• It’s a bioinformatics paper;
• I am first author there.

The second point is very important because usually for a person doing bioinformatics is more difficult to end up as first author in a paper, since most we do is “something in the middle” like data analysis. Therefore, this paper is quite important for me. Also, it deals with an interest of mine, mainly analysis of biological networks using high-throughput platforms such as microarrays. Actually I’m also interested in network reconstruction, but I need to study far more than what I’m doing right now.

In any case, let’s hope this is the first of a (hopefully long) series!

Click here to view the embedded video.

It was then that it occured to me that such applets are, in Plasma-speak, PopupApplets, which means they adjust their behavior depending if they are in a panel or “free”. Also, I knew that Plasma had panel auto-hiding. 5 seconds later, I had a solution that fit my tastes, as this screenshot shows:

I could have used auto-hide also for the lower panel, but I’m not that comfortable, as I’m used to keep an eye to the systray, taskbar, and so on. In the end, I’m very satisfied with Plasma, since with a few adjustments I made it right for my workflow. This is an example of what it can do, and I can’t wait for context (as in semantic context) aware applications…

As a nice way to break the hiatus, I’m releasing a new version of DataMatrix, my implementation of R’s data.frame in Python. Although the version bump is small, there are loads of improvements. First of all, there is proper support for file-like objects, as well as support for appending and inserting both rows and columns. writeMatrix has been substantially improved and now writes files correctly, and I have added (experimental) support for a DataMatrix object that does not require files - EmptyMatrix. Also, there is now proper documentation. Last but not least, unit tests have been added, a good way to watch out for regressions in the code.

Finally, this version marks the entrance of dalloliogm as contributor to the code. He gave quite a number of helpful hints, especially with regards to unit tests.

I’m quite satisfied on how DataMatrix behaves - as a matter of fact I use it extensively on a number of internal projects.

You can grab DataMatrix 0.7 as a source package or as a Windows installer. Comments are welcome.

• 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.