Archive for February, 2009

New Clue?

Saturday, February 28th, 2009

Without Humph?.

ffmpeg: Unknown encoder ‘mp3′

Saturday, February 21st, 2009

Aaagh. Haven’t used ffmpeg much and it took me a good 20 mins of searching to figure out why -acodec mp3, as recommended on many howtos kicking about the place, kept giving me an unknown encoder error.
It isn’t unknown, it’s just that the incantation has been changed: -acodec libmp3lame
Sigh…I will never get those [...]

Turkish Delight: A non-Newtonian pseudoplastic foodstuff

Friday, February 20th, 2009

The Rheological Properties of Turkish Delight
A paper investigating the gloopiness (“Structural and thermal properties”) of Turkish Delight at different temperatures. It is, apparently, a non-newtonian pseudoplastic foodstuff.
Seriously. There are people out there being paid to squidge Turkish Delight (or ‘TD’ as they call in the paper, presumably because nothing sounds more sciency than gratuitous [...]

HowTo: Get a list of all species in Ensembl

Friday, February 20th, 2009

From ensembl-dev mailing list: advice on how to get the current list of all ensembl species:
List lives in the compara database and can be retrieved directly with something like:

mysql -u anonymous -h ensembldb.ensembl.org -P 5306 ensembl_compara_52 \
-e “SELECT name FROM genome_db”;

Or you can do essentially the same query via the Perl API:

use Bio::EnsEMBL::Registry;
my [...]

Spotify

Friday, February 20th, 2009

Am trying out Spotify : big online music library, build your own playlists, & so on. Like LastFM or Pandora but with more music and fewer limits on what you can play and how often you can play it. Funded by (so far, fairly unobtrusive) advertising (you can pay £10ish/month for no adverts).
Windows [...]

biomaRt mapping from human illumina ID to mouse Ensembl ID

Tuesday, February 17th, 2009

Problem:
Dataset 1: ChIPseq-derived transcription factor binding sites. Mouse. Mapped to nearest Ensembl Gene ID,
Dataset 2: Human Illumina Ref6 expression array data (GPL6097, I think) from various cell lines with varying amounts of said transcription factor.
Question:
What are the targets of the transcription factor doing in the expression datasets?
Quick Mapping
As a quick approximation, map the Illumina human [...]

testing…testing

Monday, February 16th, 2009

…is this thing on?