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:
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 Presentors: 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 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
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 firstname.lastname@example.org 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): Confirmed: - 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 Unconfirmed: - 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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