Blog posts

I recently updated my set-up, and because I use a High-Performance cluster from my University (kudos to avakas) to run various simulations and analyses, I have MPI and Rmpi installed on my laptop in order to test my scripts before submitting them to the big cluster. So I installed openmpi from homebrew very easily: brew update brew install open-mpi But then I had extensive trouble installing the Rmpi package…

I just released a new package on CRAN. It’s called NPflow, it performs Dirichlet process mixture of multivariate normal, skew-normal or skew t-distributions modeling, you should check it out. I was a little worried because the check from Travis CI was returning a NOTE. And even though the NOTEs seem like mild problems, “you should strive to eliminate all NOTEs” before submitting to CRAN ! Preparing for an email exchange with a member of the R core team, I wrote the following in the submission comments:

After a bumpy road, along which I kept in mind Jeff Leak’s own worst (recent) experience, we finally got our article on Time-Course Gene Set Analysis for Longitudinal Gene Expression Data published in PLoS Computational Biology, a very nice journal ! I am really happy about it, don’t hesitate to check it out ! And there is the TcGSA R package that goes with it.

This is a quick technical post, that is as much about disseminating the information as putting it in a place where I can find it again in the future. I have been trying to use openMP in an R package that I am currently developing. openMP is supported by the popular gcc compiler. However, OS-X Xcode now ships with a clang compiler that does not support openMP. So first one needs to install gcc (from homebrew for instance).

On March 6th, 2015, I defended my thesis in front of a prestigious jury, and was awarded the title of Ph.D. in Public Health with a concentration in Biostatistics (Docteur en Santé Publique — option Biostatistique) from the University of Bordeaux. After more than 3 years of hard work, that’s an incredible feeling. For the interested reader, I give you: my Ph.D. thesis !

A couple month ago, along with other young researcher bloggers, we published a short opinion piece in the Student’s Corner of the ISBA bulletin, weighting the pros and the cons of blogging. It was awesome to get everyone insights on the matter: check it out !

I am in the process of speeding up some code, and I have been lured by the promises of Rcpp. Since the functions I am working on are mainly linear algebra, I wanted to try out RcppArmadillo. This put my googling skills to a test as I spent (way) too much time trying to figure out errors until I found this post. Thank you James Balamuta ! Be warned RcppArmadillo, microbenchmarking is on !

The American Statistical Association launched a new website thisisstatistics with general information on what being a statistician really means today. I often meet fearful looks when I meet people and present myself as a “biostatistician” (the key word being statistician here). Up to the point that I now generally say I work in “applied mathematics in medicine”, before I drop the magical “big data” keyword in the necessary explanation following this title.

The back of the hoody we received at my lab annual party:

True story :-)

At Bordeaux University, we are quite lucky. I mean as computational consumers. Indeed, we have access to a big CPU cluster, a mesocenter that has been build for all the researchers in the Aquitaine area (in the south west of France). And it’s a big one. It’s named avakas, and it has brought my Ph.D. computational projects to an other scale ! But for a few month now, I have also been granted access (for free as a I work in a national research agency) to a new kind of big computer: a net of heaters.