Workshop Description
The workshop introduces Cytoscape (https://cytoscape.org/) – an open source platform for retrieval and visualization of complex biological interactions that are available from public interaction resources: The IMEx Consortium (https://www.imexconsortium.org/), STRING (https://string-db.org/) and BioGIRD (https://thebiogrid.org/). It covers querying for interactions data using built-in search interface, interaction data cleanup and visualization as well as overlying of the in-house generated data (eg. gene expression levels) on top of the imported reference interaction network. The workshop will also provide an overview of the experimental methods of interaction determination and of the information available from the interaction resources, both necessary to critically evaluate imported interaction networks.
Workshop Materials
Day 1
Introduction to Cytoscape:
* Interaction networks
* GUI Interface
* Public interaction resources
* Interaction queries
* Data cleanup
Day 2
Day II
* Experimental methods of interaction data determination
* Information content of interaction data records
* Interaction data ambiguities
Day 3
Day III
* Data import (spreadsheets/text files)
* Visualization of expression data
* Enrichment analysis (BiNGO plugin)
Technical Requirements
Network access, recent (3.8.x) version of Cytoscape (https://cytoscape.org/download.html) installed.
Chrome or Firefox Internet Browser is recommended.
Instructor
Dr. Lukasz Salwinski is currently an assistant researcher in the laboratory of Professor David Eisenberg who, for over a decade, has been responsible for development and maintenance of The Database of Interacting Proteins (https://dip.doe-mbi.ucla.edu). He received his master degree in biology at the Jagiellonian University, Krakow (Poland) and earned Ph.D. at UCLA, in the group of Professor Wayne Hubbell where he applied EPR spectroscopy to study structure of pore-forming bacterial toxins.
Videos
Reviews
Workshop Details
Prerequisites: None
Length: 3 days, 3 hrs per day
Level: Introductory
Location: Boyer 529
Seats Available: 28
Fall 2022 Dates
Oct. 25, 26, and 27
9:00 AM – 12:00 PM
REGISTRATION IS OPEN!