Mini-Retreat Three

March 6-7, 2009

ISB, Seattle WA


Flights: arrive Thursday night, depart Saturday evening

The Official Hotel!

The Watertown Hotel in the U District has ISB rates (mention ISB):

They also have a free shuttle to and from ISB apparently.

Transportation: Shuttle from aiport to hotel (sad to say we have no decent public transit yet). Shuttle to and from ISB/hotel, there are also bus routes. Should anyone choose to stay in a downtown Seattle hotel Sarah could arrange to pick you up/drop you off. Can only take 3 though (and no one else here drives).

Schedule: THUR - nothing planned. If people would like to meet for dinner/drinks we should arrange that by Wednesday and Sarah will send cell phone number to you.

FRI - all day meeting. Breakfast at hotel. Lunch in Fremont area or we can order in sandwiches. Dinner TBD.

Meeting Schedule

Meeting Notes

in general, components will depend upon APIs, not implementations. The implementations are injected at run time. Distinguish via syntactic conventions: '-api' or '-impl

Task and Task Factory: uses a pattern that will be commonly used throughout Cytoscape Task: two basic methods, cancel and run encapsulates one unit of work. TaskFactory: created and registered with OSGI as a service Cytoscape takes task factories and makes them available Menu information is metadata Factory takes care of how to instantiate the task. Call to it is a simple getTask() method

two main XML files context: constructor with OSGI, context registers task as a service

Spring defines relation between objects basically its for wiring, constructing instances for injection

for the application level, need to take all actions and register them as services tunable as an annotation in the code

after lunch break

Hector's talk on web api plans: (see slides linked from post on cy-staff)

IO discussion

Application -- logging:


Saturday's Agenda:

1. Project management

2. Discuss web UI

3. This leads into a discussion about events

Project Management:



small note: will have to ensure that full javadoc we want to expose to plugin writers (i.e. the public api) is accessible from one place



An aside, belonging to the presentation layer: for z-order:

Web ui:

Outdated_Cytoscape_3.0/MiniRetreatThree (last edited 2011-02-24 15:33:32 by PietMolenaar)

Funding for Cytoscape is provided by a federal grant from the U.S. National Institute of General Medical Sciences (NIGMS) of the Na tional Institutes of Health (NIH) under award number GM070743-01. Corporate funding is provided through a contract from Unilever PLC.

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