EMBL-EBI: Network Analysis with Cytoscape and PSICQUIC
This workshop will guide novice users through the process of analysing interaction networks – that allow biologists to map and characterise signalling pathways and to predict the function of unknown proteins. It will use practical examples in the popular open-source tool Cytoscape and the PSICQUIC client to access several protein interaction repositories at the same time to integrate protein data from different sources. Data from external sources will then be incorporated using different Cytoscape apps to perform clustering and GO enrichment analysis over our newly created networks.
Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here.
- The workshop is aimed to biologists or computer scientists with little or no previous knowledge of Cytoscape
- Graduate students, Postdocs and Staff members from the University of Cambridge, Affiliated Institutions and other external Institutions or individuals
- Please be aware that these courses are only free for University of Cambridge students. All other participants will be charged a registration fee in some form. Registration fees and further details regarding the charging policy are available here
- Further details regarding eligibility criteria are available here
Basic knowledge of interaction data resources and techniques is recommended
Number of sessions: 1
| # | Date | Time | Venue | Trainer | |
|---|---|---|---|---|---|
| 1 | Wed 17 May 2017 09:30 - 17:00 | 09:30 - 17:00 | Bioinformatics Training Room, Craik-Marshall Building | map | Pablo Porras |
Bioinformatics, Pathway or network analysis, Pathway or network visualisation
After this course you should be able to:
- Understand how the PSICQUIC client can help you to integrate molecular interaction data from different public repositories
- Utilise a range of Cytoscape apps to generate and analyse interaction networks
During this course you will learn about:
- Molecular interaction network analysis
- PSICQUIC and molecular interaction data integration
- Basic principles of network analysis
- Basic Cytoscape functionality and use of apps for clustering and GO enrichment analysis
Presentations, demonstrations and practicals
| Time | Topics | Speaker(s) |
| 09:30 - 10:30 | Introduction to PSICQUIC and MI data integration | Pablo Porras Millan |
| 10:30 - 11:00 | Introduction to network analysis and Cytoscape | |
| 11:00 - 11:15 | Tea/Coffee break | |
| 11:15 - 12:30 | Cytoscape basics (hands-on) | Pablo Porras Millan |
| 12:30 - 13:30 | Lunch | |
| 13:30 - 15:00 | Cytoscape basics (hands-on) cont'd | Pablo Porras Millan |
| 15:00 - 15:15 | Tea/Coffee break | |
| 15:15 - 17:00 | Cytoscape basics (hands-on) cont'd | Pablo Porras Millan |
| 17:00 | End of workshop | |
- Free for University of Cambridge students
- £ 50/day for all University of Cambridge staff, including postdocs, and participants from Affiliated Institutions. Please note that these charges are recovered by us at the Institutional level
- It remains the participant's responsibility to acquire prior approval from the relevant group leader, line manager or budget holder to attend the course. It is requested that people booking only do so with the agreement of the relevant party as costs will be charged back to your Lab Head or Group Supervisor.
- £ 50/day for all other academic participants from external Institutions and charitable organizations. These charges must be paid at registration
- £ 100/day for all Industry participants. These charges must be paid at registration
- Further details regarding the charging policy are available here
One full day session
A number of times per year
Booking / availability