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Archive for June, 2012

Glascow

June 30, 2012 Leave a comment

After some months of work, we had our article accepted in bioinformatics and the accompanying  software GLASCOW released (available on the GIGA website).

Basically, the software perform a generalized linear mixed model analysis on (preferably) hidden states (obtained e.g. with PHASEBOOK) after a correction for population stratification. This approach has already been successfully applied in : Durkin et al, Sartelet et al, Dupuis et al.

I contribute to the software with some optimizations and code rewriting. The code is thus a mix of several coding practice and style, I must admit that to some extent this can made the code hard to follow.

Seen on this blog

Concerning programming, several details of the package are available on the blog  :

  1. The general framework of the package was set by the script LancementProjet.sh
  2. I use command argument as described here 
  3. The use of Lapack is conditional, and therefore I add some preprocessor instructions in the code
  4. In order to get info on date of compilation I also add some preprocessor instructions

…coming soon on this blog ?

Others key features are :

  • A parallelized reading of the files (we rely on the use of one phase/hidden states file per chromosome, obtained with PHASEBOOK), this trick plus a neat storage of the partial relationship between individuals allow to obtain great speed improvements and lower memory consumption.
  • The computation of score on residuals allow both a general speed-up and an ability to restart analysis only from these last steps.
  • Permutations are done in parallel, nevertheless this last part was very tricky to implement, and I must says that the speed-up didn’t fulfill my expectations….I’ll try to see how to fix this.
  • We add an option for outputting results in a “.assoc” file for a better viewing experience in IGV.

So even if the code still contain some old fashion Fortran (goto etc…) the adventure was fun, inspired me some posts, give me some experience in glmm and add one article to my publications list ! Not so bad, isn’t it ?

Look as if nothing has chanded but…

June 7, 2012 Leave a comment

I almost forgot this, but yesterday was the WorldIPV6 launch.

Surprisingly, it doesn’t sound as if anything special has changed but just imagine what would happened if we were to add all over the world two extra digit to every ZIP code ! It could be potentially a mess ! So this almost imperceptible change worth being noticed as not only it make a change (and allow evolution for the web), but also it is really invisible for the end-user. I wish I could make such big changes to my software with none of their user noticing it ! (Ok it also took 16 years to be set-up, may help a bit)

To test if you are ready for this change google set a test here

To have more info have a look here, or here.

And for a very nice explanation of why ipv6 is a solution to a pending problem have look at this video

Categories: Uncategorized

Software update

June 5, 2012 2 comments

Last month a bunch of software I recently used got updated  :

GATK 1.6 

This new version came few time (2 month) after last version. A lot of promise concerning indel handling, i am eager to test it by my self.

GCTA 1.0

Add the conditional and joint GWAS  analysis  option, presented Yang et al. The source code is not available (sigh).

MAGMA 1.2

This library allow to easily use GPU for computation.  A fair amount of lapack subroutine are already available. I unfortunately had more difficulties to set-up this version then the previous one. But this project definitely deserve attention.

LLVM 3.1

This free compiler is hip ! Fortran compilation are recently available (with dragon egg), and more and more group are having an eye on it (e.g. nvidia freebsd), so I guess we should keep an eye on it too !

Categories: Linux