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Programming Jamboree IV: Stanford Dec 6-10, 2002

The fourth MGED programming jamboree will be held at Stanford University in in Stanford CA from Dec 6 through Dec 10.

Hotel Information and directions

Go to the Stanford Jamboree page for more details.

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.

Here is a proposed itinerary

Important issues:
 * documentation: good examples, tutorials
 * DB: finish generation of Postgres schema, work on mapping layer
   started by Angel, look into automatic generation of DB adaptor code
 * XML Schema: in order to use MAGE with BioMOBY/MyGrid we need to
   generate a modular XML Schema - this can then be converted to a DTD
   if necessary for backwards compatibility.
 * finish Python support
 * ensure that XMI parsers fully support Poseidon/Argo XMI
 * Perl: move XML Reader to a module, add better hooks to customize
   writing and reading of XML
 * test MAGEstk with other data models 

Agenda for Friday, Dec 6

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

Jason Stewart: OpenInformatics and MGED
Plus other guests

Tentative Schedule:
  09:00-11:30 - Model Overview
  11:30-13:30 - long lunch break
  13:30-15:30 - Model Overview / MAGEstk Overview
  15:45-16:00 - break
  16:00-17:45 - User presentations (SMD, UPenn, ISB?, ?)
  17:45-18:00 - wrap up


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


To register, go to the Stanford Jamboree page.


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 and I'll update.

If you are attending, either just the tutorial or the full week, you should subscribe to the jamboree mailing list. All announcements will go through that list.

All week (Friday + coding work Sat-Tue, or part of it anway):
- Jason Stewart   Open informatics
- Michael Miller  Rosetta BioSoftware
- Angel Pizarro   University of Pennsylvania
- Paul Spellman   UC Berkeley
- Ronald Taylor   University of Colorado
- Charles Troup   Agilent Technologies
- Steven Zhang    Stanford University
- Michael Fero    Stanford University
- I-Ping Tu       Stanford Functional Genomics Facility
- Rami Rauch      Stanford
- Albert Leung    Johnson & Johnson Pharmaceutical Research Institute	
- Allen Day       Human Genetics, UCLA Medical School
- Todd Thal       NA-UC
- Bill Martin     Attotron
- Sung-Joon       Lee
- John Matese     Stanford University
- Catherine Ball  Stanford Univeristy
- Nick Moseyko    Carnegie Institution of Washington
- Tina Boussard   Stanford University
- Karsten Hokamp  Simon Fraser University
- Greg Finney     contractor

- Jeremy Gollub (Stanford)
- Brandon King  (Caltech Wold Lab)
- Diane Trout   (Caltech Wold Lab)
- Eric Deutsch  (ISB)
- Robert Hubley (ISB)

Friday Tutorial only
- Siobhan Pickett       Axon Instruments
- Shawn Handran         Axon Instruments
- Luis Allegri          Amersham Biosciences
- Peter Schattner       University of California, Santa Cruz
- Christian Rees        Zyomyx Inc.
- Greg Rokita           Zyomyx Inc.
- Joan Hebert           Stanford University
- John Coller           Stanford University
- boussard              Stanford
- Susan Holmes          Stanford
- Todd Stephan          PerkinElmer
- Chiao-Jung Tsai       Stanford University
- Shufang Yang          Stanford University
- Daniel DiGiulio       Stanford University Medical School
- Verbus M. Counts      Advanced Open Source Solutions, inc.
- Peter Webb            Agilent Technologies
- Robert Horton         Attotron Biosensor Corporation
- rajendra shrivastava  Advanced Open Source Solutions, inc.
- Mark Sornson          Stanford University
- Nigam Shah            Penn State
- Gail Binkley          Stanford University
- Mykola Dudar          UNM HPCERC
- Margarita Garcia      CArnegie Institution of Washington
- Peter Eastman         Silicon Genetics

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