Welcome to the RG Lab

King Eloi

Raphael Gottardo — Fri, 08 Jan 2010 20:04:40 +0000

This week was Epiphany and as a French tradition, the lab decided to buy a “gallette des rois” to celebrate. Eloi was lucky enough to get the trinket. To remember this day forever we have decided to post a picture of King Eloi with his crown. Enjoy!

Congratulations to Marie-Pier and Greg!

Raphael Gottardo — Mon, 09 Nov 2009 16:57:53 +0000

Congratulations to Marie-Pier Scott-Boyer and Greg Finak who have both won a prize in the poster competition at the 2009 Robert-Cedergren colloquium in Bioinformatics. Marie-Pier won the best poster in the PhD category for her work on “Modeling gene expression networks with genomic data to identify determinants of complex quantitative traits in mouse hearts” and Greg won best poster in the postdoc category for his work on “Merging mixture components for cell population identification in flow cytometry”. Great work!

flow cytometry special issue

Raphael Gottardo — Thu, 08 Oct 2009 15:49:11 +0000

Some of the papers to be published as part of the special issue on bioinformatics approaches to flow cytometry have started to appear online. I expect that all papers accepted will be available soon, including our own paper on flowMerge. If you have not looked at flowMerge yet, please try the R package available from bioconductor.

rMAT soon to support Grand Central Dispatch

Raphael Gottardo — Sun, 27 Sep 2009 22:24:48 +0000

In my spare time, I have been playing a bit with GCD, and the R package rMAT. My first impression is that it’s very easy to use and works as advertised. I have actually used it to parallelize the normalization processing of multiple tiling arrays. This will soon be incorporated in the R package rMAT, available from Bioconductor. In comparison to standard parallel computation in R done via, for example, snow and/or snowfall, with GCD you do not have to worry about cores/processors initialization. In particular, you do not have to specify the number of cores to be used, the optimum number will be decided at run time depending on resources available. The downside, is that currently, such optimization can only be used on Snow Leopard (and of course a Mac). If you do not have Snow Leopard, nor a Mac, then don’t worry, the code should still compile on your machine using the serial version. A machine specific compilation can be done using #ifdefs such as:

#if defined(__APPLE__) || defined(macintosh)

#ifdef __MAC_OS_X_VERSION_MIN_REQUIRED

// Use Grand Central on Snow Leopard

// note use of 1060 instead of __MAC_10_6

#if __MAC_OS_X_VERSION_MIN_REQUIRED >= 1060

The bottom line is that it’s great, and it’s very likely that future code/packages coming out of our lab will take care of such optimization. So perhaps you should buy a Mac .

#if defined(__APPLE__) || defined(macintosh)

#ifdef __MAC_OS_X_VERSION_MIN_REQUIRED

// Use Grand Central on Snow Leopard

// note use of 1060 instead of __MAC_10_6

#if __MAC_OS_X_VERSION_MIN_RE

Grand Central Dispatch

Raphael Gottardo — Fri, 18 Sep 2009 02:20:51 +0000

A few days ago I finally upgraded to Snow Leopard. I was writing a few grants, so I did not want to take the chance to upgrade before submitting these grant applications. Anyway, I am now running Snow Leopard, and even though there are no “new” apparent features, it is a great upgrade. In my opinion, the best of all OS X upgrades so far, as it really brings great improvement under the hood, including “full” 64 bit support, openCL, and Grand Central Dispatch. For more details check out the Apple webpage. To say the least, I am very exited about Grand Central and trying to use it in some of our work. I thought it would be rather complicated to take advantage of it, but in fact it looks pretty easy. The folks at macresearch have posted a simple example that makes me want to try it ASAP. It looks even easier than openMP, and perhaps more efficient.

I will try to post an update as soon as we have tried it.

Job inquiries

Raphael Gottardo — Fri, 18 Sep 2009 02:06:44 +0000

I receive a lot of emails regarding job openings in our lab, which is fine of course because we are always looking for bright people to join our team. This said, I am sick and tired of receiving emails from people saying that they are very interested in joining our lab but they have no idea of what we actually do! You know what, it’s right on this website, so at least please have a look at our research interest before you do send an email. In particular, as of yet, we do not work on structural biochemistry, we do not have a wet lab, etc.

Thanks for doing your homework before sending an email.

MonBug symposium

Raphael Gottardo — Thu, 03 Sep 2009 18:13:16 +0000

Today is the monbug symposium, and I thought I would send a quick note from the IRCM where it is currently taking place. We have already

seen a series of great talks and I can’t wait for the next edition. You can see on this picture, Elaine Mardis, giving the second keynote lecture of the day.

– Post From My iPhone

Statistics is sexy!

Raphael Gottardo — Tue, 18 Aug 2009 18:49:25 +0000

An interesting article was published in the NY Times on Aug 5, 2009 stating how important statistics is in today’s world. To quote a sentence from the article: “I keep saying that the sexy job in the next 10 years will be statisticians,” said Hal Varian, chief economist at Google. The original article can be found on the NY Times website. I meant to post this a few weeks ago, but I have been a bit lazy …

Similarly, statistics is prone to play an important role in genomics for the next decade at least with the introduction of next generation sequencers and other high throughput machines that are yet to be invented. This is good news for us, statisticians and computational biologists!

JSM Talk

Raphael Gottardo — Mon, 10 Aug 2009 11:00:24 +0000

I have received a few emails asking me for my slides of my JSM talk on ChIP-Seq, so I have decided to post them online. You can download the slides here. If you have any questions please do not hesitate to contact me.

flowMerge

Greg Finak — Fri, 05 Jun 2009 13:49:19 +0000

A new package for improving automated gating of flow cytometry data is now available in BioConductor development release 2.5. flowMerge improves identification of complex cell subpopulations in flowClust models by allowing multiple components to represent the same cell subpopulation. Version 0.3.5 is now in the public repository.