UVa Update - Tom Laudeman

Things have been quiet lately. I hope everyone is making good progress.

We're putting a new version live today: 1.5.20

We just created a raft of changes/features requested mostly by the microarray center here (the BRF). They wanted all studies, experimental conditions, orders, samples, and hybridizations (arraymeasurement records) to be owned by the Primary Investigator, with a created_by field. That was exciting. In doing that I found some bugs.

We also added loading and viewing the Affy quality control data. I added quite a bit more detail to some of the curator's order views.

Teela got the back end for the Analysis Trees 98% complete. As far as we can tell there are a couple of tiny tweaks at the Web/UI side, and Analysis Trees will be fully functional.

BTW, we changed the logo from "Va GeneX" to "GeneX Va" due to an alternate (funny, unfortunate) way to understand the letter combination

v a g e n e x

Sadly, we neglected to do the "does this spell something funny" test before finalizing the name. Sheez.

Cheers!

Caltech Update - Brandon King

I've been busy trying to document and get Pymerase to the level where other developers would consider using it. One of these days we hope to make the changes which will make the generatedm Python API compatible with Genex 2.x. We have also just setup the Bug / Feature Request tracker for the Pymerase project. I personally like it and think it might be worth using in the GeneX world.

On another note, my laptop has suffered from a RAM Slot Failure. It has been sent back to sony for repairs. Unfortunately, it had our only copy of GeneX 2.x. So, we are going to install GeneX 2.x on our database server soon, as Joe Roden would like to use the database. Any comments or suggestions about installation from a CVS checkout? Is it in a stable state? Any big changes planed soon?

Joe is hoping to load Affy U133 data into the database. Are the MAGE-ML file available to doing such a thing?

My goal for the next couple of weeks is to continue preparing Pymerase for release in the hope that other will use it and maybe even contribute to it. I also would like to get a better understanding of where GeneX 2.x currently stands? We would love to see GeneX 2.x regain the momentum it had before the holidays... Maybe it has, but we've just been out of touch?

Caltech Update - Brandon King

Accomplishments:
-Generate Graphviz diagrams which look like UML using Pymerase
-Wrote setup script for installing Pymerase

Next Week:
-Pymerase generation of GUIs
-More setup script improvement

UVa Update - Tom Laudeman

- Jodi cleaned up the schema some. We added a table to the security system so we can keep track of primary investigators (PI). Traditional groups aren't enough
-- the Microarray Center (called the BRF here at UVa) wants to know who the PI is. Jodi also removed loads of legacy stuff in the schema that isn't being used.

- Teela is back on our project for several weeks and is putting the final touches on the back end of the Analysis Trees.

After a couple of weeks working on other projects, I added some user requested features:

- Curator order view has a link to order owner's contact info

- Curator order view has a link to the QA data which is now being loaded from the RPT and EXP files.

- Curator order view has a link to the study. In yet another triumph for the security system, since the experimental conditions are not owned by the curator and therefore not writable, they render as text, not form fields. The triumph comes from not modifying the any existing code to achieve this.

- A couple of weeks ago I added a 'view one order' feature for the curators.

- I created the 'add PI to a specific user' and 'change user's PI' features.

- Fixed admin_cli.pl that we use to create new accounts to take PI as an argument.

- Patrick at George Washington U. has installed Va GeneX and found a bug in loading XLS Affy MAS5 data. I fixed that, added a new item to our test plan (since we missed the bug) and generally did some much needed cleaning in the loading scripts.

Next:
- allow users to chown orders and studies to the PI. Current thinking is that chown'ed records keep their group and group permissions.

- allow curators chown orders to the PI so that when the data is loaded, the PI will own it. Loaded data is owned by whoever owns the order.

- Analysis Tree work continues

- Additional reports for the curators in the microarray center