castanyes blaves

... 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:

http://takingliberties.squarespace.com/ 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...

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.

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

http://code.open-bio.org/svnweb/index.cgi/bioperl/revision?rev=14681

Excellent!

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.

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

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

Click on Accept UNO connection

=VALUE(SUBSTITUTE(SUBSTITUTE(SUBSTITUTE(SUBSTITUTE(MID(INDEX(ImportHTML("http://finance.google.com/finance/converter?a=1&from="&A1&"&to="&B1&"&workaround="&INT(NOW()*1E3)&REPT(GoogleFinance("GOOG");0);/10000

cd
mkdir src
cd src
cvs -d :pserver:cvs@code.open-bio.org:/home/repository/bioperl login # password is cvs
cvs -z3 -d :pserver:cvs@code.open-bio.org:/home/repository/bioperl checkout -r bioperl-release-1-2-3 bioperl-live
cvs -d :pserver:cvsuser@cvs.sanger.ac.uk:/cvsroot/ensembl login # password is CVSUSER
cvs -z3 -d :pserver:cvsuser@cvs.sanger.ac.uk:/cvsroot/ensembl checkout -r branch-ensembl-49 ensembl
cvs -z3 -d :pserver:cvsuser@cvs.sanger.ac.uk:/cvsroot/ensembl checkout -r branch-ensembl-49 ensembl-compara
PERL5LIB=${PERL5LIB}:${HOME}/src/bioperl-live
PERL5LIB=${PERL5LIB}:${HOME}/src/ensembl/modules
PERL5LIB=${PERL5LIB}:${HOME}/src/ensembl-compara/modules
export PERL5LIB

It's easy :-)

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

http://hmg.oxfordjournals.org/cgi/content/short/17/11/1569?rss=1

The Ensembl Compara GeneTree for NRXN1 shows:

http://www.ensembl.org/Homo_sapiens/genetreeview?db=core;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:

http://www.treefam.org/cgi-bin/TFinfo.pl?ac=TF321302

Examples

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/

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

http://www.nytimes.com/interactive/2008/05/03/business/20080403_SPENDING_GRAPHIC.html