DataMatrix 0.7 has been released

Finally a new entry! I’ve been extremely busy with other things, that is why I did not have time to write more. One of the main reason is related to an important landmark in my professional career, but I’ll write more about it after January 1st (hint: those who follow my Twitter updates may have already understood). As a nice way to break the hiatus, I’m releasing a new version of DataMatrix, my implementation of R’s data.

November 2, 2008

The plague of cross-database annotations

Recently I had to annotate a large (10,000+) number of genes identified by Entrez Gene IDs. My goal was to avoid “annotation files” (basically CSV files) that a part of wet lab group likes, because I wanted to stay up-to-date without having to remember to update them. So the obvious solution was to use a service available on the web, and in an automated way. For reference, I just tried to attach gene symbol, gene name, chromosome and cytoband.

October 22, 2008

Alternatives to Kubuntu for the Eee PC?

Currently I have Kubuntu 8.04 (Hardy) installed on my Eee PC. Version 8.10, the Intrepid Ibex, is due on October 30th. However, I will not install it. The reason is that Kubuntu developers intentionally disabled the zoom function, and I have three activities on this machine. How come I’m supposed to use them? Also, space is pretty tight so install a build environment just to remove one patch seems overkill. So, I’m moving away from it.

October 12, 2008

DataMatrix page up

Ok, ok… my definition of “tomorrow” is not like what most people use, apparently. Although I took quite a while, now [there is a static page on DataMatrix]({{ site.url }}/projects-2/datamatrix). There you will find a summary of wht I wrote in my other blog posts regarding this module. Of course, it will be kept up-to-date should I release a new version. Aside that, I put a contact form on this blog.

September 20, 2008

Posting from KOrganizer

Following the instruction from Mike Arthur’s post on planetkde, I tried posting on dennogumi.org from KOrganizer (KDE 4.1.1). Lo and behold, it works! It’s always better to use an application rather than a clunky web user interface…

September 19, 2008

DataMatrix 0.5

At last, since it’s been like ages, I decided to put out a new version of DataMatrix. For those who haven’t seen my previous post, DataMatrix is a Pythonic implementation of R’s data.frame. It enables you to manipulate a text file by columns or rows, to your liking, using a dictionary-like syntax. 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).

September 13, 2008

New PC, at last

All right, it didn’t quite turn out as I had expected. This post wasn’t “soon"as I predicted originally. The reason? The fact that the video card I bought died after three days of usage, and getting a replacement took a while. Finally though, I have a functional system. It’s a Core 2 Duo CPU (7200) with 2 Gb of RAM and an ATI Radeon 3870 HD video card. I installed Linux on it, of course, but instead of Kubuntu I gave openSUSE a try.

August 27, 2008

I'm back

Sadly (for me) I’m back from the holidays. For those of you who wondered why the updates on Japan stopped: when I got back to Tokyo I didn’t have an Internet connection, so I had no means to update. The whole holiday was a blast, though, and we’re considering getting back in two years. Aside from that, work has picked up a really fast pace immediately (why on Earth journals don’t accept LaTeX-produced PDFs?

August 8, 2008

Japan - Day 6

Today we went to Nar, site of the first capital of Japan, especially to see the Todaiji Temple, designated as a World Heritage site by UNESCO. We used an express train to get to Nara and then a bus to get to the Todaiji itself (actually it’s a quick walk, I just didn’t know the distance was so short). The temple lies inside the Nara-koen, or Nara park, which is famous for its 1200 tame sacred deers.

August 7, 2008

Japan - Day 5

It’s been a hot day here in Kyoto. And I don’t mean lame second meanings, just that the temperature was really over the top. As a consequence, we changed our plans: we were supposed to visit the so-called “path of the philosophy” but instead we set for Nijo Castle. Nijo Castle was the Kyoto residence of Ieyasu Tokugawa (I suspect to tell the emperor who was the real person in power) and it can be visited.