Genetics, Bioinformatics and Systems Biology Colloquium
Thursdays, 12:00 pm – 1:00 pm
UC San Diego, Powell-Focht Bioengineering Hall, Fung Auditorium
Complete schedule here

Cytoscape Workshop 2016

Thursday, May 19, 2016 from 1:30 pm – 6 pm

Sanford Consortium for Regenerative Medicine

Organized by Barry Demchak

Cytoscape is the most popular software for visualizing molecular networks and biological pathways and for integrating these networks with annotations, gene expression profiles and other state data. Although Cytoscape was originally designed for biological research, now it is a general platform for complex network analysis and visualization. In this workshop, the Cytoscape development team from Trey Ideker’s lab will present a series of lectures and hands-on demonstrations covering a range of issues for both beginning and advanced users.


Please visit here to register.


Note: Please register for the beginner OR advanced session, not both. The only difference between ticket types is the information presented during the 3:15pm session. The software requirements for each session can be seen here, and you may need to download software prior to the session.



1:00 pm Registration (upstairs terrace)
1:30 pm Barry Demchak
Welcome (main auditorium)
1:35 pm Keiichiro Ono
What’s new in Cytoscape? (main auditorium)
2:30 pm Dexter Pratt
NDEx – the Network Data Exchange (main auditorium)
3:00 pm Coffee break (upstairs terrace)
3:15 pm Barry Demchak
Hands-on Workshop – Beginning Cytoscape (main auditorium)
3:15 pm Keiichiro Ono
Hands-on Workshop – Beginning Cytoscape (classroom near lobby downstairs)
4:45 pm Happy Hour (upstairs terrace)



What’s New in Cytoscape:

  1. Brief introduction to Cytoscape
  2. Cytoscape v3.3 and v3.4 improvements
  3. Futures: Cytoscape v3.5 and the Cytoscape CI


  1. What is NDEx and why is it valuable?
  2. How to use NDEx web site
  3. How to use NDEx in applications

Beginning Cytoscape:

  1. Understand networks
  2. Understand Cytoscape
  3. Goals: Be able to load a network, import annotation data, layout network, and visualize an important relationship

Advanced Cytoscape

  1. Understand how Cytoscape and custom applications can interact
  2. Goals: Be able to import data with Pandas, analyze data with NetworkX, visualize data in Cytoscape, and share notebooks and visualizations


No Show Policy

While we do not charge a fee to attend this event, these programs would not be sustainable and available to all wanting to attend, unless all registrants abide by the 48 hour cancellation notice policy. A no-show will also limit your ability to book our events in the future. Thank you in advance for your cooperation.


Free parking at the Sanford Consortium’s east lot will be provided on a first-come, first-serve basis. Hourly parking is also available for puchase at the ticket booth. There is also additional parking near the Torrey Pines Gliderport, which is within walking distance.  The UCSD Shuttle Route has two drop off locations within walking distance to the Sanford Consortium.


Pictures of scientists having fun

2016 05 SDCSB Cytoscape2016 05 SDCSB Cytoscape-2 2016 05 SDCSB Cytoscape-3 2016 05 SDCSB Cytoscape-5 2016 05 SDCSB Cytoscape-6

With additional support provided by Flu-OMICS

Flu-OMICS is funded by a grant from the NIH/NIAID U19AI106754