Caltech Update - Brandon King

Summery:
-Worked on updating pymerase output modules
-Wrote an output module for generating Python Tk Widgets. (Partially Implemented)
--Currently handles varchar and text fields.

Next Week:
-Add support for other datatypes to Python Tk Widget generation
-Automaticly hook up the Python Tk Widgets to generate Python Tk Widgets as a option
-Test GeneSpring connection

Caltech Update - Diane Trout

* Current progress

** sent to rosetta to investigate resolver. ** in getting the XMI reader working for pymerase I broke the GeneX Table.dtd reader. I'm currently fixing it.

* Next week ** Try and generate python MAGE objects
** More pymerase bug fixes.

* Thoughts

Since we're auto creating an API and database to for the user, would it be possible to choose between storing array expression data as relational records or as NetCDF (or similar open matrix file format)?

UVa Update - Tom Laudeman

- Implemented chgrp and chmod types of functionality in the web UI.

- Fixed a host of small bugs

- Tested, and installed a new version in production (1.5.15)

- Started integrating UI of the Analysis trees with the back end. The UI now reads user parameter values, and new nodes created from the UI get default values.

UCI Update - Harry Mangalam

* worked on getting the configure/installer to install the analysis apps again (cybert, xcluster, rcluster)
* the changes are just about ready to check in (the infamous Mangalam Real Soon Now). The installation works for CyberT, xcluster, but not yet for rcluster (perl lib location problem).
* in doing so, spent some time fixing the app cores and interfaces for cybert
* another GeneX install from scratch; more mods to the installation docs.

Open Informatics Update - Jason Stewart

Progress:
* jamboree at Stanford - added support for persistence in XML::Reader
* added array tools to support MAS5 (fix-array, tab2AD, qtdim)
* loaded and verified MAS5 dataset

Goals for next week
* be happy
* build Genex persistence subclass for XML::Reader
* load U133 array design
* load .CEL data

Caltech Update - Diane Trout

* current work

Spent week vacationing.

Actually I discovered that the packages satisfying some of the dependencies I'd built for GeneX were accidentally deleted.

I've managed to rebuid them.

* next week

other internal work, (high probability of being done).

start working on updating pymerase for the most recent GeneX database format. (e.g. support row level security). (med priority)

Perhaps make a few more debian packages. (low-med priority)

UCI Update - Harry Mangalam

Last week largely lost to travel prep and travel. Met and talked with a number of people at GMU, NRL. Installed GeneX with some success and tried to load data, with less success.

During last week, more time 'lost' to Thanksgiving, but GeneSpring connection up and running mostly. Have documented the protocol level connection and am continuing to extend the connection to provide user-level useful data and provide mappings so that more of GeneSpring capabilities can be used.

This process somewhat delayed by problems in data loading, somewhat resolved now and personal ignorance of finer points of SQL.

Also for GeneSpring connectivity, am testing scalability of GeneX DB (sometimes by intent, sometimes by ignorance)...

Caltech Update - Brandon King

Summery:
-Created GenePix-GPR-1.0 FeatureExtractionSoftware
-Tested Uploading of GPR files (success)
-Documented the creation process of
---FeatureExtractionSoftware
---ArrayDesign
---ExperimentSet
---Data Upload
-Finished Agilent 5.1.1 FeatureExtractionSoftware XML
-Created BioGenex Python package
---GPR Parser (Diane's Creation)
---Agilent Parser
---GeneX 2.x Config Parser
---bin/fixarray-gpr.py (for preparing arraydesigns from a GPR file)
---bin/tab2ADgui.py (GUI for running tab2AD.pl)
---setup.py for installing BioGeneX package

Next Week:
-Finish testing Agilent data upload
-Help Diane (if possible) with updatinge Pymerase for GeneX 2.x.
-Start on ideas for GeneX 2.x GUIs

UVa Update - Tom Laudeman

Open Informatics Update - Jason Stewart