Cytoscape Workshop 2016

Ideker Lab

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. 
 
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 <A HREF="https://drive.google.com/file/d/0B3Uru2yfZaXFc1pQcHM2NXdJa3c/view?usp=sharing" TARGET="_blank" DATA-MSYS-CLICKTRACK="0" REL="nofollow noopener noreferrer">here</A>, and you may need to download software prior to the session. 
 
Schedule 
<TABLE BORDER="0">
<TBODY>
<TR>
<TD>1:00pm</TD>
<TD>Registration</TD>
<TD> </TD>
</TR>
<TR>
<TD> </TD>
<TD>Upstairs terrace </TD>
<TD> </TD>
</TR>
<TR>
<TD> </TD>
<TD> </TD>
<TD> </TD>
</TR>
<TR>
<TD>1:30pm  </TD>
<TD>Introduction </TD>
<TD> </TD>
</TR>
<TR>
<TD> </TD>
<TD>Barry Demchak</TD>
<TD> </TD>
</TR>
<TR>
<TD> </TD>
<TD>Main auditorium </TD>
<TD> </TD>
</TR>
<TR>
<TD> </TD>
<TD> </TD>
<TD> </TD>
</TR>
<TR>
<TD>1:35pm</TD>
<TD>What’s new in Cytoscape? </TD>
<TD> </TD>
</TR>
<TR>
<TD> </TD>
<TD>Keiichiro Ono</TD>
<TD> </TD>
</TR>
<TR>
<TD> </TD>
<TD>Main auditorium</TD>
<TD> </TD>
</TR>
<TR>
<TD> </TD>
<TD> </TD>
<TD> </TD>
</TR>
<TR>
<TD>2:30pm</TD>
<TD><A HREF="http://www.ndexbio.org/" TARGET="_blank" DATA-MSYS-CLICKTRACK="0" REL="nofollow noopener noreferrer">NDEx – the Network Data Exchange</A> </TD>
<TD> </TD>
</TR>
<TR>
<TD> </TD>
<TD>Dexter Pratt </TD>
<TD> </TD>
</TR>
<TR>
<TD> </TD>
<TD>Main auditorium</TD>
<TD> </TD>
</TR>
<TR>
<TD> </TD>
<TD> </TD>
<TD> </TD>
</TR>
<TR>
<TD>3:00pm  </TD>
<TD>Coffee break</TD>
<TD> </TD>
</TR>
<TR>
<TD> </TD>
<TD>Upstairs terrace </TD>
<TD> </TD>
</TR>
<TR>
<TD> </TD>
<TD> </TD>
<TD> </TD>
</TR>
<TR>
<TD>3:15pm</TD>
<TD>Hands-on Workshop – Beginning Cytoscape            </TD>
<TD>Hands-on Workshop – Advanced Cytoscape          </TD>
</TR>
<TR>
<TD> </TD>
<TD>Barry Demchak </TD>
<TD>Keiichiro Ono</TD>
</TR>
<TR>
<TD> </TD>
<TD>Main auditorium</TD>
<TD>Classroom near lobby downstairs </TD>
</TR>
<TR>
<TD> </TD>
<TD> </TD>
<TD> </TD>
</TR>
<TR>
<TD>4:45pm </TD>
<TD>Happy hour</TD>
<TD> </TD>
</TR>
<TR>
<TD> </TD>
<TD>Upstairs terrace </TD>
<TD> </TD>
</TR>
</TBODY>
</TABLE>
 
Agenda 
What’s New in Cytoscape: 
<OL>
<LI>Brief introduction to Cytoscape</LI>
<LI>Cytoscape v3.3 and v3.4 improvements</LI>
<LI>Futures: Cytoscape v3.5 and the Cytoscape CI</LI>
</OL>
 NDEX: 
<OL>
<LI>What is NDEx and why is it valuable?</LI>
<LI>How to use NDEx web site</LI>
<LI>How to use NDEx in applications</LI>
</OL>
 Beginning Cytoscape: 
<OL>
<LI>Understand networks</LI>
<LI>Understand Cytoscape</LI>
<LI>Goals: Be able to load a network, import annotation data, layout network, and visualize an important relationship</LI>
</OL>
 Advanced Cytoscape 
<OL>
<LI>Understand how Cytoscape and custom applications can interact</LI>
<LI>Goals: Be able to import data with Pandas, analyze data with NetworkX, visualize data in Cytoscape, and share notebooks and visualizations</LI>
</OL>
 
No Show Policy
While we do not charge a fee to attend this event, these and our other events would be unsustainable unless those unable to attend cancelled their reservations no later than 2 days before the event. A no-show can limit your ability to book our events in the future. Thank you in advance for your cooperation.
 
  
Parking
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.

Sanford Consortium for Regenerative Medicine

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Cytoscape Workshop 2016

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