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Programming Jamboree III: Seattle May 20-24, 2002

The third MGED programming jamboree was held at the Fred Hutchinson Cancer Research Center in Seattle Washington from May 20th through the 24th.

Hotel Information

You can find hotel information in the following email from Robert Hubley.

Schedule

Official initial start time is Monday 10:00a in Sze Conference Room. Setup and preparation will start earlier, beginning 9:00a. After lunch we'll be in B1-072/074.


  Mon May 20 10:00a - 1:00p:  Sze conference room, Thomas Bldg
                    - 6:00p:  B1-072/074, Thomas Bldg
                    - 6:00p:  Room J2-108, Yale Bldg
  Tue May 21  9:00a - 6:00p:  Room J2-108 + J2-515, Yale
  Wed May 22  9:00a - 6:00p:  Room J2-108
  Thu May 23  9:00a - 6:00p:  Room J2-108
  Fri May 24  9:00a - 6:00p:  Room J2-108 + J2-515

Maps of the Fred Hutch area:

Directions:

To get to Monday morning's session: Drive onto Yale Ave from Fairview Ave (top of map) and then around to the Parking "P" adjoining the Thomas building (the building labeled "1" on the maps). Enter the building through the main entrance at the NE corner of the parking lot. The reception desk is on the right just after you've entered. Give the receptionist your license plate number and indicate that you'd like to park all day for the "MAGE Conference". The Sze conference room is just past the reception desk in the Thomas building. Room B1-072/074 is farther down the main corridor on the right, opposite the Double Helix Cafe.

If parking here runs out, you may need to move to the Yale Building parking lot (below) or resort to street parking (unlikely).

To get to J2-108/J2-515: Drive onto Aloha St from either Eastlake Ave or Fairview Ave and then into the Parking "P" in front of the Yale Building, labeled "5". Walk into Yale, giving the receptionist your license plate number and indicating that you'd like to park all day for the "MAGE Conference". Go up to the second floor to find J2-108 and J2-515 (adjacent).

The Marriott is due West of building "6" in the triangle block bounded by Minor, Fairview, and Valley. The Silver Cloud is East of building "2" in the sliver of land between Fairview and Eastlake.

Rosetta has kindly offered to provide box lunches on Monday. We'll go foraging at the Fred Hutch cafeteria or elsewhere for the rest of the week.

Don't forget a computer! There are no public computers available so you must bring a laptop or other computer to work with for Tue - Fri.

The Seattle Folk Life festival begins Friday the 24th and goes through the weekend. See http://www.nwfolklife.org/P_F/Schedule.html for more information. There was talk of going on a hike in the mountains on one of the weekend days, too, weather permitting. If you're interested in doing that, bring hiking boots, preferably somewhat waterproofed. Hiking may well be on snow, depending on where we go.

Overview of the week

There are two main goals for the jamboree:

  1. A full-day seminar to educate people about MAGE and MAGEstk.
  2. A four day programming marathon to improve MAGEstk.

The full day seminar is open to anyone who wants to attend and learn more about MAGE. The programming marathon will be limited to around 20 developers.

You can find the detailed itinerary in the following email from Jason Stewart.

Agenda for Monday May 20


Title: A Tutorial on MAGE, the MicroArray Gene Expression project

Presentors:
Jason Stewart: OpenInformatics and MGED
Michael Miller: Rosetta BioSoftware
Plus other guests


Tentative Schedule:
  10:00-11:30 - Model Overview
  11:30-11:45 - break
  11:45-13:00 - Model Overview
  13:00-14:00 - lunch
  14:00-15:30 - Model Overview / MAGEstk Overview
  15:45-16:00 - break
  16:00-17:45 - User presentations (ISB, SMD, TIGR, ?)
  17:45-18:00 - wrap up


Abstract: 

The goal of the MAGE project is to provide biologists and developers
with a unified description of microarray expression data, which we hope
will become the de facto community standard.

MAGE consists of three main components:
1) MAGE-OM - The MAGE Object Model, a UML data model
2) MAGE-ML - The MAGE Markup Language, an XML data format
3) MAGEstk - The MAGE Software ToolKit, a suite of software for
   handling MAGE data

The MAGE-OM was developed by a collaborative effort of a number of
different groups, including participants from MGED - the MicroArray Gene
Expression Database group, Rossetta BioSoftware, Agilent, and
Affymetrix. It was accepted as an official data specification by the
Object Management Group (OMG) in January 2002. MAGE-OM defines the high
level objects in microarray data and their relationships with one
another using UML, the Unified Modeling Language. 

Since communication of data was one of the primary goals of the project,
an XML markup language, MAGE-ML, was created that is derived directly
from object model by means of software. 
Finally, in order to assist in the adoption of MAGE, an Open Source
software suite, MAGEstk, was developed to enable programmers to generate
and parse MAGE-ML information, as well as interact with a persistent
data store, such as a relation DB system.

This full-day tutorial will cover the following areas:

1) What is MAGE-OM, MAGE-ML, MAGEstk
2) What is the status of MAGE, and where is it going
3) A full discussion of MAGE-OM (and why we will not discuss much
   about MAGE-ML)
4) Examples of how to use MAGEstk, for pulling data out of a DB and
   exporting XML in Java and Perl

The target audience for this tutorial is anyone who
1) wants a better understanding of MAGE-OM
2) has questions about converting existing data to MAGE
3) has issues/concerns about whether MAGE can handle what they need
4) developers who want to support MAGE, either in their own software
   or by adding to the MAGEstk suite

Attendees

And finally, here's the list of attendees as I have it in no particular order. If you have any additions/corrections to make, please send them to edeutsch and I'll update.

Monday only (Model tutorial and public session/discussion):
- Jeremy Gollub (Stanford)
- Janos Demeter (Stanford)
- Catherine Ball (Standford)
- Tina Hernandez-Boussard (Stanford)
- Don Brocha (Applied Precision, LLC)
- Mike Wood (Applied Precision, LLC)
- Tom Milac (U of Washington)
- PaulBen McElwain (U of Washington)
- Wayne Yamamoto (U of Washington)
- Steve Lasky (ISB)
- Paul Shannon (ISB)
- David Reiss (ISB)
- Chris Lausted (ISB)
- Tim Dahl (ISB)
- George Lake (ISB)
- Vesteinn Thorsson (ISB)
- Bruz Marzolf (ISB)
- Tatiana Gill (ISB)
- Mark Aronszajn (Fred Hutch)
- Bill Carrick (Fred Hutch)
- Mark Ashworth (Fred Hutch)
- Natalie Hawkins (Fred Hutch)
- Jack Hwang (Fred Hutch)
- 3 +- ? other people from Fred Hutch
- 3-10 other people from Rosetta


All week (Monday + coding work Tue-Fri):
- Jason Stewart (Open informatics)
- Michael Miller (Rosetta)
- Angel Pizarro (U Penn CBIL)
- John Matese (Stanford)
- Teemu Toivanen (Turku Centre for Biotechnology, Finland)
- Tero Raitanen (Turku Centre for Biotechnology, Finland)
- Terry Barrette (U Michigan)
- Brandon King (Caltech Wold Lab)
- Benjamin J. Bornstein (Caltech Wold Lab)
- Diane Trout (Caltech Wold Lab)
- Eric Deutsch (ISB)
- Michael Johnson (ISB)
- Robert Hubley (ISB)
- Michelle Whiting (ISB)
- Paul Edlefsen (ISB)
- Rowan Christmas (ISB)
- Joe White (TIGR)
- Jerry Li (TIGR)
- Gonzalo Garcia Lara (EBI)
- Mike Terry (U of Nebraska)
? Hilmar Lapp (GNF)

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