• UCSC Genome Browser: it has a MySQL server but it’s rather slow and I did not want to clog it up. Using their tables and .sql files I managed to get a first shot at annotation, but about 2,000 genes were without annotation!
• NCBI’s own Entrez Gene: This needs EUtils, and in Biopython there is not a parser for Entrez Gene XML entries. I had to scrap the idea because I did not have time.
• Ensembl: I decided to use the Biomart service, through Rpy. There were missing genes, and sometimes the IDs were “converted” in something else (I had no time to figure out what was happening). Also some perfectly valid genes (in Entrez Gene) were not present in Ensembl.

In the end I just grabbed Bioconductor’s “org.Hs.eg.db” package and used its sqlite gene database (from Entrez Gene) to annotate the list, with only 97 missing IDs (mostly genes that had changed identifiers). However, this effort revealed a problem:the annotations are not consistent between databases. This is a real pain when doing microarray-based analysis, because you often have large number of genes and perceived lack of annotation might get lead to a number of them getting discarded.

I thought the situation was better than this. If I annotate genes in different databases with the same ID, I expect to get identical results. I mean, it’s not like Gene or Ensembl have little resources… or am I wrong?

Aside that, I put a contact form on this blog. It may be useful for reports that aren’t directly related to the posts.

In this new version there have been a few improvements and correction to a couple bugs (for example saveMatrix did not really save) and the start (only a stub at the moment) of an append function to add more columns (I’ll also think about a function to add rows).

DataMatrix is licensed under the GNU GPL, version 2 only. You can download the installer (Windows) or the source distribution (Linux and other *nixes). The only requirement is Python 2.5 or later installed on your system.

The README currently is a stub, but you can browse the pydoc generated documentation, which details how to instantiate and use DataMatrix objects (or you can turn to my older post).

Also, since git is the new “cool feature of the day”, DataMatrix is is hosted on github’s repository, and you can grab the source with

git clone git://github.com/cswegger/datamatrix.git

Comments and suggestions are welcome. I’ll be putting a static page on DataMatrix tomorrow, if time permits.

I installed Linux on it, of course, but instead of Kubuntu I gave openSUSE a try. It’s quite polished, although I had to go through some hoops to enable font hinting, especially in Firefox (not that I use that browser a lot, but I still need it for some things). I’ll be keeping Kubuntu on the Eee, as there’s a larger community for customization.

With this PC, I can do a few things, such as trying out FFXI on WINE and also try out some web application using the Django framework.

By the way, if you have seen some downtime in this blog it’s due to the absolutely awful Wordpress upgrades I attempted, and mostly Wordpress’s fault anyway.

Aside from that, work has picked up a really fast pace immediately (why on Earth journals don’t accept LaTeX-produced PDFs?) and I expect a round of meetings and planning to start soon to plan the next three months. I had a poster accepted at the ECCB 2008 conference, but the steep fees (1200 euro for flight, registration and lodging) made me reconsider. Better luck next time, I guess.

On other fronts, I read that FFXI can run on WINE now. I’ll be sure to try it once I finish preparing my new PC (I’ll write about it soon).

That’s all for now.

There are lots of them. Everywhere. Literally. As they’re tame, they approach people and aren’t really scared (save for the younger ones). You’ll see some photos of them in the gallery. After that, I got to see the Daibutsu (BIG BUDDHA, for NRK). It’s a huge statue of the Buddha, in bronze and gold. Along with that, we paid a visit to the Nara Museum (1200 yen - ick) to see an exhibition on the thirty-three shrine pilgrimage in Japan. Nice exhibits, just a little short for the price.

The afternoon was spent looking for electronics at the BIC CAMERA store near the Kyoto station. Tomorrow we’re back to Tokyo - last two days of shopping before going back to Italy. The gallery has been updated, as usual.

After that we stopped for lunch in the Kyoto Station, a rather controversial piece of architecture built in the ninieties of the last century. I can say it’s huge, and filled with stores and even a hotel(!).

In the afternoon, we went gain for shopping, targeting the local Animate, Gamers, and Melon Books stores. My brother snatched up a non-H, FFXI-related dojinshi from Melonbooks, and I grabbed a limited edition of Aquaplus’s latest PS3 title, Tears to Tiara (photos coming up tomorrow). Tomorrow, we’ll be (weather permitting) heading for Nara to view the Todaiji Temple. That will be our last day in the Kansai region, as the day after that we’ll return to Tokyo via shinkansen. New photos have been uploaded to the gallery, of course.

By the way, I managed to view Slayers Revolution last night on TV Tokyo, and here is the obligatory photo:

Today instead we transferred by Shinkansen to Kyoto (very fast trip) and settled in the new hotel here (definitely larger, although I have to access the net from a lobby). Tomorrow we’ll go for some sightseeing in the morning and shopping in the afternoon (Gamers and Melon Books have branches here, near the hotel even).

New photos have been put up in the gallery.