web browser: https://www.google.co.uk/chrome/ (other browsers don’t work well with our virtual environment - especially Safari).
However, if you would like to set up a local installation you can follow the instructions here
If you choose this route during the course please be prepared to switch over to the virtual desktop environment in case of installation issues (we are happy to help debug these issues after the course).
Don’t worry if you don’t have this installed in time as you can use the Cytoscape installation on the virtual desktop environment to access this app during the course.
We recommend that, if possible, you have access to a second screen for the duration of the course.
Timetable
Date Time Topics
Day 1 09:30 - 09:45 Welcome and course admin
09:45 - 10:45 Introduction (~1h)
a. Network analysis basics
b. Molecular interactions and interaction databases: IntAct
c. Cytoscape
10:45 - 11:00 Comfort Break (~15')
11:00 - 13:00 Cytoscape practical
Accessing interaction data through the IntAct app (~2h)
a. Search modes
b. View modes
c. Filtering and finding data
Day 2 09.30 - 10:00 Cytoscape practical
Data integration in Cytoscape (~30')
10:00 - 11:00 Cytoscape practical
Topological analysis in Cytoscape: clustering with MCODE / ClusterMaker2 (~1h')
11:00 - 11:15 Comfort break (15')
11:15 - 13:00 Cytoscape practical (continued)
Enrichment analysis in Cytoscape: ClueGO (~1.75h)
Feedback survey
After the course, we would really appreciate it if you could share your thoughts with us regarding these sessions. We are interested in your opinions, how you feel the experience has benefited you and how it could be improved!
Zoom recordings
Links to the recordings will be made available after each session. These recordings are intended for course attendees only for private study. Please do not share these links! The links will continue to work for around a month after the course but you may download the videos for a permanent copy if you wish.
Day 1 recording - mhAhv0^j
Day 2 recording - 3yaK!s5%
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