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Tag: Science (Page 2 of 2)

ProbABEL v0.3.0 released

4 January 2013 / / 0 Comments

On New Year’s day I released version 0.3.0 of ProbABEL, almost two months after the previous release.

This update contains a few small bug fixes, but the most important feature of this new release is that thanks to the work of Maarten Kooyman we have a four to five-fold speed increase for the types of GWAS we run at work. In his e-mail to the GenABEL developers list he explains what he did to achieve this. The take-home-message of it is that you should always look for a suitable library for important tasks of any program you write. The old ProbABEL was based on a self-written matrix class that handled things like matrix multiplication and matrix subsetting. In the new release we make use of the Eigen C++ template library, maintained and developed by people who know much more about fast implementations of linear algebra than we do.

For those of you running Ubuntu Linux (or one of its derivatives and probably also Debian) I have set up the GenABEL PPA (personal package archive) where you can download and install the ProbABEL .deb package and stay up to date with future updates.
ProbABEL is also available for MS Windows, although we don’t have much experience running it on that platform.

Development of ProbABEL (and other members of the GenABEL suite) takes place on this R-forge page. If you are in search of an open source project to contribute to, feel free to contact us!

User support for the GenABEL suite can be found at our forum.

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The Raspberry Pi runs ProbABEL

21 November 2012 / / 1 Comment

One of the first things I tried on my Raspberry Pi was to compile ProbABEL and see if it runs. Since the Raspberry Pi has an ARM processor I wasn’t sure whether our code was portable to it. Apparently it is! Compiling ProbABEL (r.1027 from SVN) took 30 minutes (single threaded of course) compared to 34 seconds on my Desktop (4 threads on an Intel Core i3 processor), but hey, it worked :-). Surprisingly it also passed all the checks in make check.

Once I hook up some more storage to device I will try to run ProbABEL on some real data. It will be interesting to see how much time it takes to run a linear regression on e.g. chromosome 22 of HapMap3 imputated data for a few hundred samples…

Will the Raspberry Pi be the next platform for GWAS ;-)?

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ProbABEL 0.2.2 released

21 November 2012 / / 1 Comment

On November 7th I released version 0.2.2 of ProbABEL, a set of programs that allow scientists (usually geneticists and epidemiologists) to run Genome-wide association studies (GWAS) in a fast and efficient way, even on machines with low amounts of RAM.

ProbABEL is part of the GenABEL suite, wich is a set of open source package for statistical genomics. Its main developer is Yurii Aulchenko, my former supervisor at the Erasmus Medical Centre.

This update contains a few small bug fixes and an update of the probabel.pl wrapper script that enables the use of chunked imputation output files as input. For more detailed changes, check the announcement.
For those of you running Ubuntu Linux (or one of its derivatives and probably also Debian) I have set up the GenABEL PPA (personal package archive) where you can download and install the ProbABEL .deb package and stay up to date with future updates.
ProbABEL is also available for MS Windows, although we don’t have much experience running it on that platform.

Development of ProbABEL (and other members of the GenABEL suite) takes place on this R-forge page. If you are in search of an open source project to contribute to, feel free to contact us!

User support for the GenABEL suite can be found at our forum.

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Subversion: merging updates in trunk to a branch

25 October 2012 / / 0 Comments

Yesterday I was working on ProbABEL, an open source package for running GWAS (genome-wide association studies). We use R-Forge and they provide us with a Subversion (SVN) server for revision control.

Some time ago we created a branch in which one of the co-developers is doing some major refactoring of the code. In the mean time I have been fixing bugs and adding new features to trunk. Now that the work in the refactoring branch comes to an end I thought it was high time to integrate the changes in trunk with the changes in the branch so that we can later promote the branch to trunk.

Since I had never done this before I decided to try the merge in the doc directory first, because I knew that in that directory nothing had changes since the branch was created, so all changes from trunk should be imported. At first I followed the SVN book instructions so I went into the doc dir in the branch and ran

$ svn merge ^/pkg/ProbABEL/doc

Unfortunately that didn’t work out. For some reasons conflicts appeared as wel as files that weren’t supposed to be there at all.

Thanks to Google and this blog post I found a solution. It boils down to explicitly telling SVN which revisions to use for the merge.

First I used

$ svn log | grep -C3 branch

to find out at which revision I created the branch:

------------------------------------------------------------------------
r864 | lckarssen | 2012-03-27 17:38:05 +0200 (Tue, 27 Mar 2012) | 1 line

Creating ProbABEL branch for code refactoring

Next I went to trunk and ran

$ svn update
At revision 987.

to find out at which revision trunk currently was. Back in the doc directory in the brach I ran

svn merge -r 864:987 ^/pkg/ProbABEL/doc

to merge al the changes since the branch was split off and it worked like a charm! All changes in trunk applied cleanly.

I then id the same for the other directories which also had changes in the branch. It turns out that when SVN find a conflict it is easier to postpone resolving the conflict because Emacs has a great SVN merge minor mode called SMerge! It highlights your changes vs. the incoming ones and allows you to select a resolution and move to the next conflict with a few easy keystrokes. After all conflicts have been resolved Emacs automtically removes the intermediate files SVN created and you are ready to commit.

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Ubuntu 12.04: LaTeX siunitx package and the correct font in beamer

20 May 2012 / / 0 Comments

When writing scientific text I normally use the siunitx package to typeset numbers (using \num{}) and numbers with units (e.g. \SI{4.0}{TB}) in LaTeX.
Something that bothered me for a while was the fact that when making presentations in Beamer, numbers and units would be typeset in a serif font, whereas beamer uses sans-serif fonts.
The solution is actually documented in the manual, but what to me a while to figure out was that in Ubuntu 12.04 (and therefore in Debian as well, I presume) the version of the siunitx package is lagging compared to what is available on CTAN. Ubuntu 12.04 still has version 1.3a of the siunitx package, which was released in September 2009. For this version the solution is to add the following to the preamble of your document:

\sisetup{obeyfamily=false,mathrm=mathsf,textrm=sffamily}

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RefTeX, how could I have missed this?

21 August 2011 / / 1 Comment

I’ve been using Emacs and LaTeX for more than ten years now and still I keep learning. For example, last Friday I came across Stephen Eglen’s ESS (Emacs Speaks Statistics) tutorial. In his slides he mentioned RefTeX. I had heard of it before, but for some reason I thought it was either a set of LaTeX styles or an AUCTeX replacement and consequently, I never looked into it.

This time, however, I made the small effort of looking up RefTeX’s website and lo and behold, it’s neither of the two things I thought it was. Instead, it is an extension to LaTeX that makes inserting citation, references, index entries and labels a breeze. Even if you don’t (want to) use all its capabilities, the following keystrokes are worth the effort:

C-c = Show table of contents of the document (also a great way to walk through your document)

C-c ( Insert a label at point
C-c ) Insert a reference to some label
C-c [ Search in your bibliography (either BibTeX or thebibliography environment) to insert citations

To start using RefTeX in a document you are already editing simple run

M-x reftex-mode

Insert the following in .emacs file if you want to load RefTeX on startup

;; Enable RefTeX
(add-hook 'LaTeX-mode-hook 'turn-on-reftex)   ; with AUCTeX LaTeX mode
(add-hook 'latex-mode-hook 'turn-on-reftex)   ; with Emacs latex mode

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