Where Pedro has gone

2009-01-15

Previously, I asked where Pedro had gone. Well, I’m delighted (although mystified) to find that he seems to have actually read my blog, because he’s left a comment on it.

I’m not quite sure why I had such troubles finding him on Google — possibly a bad day; I think mostly it was just that his website doesn’t mention Pedro’s tools anymore. He’s been building CAZy, which I know of, although I don’t think I’ve used it. Poking through his bibliography, he’s published on semantic similarity, one of my pet topics.

It’s amazing to me how much traction Pedro’s tools has got with bioinformaticians/biologists; during the Ontogenesis at which I was present last night, I mentioned the website and the three who were old enough all perked up, saying "yeah, Pedro’s tools was excellent". We started comparing Pedro numbers; for the record mine is currently 4 (me, Norman Paton, Mike Cornell, Pedro albeit via a genome paper), although if I get lucky with a paper under submission this will go to 2 (you’ll have to wait to find out how…).

As he says, it’s rewarding to observe how bioinformatics has moved on to become central to all biology; of course, it’s also amazing how the web has become commonplace to the rest of our lives. At the time, it was image-poor, slow and clunky. Most of us hardly knew how to use bookmarks (if they’d been invented then, I don’t remember), search engines were in their infancy, URL naming was inconsistent and changeable; it was really hard to navigate, to discover. It’s perhaps not surprising that the website was such a success and remembered so fondly; the only question that remains is, how the hell did everybody find out about it in the first place?

His comment finishes with the statement that "And, if there is a final message, [it] is that with some good will, anyone can make a difference in Biology and elsewhere." What a cool bloke!

Anyway, in case my comment engine goes awry, I reproduce the quote here…

Where has Pedro gone? Well, I’ve been happily busy researching and teaching on my favorite subjects.

After a PhD in (Bio)Chemical Engineering at Iowa State University (ISU) in 1996, I did a Post-Doc in Grenoble and Marseille, France. In 1999 I got a faculty position in Biological Engineering at the Instituto Superior Tecnico, Lisbon, Portugal. From 2002 onwards, I moved to a new a faculty position at the University of Provence in Marseille, France where I presently teach Biocatalysis and Bioinformatics.

Since 1998, I’ve been developing and maintaining a database on Carbohydrate-Active Enzymes (CAZy, http://www.cazy.org), that presently constitutes a reference resource in Glycobiology and a research tool for Glycogenomics.

The "Pedro’s Biomolecular Research Tools" adventure lasted from late 1993 to early 1997. It was a great learning moment for me and I’m proud of leaving my little brick on the wall of Bioinformatics. Initially developed as the web complement to an internal software locker that I maintained, the list grew up in importance thanks to the positive response from the burgeoning community of web-aware Biologists and the many encouragements and suggestions I received from users from all over the world. It was a (hopefully) good index for those pioneering days where I intuitively tried to reveal the potential of the new discipline. Naturally, I used my on research subjects to test the different tools available at the time, and this had some impact on my thesis. However, the most rewarding and interesting was to observe how Bioinformatics moved on in a few years from an obscure and marginal discipline to become absolutely central to almost all aspects of Biology and its applications. As a community, Biologists created since then an impressive dynamic that makes other scientific communities envious. And, if there is a final message, is that with some good will, anyone can make a difference in Biology and elsewhere.

Originally published on my old blog site.