arrayCGHbase - The Dresden Build

Aside from the mobile/semantic/design stuff that this blog is primarily about, I'm also supporting a build of the php application ArrayCGHbase, which I'm now calling "The Dresden Build". It is up for demo viewing here:

http://www.cultureset.com/arrayCGHbase/index.php

If you'd like the demo password, please send email to acgh_base@cultureset.com. Let me know a little about you: what lab you are working at, what's your experience with ArrayCGHbase or other tools like it.

I found a couple of glaring bugs just before putting this version up, and I'm packing to go to California tomorrow, so I probably won't fix them for a few days. Just so you know:

- checkboxes are acting strangely in the experiment list page

- in normalization, if you do an add/update, the query mode controls appear at the bottom, even though you're not in query mode yet.

- I'm still tweaking the settings at the host; for now, loading more than about 6 oligo experiments, or 8 of the smaller experiments, will cause the upload page to time out. (Note that in this version of ArrayCGHbase, users copy experiment data files into a directory on the same server as the app; the files are then available via a pulldown in the experiment upload section. I've only uploaded 3 sets of CGH files into this directory).

Also, please note that in normalization, the checkbox for "Use Smoothed Ratios" refers to performing the normalization on a column of pre-smoothed ratio data, rather than the normal (non-smoothed) ratios column.

There are some reports still disabled in the pulldown in the experiment list page. We've got a list of open issues on those reports, which Beta users are welcome to peruse. (Beta users also get a tool for enabling those reports so they can try them out.)

So, if you don't the dust while I get some things worked on, please enjoy trying out this version. Let me know (at the above email address) if you're interested in downloading and installing The Dresden Build. I've written a quick but comprehensive manual for doing the install, which takes you through setting up your own LAMP (or WAMP/MAMP) server, tweaking it a bit, and installing our code. (Again, let me know what lab you're working with, and what experience you've had with ArrayCGHbase or other similar tools in the past.)

enjoy!