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Tita (my grandmother) called this morning and urged me to go to visit her. Since today was Children’s day, she wanted to celebrate it with her “children”. We spent a nice evening talking and eating the fabulous lunch that my aunt Susana prepared. I guess sometimes Tita has more of a child’s spirit than all of us together. She’s definitely great!

[Footnote] This weekend I logged another 1,600 meters of climbing. My ankle is recovering well and I’m just waiting for the day to get back into the hard bouldering (and hard falling) business…

EMBOSS, the European Molecular Biology Open Software Suite, has received new funding from the Biotechnology and Biological Sciences Research Council (BBSRC) in the United Kingdom that ensures its survival as an open-source utility, at least for the next three years.

The fate of the EMBOSS project had been in doubt for the past two years, following the closure last summer of the Rosalind Franklin Centre for Genomics Research (RFCGR), which had hosted the project…

Bio-IT World: New Funding for EMBOSS Bioinformatics Tools

Where the hell have all people gone?

I upgraded the port from 0.6.2 to 1.0.0 and created an interactive menu to optionally install the necessary Ruby extensions (xmlparser, bdb4, MySQL and PostgreSQL) for using its extra features.

Thanks to Pav Lucistnik for committing it!

IBM today announced its researchers have discovered numerous DNA patterns shared by areas of the human genome that were thought to have little or no influence on its function and those areas that do.

As reported today in the Proceedings of the National Academy of Sciences (PNAS), regions of the human genome that were assumed to largely contain evolutionary leftovers (called “junk DNA”) may actually hold significant clues that can add to scientists’ understanding of cellular processes. IBM researchers have discovered that these regions contain numerous, short DNA “motifs,” or repeating sequence fragments, which also are present in the parts of the genome that give rise to proteins.

If verified experimentally, the discovery suggests a potential connection between these coding and non-coding parts of the human genome that could have a profound impact on genomic research and provide important insights on the workings of cells…

Genetic Engineering News: IBM Discovery Could Shed New Light on Workings of the Human Genome

Here is XML’s grammar expressed as an automaton in XML syntax. It is based on Tim Bray’s Lark grammar, which Tim has recently released.

I’ve XML-ified it to give a headstart to anyone interested in making their own XML processor: you could write an XSLT script to generate code for example. The XML version is based on a finite state machine, but with a couple of extra attributes that act on stacks. There are various Lark-specific actions included in the transitions: these provide a good guide for some of the processing required for a complete XML processor. However, of course you might prefer to annotate it with your own actions…

O’Reilly XML Blog: XML in XML

1. The way you want them to be.
2. The way that you plan them.
3. The way they actually happen.

So far, the 3rd always wins and never has to do with the first other two. As you can see, the lesson repeats over and over: don’t plan ahead too much, or better yet, don’t make any plans!

Oh yeah, my “phylosophy” of life…

[Footnote] I logged a total of 1,600 meters of climbing in this two days. Not everything had to be bad in life, huh? I think I was missing that training wall too much…

In the lore of marathoners and extreme athletes, lactic acid is poison, a waste product that builds up in the muscles and leads to muscle fatigue, reduced performance and pain.

Some 30 years of research at the University of California, Berkeley, however, tells a different story: Lactic acid can be your friend…

UC Berkeley News: Muscles burn lactic acid as well as carbos

Today, Fer’s car didn’t ignite also (even though she kept it in use all the time). It needed some gas and electricity to get back to normal. So strange it died all of a sudden…

After 2 days of technicians at home and fixing other stuff by myself, I got a decent dinner and a few hours of great conversation. No more complaints!