Cytoscape 3 Hackathon

• October Thur 29 - Friday 30, 2009 (2 days)

• UCSF Mission Bay, 1650 Owens St. San Francisco, CA 94158 (The Gladstone Institutes)

• Contacts: Alex, Allan, Scooter

Logistics

• Flights:

  • arrive Wednesday 28th in the evening, or early Thursday morning.

  • depart Friday evening (not afternoon!), or Saturday.

• The Official Hotel!

  • The Queen Anne is particularly recommended (1-800-227-3970) Ask for the UCSF group rate. http://www.queenanne.com/ ($125; It's not close by, however. We would have to organize pick ups/ drop offs)Check for bed bugs!

• Transportation: You can take BART to and from the SFO airport. And there is the K/T-line train that connects downtown SF to the campus (takes ~20min).

• Schedule: All day Thursday and Friday. We will organize breakfast and lunch both days, plus Thursday dinner.
• We'll be on skype... and email, of course.

Goals

• Get a grip on 3.0 core and plugin development
• Port the core plugins to 3.0

Tasks to Tackle

People should add their plugins/core plugins that they are most interested in porting. We also need to define teams (pairs or tuples) of people to work together (Extreme style) on these projects. Ideally, each team will have a maven/spring/osgi/3.0 guru.

• Discuss Integrated Search Bundle - QuickFind, Filters and ESP (Maital).

• Metanodes port (Scooter). Maital - expressing interest in Metanodes.
• 3.0 Plugin Manager (Sarah?)
• Editor (Allan)
• Attributes/CyDataTable Browser (?)

Homework

Before the Hackathon, please setup your development environment for OSGi/Maven projects:

• Install Java 6 to your laptop!

• Learn basics how to create/wrap bundles (This is a good introduction)

• Read developer's guide for Cytoscape 3

Eclipse

• Install latest version of Eclipse (3.5 Galileo)

• Install Cytoscape IDE

• Try this tutorial

NetBeans

Commandline

• Install Maven

Agenda

Thur 29

Conference Rooms A & B on the ground floor of Gladstone. Video conferencing systems available for the morning session. Connection details coming...

• 9:15AM - 10:30AM => intializing (12:15NOON-9:00PM EASTCOAST; 5:15PM-2:00AM CET WORLDCLOCK)

• 10:30 - 12:00PM => discuss overall goals of projects and split into teams

• 12:00PM - 1:00PM => lunch

• 1:00PM - 6:00PM => HACK!

• 6:00PM => Japan town: Fuku Sushi

Fri 30

Conference Rooms C & D

• 9:30AM - 4:00PM => HACK!

• 4:00PM - 6:00PM => report and wrap-up

Pre-meeting Questions & Comments

Discussion Notes

• Day One

• Day Two

Attendees

I need a head count to help organize the event. Please contact Alex if you're are coming or might be coming. Please add your name below, including your approximate arrival and departure times.

• Sarah - arriving: departing:
• Kei - arriving: Wed 28th, evening, departing: Friday evening 9PM flight
• Peng - arriving: Wed 28th, evening, departing: Friday evening 9PM flight
• Mike - arriving: Wed 28th, evening, departing: Friday evening 9PM flight

• Allan - local

• Alex - local

• Kristina - local

• Scooter - local

• Maital - arriving: Wed 28th, evening. departing: Saturday noon flight

Remote

• Skype call

• Ustream channel