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I'm Leonardo de Oliveira Martins, a Brazilian postdoctoral researcher working in Spain on evolutionary genomics . This blog is not affiliated in any form to my employers, and all opinions are mine.Before joining the discussion, please take a look at the comment policy of the blog.
This site has moved. Its new home is at http://biomcmc.blogspot.com
Copyright
The works by Leonardo de Oliveira Martins originally presented here are licensed under a Creative Commons Attribution-Share Alike 3.0 Unported License. In a nutshell you are free to share, copy, and modify his works as long as you accredit him and preserve this license.Labmates at Univ. of Vigo
Shared articles- A New Method for Inferring Hidden Markov Models from Noisy Time Sequences January 11, 2012 David Kelly et al.
- Conservation science: A market approach to saving the whales January 11, 2012 Leah R. Gerber
- Don't censor life-saving science January 11, 2012 Peter Palese
- Scientific misconduct: Latest MMR 'dispute' is a straw man January 11, 2012 Brian Deer
- Call for more mobility January 11, 2012 (author unknown)
- Homing in on the ‘Homer Simpson Effect’: reply to Dugdale et al August 22, 2011 (author unknown)
- Biased sampling: no ‘Homer Simpson Effect’ among high achievers September 6, 2011 (author unknown)
- [Letter] NextGenVoices — Results January 5, 2012 Asgeir Kobro-Flatmoen
- Phylogenetic Inference via Sequential Monte Carlo January 5, 2012 Bouchard-CoTe, A., Sankararaman, S., Jordan, M. I.
- CATCHprofiles: Clustering and Alignment Tool for ChIP Profiles January 4, 2012 Fiona G. G. Nielsen et al.
- Controversies in modern evolutionary biology: the imperative for error detection and quality control January 4, 2012 Julie Thompson
- Reach out about climate January 4, 2012 (author unknown)
The GPU hype and bioinformatics algorithms
I am a big fan of GPU computing (and other “alternative” hardware), but it was refreshing to read this commentary by Lars Jensen, which I could summarize by this statement:
The first time I heard a similar criticism was by Alexandros Stamatakis, who alerted that we should always compare the performance of a GPU algorithm to the same effort focused on a multi-core CPU environment. Since then I try to be more cautious about grand statements of improvement. And yes, I completely agree with them, even though I don’t give so much importance to speed gains.
My feeling is that thinking about novel GPU algorithms is always worth the effort since a different path for doing a given computation, though currently slow or inefficient, can lead to faster algorithms in the future. And can also give feedback to vendors as to where they should put their efforts into – provided there’s competition, which in end is the problem with the GPU approach…
(via Jason Stajich)
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About Leonardo de Oliveira Martins
I am currently a postdoc working in David Posada's lab at the University of Vigo, Spain. I did my Ph.D. at the Universty of Tokyo, and have both an M.Sc. in Biotechnology and a B.Sc. in Molecular Sciences completed at the University of Sao Paulo, Brasil.