castanyes blaves

Random ramblings about some random stuff, and things; but more stuff than things -- all in a mesmerizing and kaleidoscopic soapbox-like flow of words.



One of the wonders of the Internet...

... is that, like newspapers, Internet content generated today will remain available for future generations to read in a decade, a century and so on.

In the same manner as slavery was accepted by some a couple hundred years ago, tobacco smoking is today accepted by still a lot of people as something people can freely do, given you don't affect the liberties of others while smoking. Because we all have the right to enjoy a smoke-free pub or restaurant, I think in the future nobody will doubt that banning smoking on public paces is the right thing to do.

So, one of the wonders of the Internet is that, like newspapers, Internet content generated today, like this blog by Simon Clark: a blog about defending smoking, will be available for future generations to read.

A couple of centuries ago, there were lobbies defending slavery, and today there are people who are defending smoking. Yes, nobody is defending slavery nowadays, but there are people, like Simon Clark, who are still defending smoking today...



Ensembl GeneTree for CTNNBL1: a novel gene for obesity

CTNNBL1 (Beta-catenin-like protein 1 (Nuclear-associated protein) (NAP) (Testis development protein NYD-SP19)) is a gene recently linked to obesity (HMG).

The domain structure shows an "Armadillo" SMART domain and a shorter PFAM domain
at the beginning of the protein:

The Ensembl Compara GeneTree for CTNNBL1 shows:

A high degree of conservation across a wide range of species, down to the nematode C. elegans. We unfortunately
have partial predictions for platypus, and a suspiciously partial prediction for cow, as well as the cat and shrew 2x genomes.




Bio::Perl PHYML wrapper

Heikki has added a Bio::Perl wrapper around PHYML:




Very cool new OLPC



Distributed Annotation System (DAS) -- Andy Jenkinson

Two interesting points from Andy Jenkinson's DAS talk:

(a) Current clients (e.g., Ensembl) can identify that the data from an external server (Lab X) is based on an old coordinate system/assembly (OldCS), project from the old coordinate system to the new one, and prepend "OldCS_" to the names for that track.

(b) When sending BED/WIG/GFF files to current clients (e.g., Ensembl), the files are parsed, a temporary DAS is created in a server, and the data is served to the client as if it were from a DAS server. This is specially attractive for very dense feature sets that need to be visualized in queries of small segments of a chromosome. If the uploading of the file is done in compressed format, the whole operation is very efficient. This is still not the case for URL-based files, which can make your browser painfully slow.




Using Bibus with OpenOffice in Ubuntu Gutsy 7.10

To make the connection, you have to open this file:

ooffice /usr/share/bibus/Setup/UnoConnectionListener.odg

Click on Accept UNO connection



EURUSD finance converter for Google Spreadsheets



Install the Ensembl Compara API in 12 lines

mkdir src
cd src
cvs -d login # password is cvs
cvs -z3 -d checkout -r bioperl-release-1-2-3 bioperl-live
cvs -d login # password is CVSUSER
cvs -z3 -d checkout -r branch-ensembl-49 ensembl
cvs -z3 -d checkout -r branch-ensembl-49 ensembl-compara
export PERL5LIB

It's easy :-)




Ensembl GeneTree for NRXN1/NRXN3

Significant association of the neurexin-1 gene (NRXN1) with nicotine dependence in European- and African-American smokers

The Ensembl Compara GeneTree for NRXN1 shows:;gene=NRXN1

that the NRXN1 subfamily is closely related to the NRXN3 subfamily, and there is a third member, NRXN2, that is also related to the other two. The TreeFam tree shows NRXN2 on top of the tree:




Copying files with rsync


Copy only the directory structure without copying any files:

$ rsync -a -f"+ */" -f"- *" source/ destination/

The two -f arguments mean, respectively, "copy all directories" and then "do not copy anything else".

Copy only directories and Python files:

$ rsync -a -f"+ */" -f"+ *.py" -f"- *" source/ destination/

This is really handy for replicating the general directory structure but only copying a subset of the files.

Copy everything but exclude .git directories:

$ rsync -a -f"- .git/" -f"+ *" source/ destination/



Great plot

There is a great plot in the NYTimes this weekend: the spending graphic of americans and inflation during 2007-2008:


200409   200412   200501   200502   200503   200504   200505   200506   200507   200508   200509   200510   200511   200512   200601   200602   200603   200604   200605   200606   200607   200608   200609   200610   200611   200612   200701   200702   200703   200704   200705   200707   200708   200709   200710   200711   200712   200801   200802   200803   200804   200805   200806   200807   200808   200809   200810   200811   200812   200901   200902   200903   200904   200905   200906   200907   200908   200909   200912   201001   201002   201003   201004   201007   201009   201011   201102  

This page is powered by Blogger. Isn't yours?

Subscribe to Posts [Atom]