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.



Because Organic is not always the same as environmentally friendly

Flown-in organic food rule change

Food flown into the UK will be stripped of its
organic status unless it meets new stricter ethical standards, the Soil
Association has warned.



On MS Word and Openoffice comments/notes interop


Anton Enright -- Network based clustering and analysis of the Mouse Transcriptome

MCL -- [M]arkov [CL]uster algorithm -- Stijn Van Dongen

a graph with weights -- a matrix with markov transition probabilities

inflation and expansion operators

from a one step to a two step path -- promote the flow in the strong paths -- third step -- fourth -- etc... obtain centers of flow

cytoscape -- tool to draw graphs -- seemed all done

application to expression data -- relate two genes in terms of their expression

did biolayout express 3D -- implemented in 3D using OpenGL (JOGL)

protein protein interactions? yes, we tried
Stijn is now working on hierarchical MCL


I find this program absolutely delightful

I mean, how can you say that a burger or a pizza is "bad food"?

It could be bad to eat a burger or a pizza from a fast food chain, but this guy, Heston Blumenthal, can really change your
opinion about this sort of food :)


Ewan Birney -- ENCODE project

Neutrality for biochemical events!!

Functional conservation non coincident with orthologous sequences?

Transcription is a special case -- connectivity component difficult to assess


Climate threat to biodiversity

if one can call me "conservative" in any sense, it is in terms of "biodiversity conservative" :)



Diet choices written in genes



'Slight recovery' for cod stocks


Lab suspends DNA pioneer Watson



Sanganchao!!! sanganchao!!! En la puzolana!!!


Just when you thought everything was already invented...



Foreign affairs -- USA presidential candidates

and also


Apple starts supporting ODF



Yet another Perl Emacs tip

near your emacs 22 :)


Appetite 'control centres' found

A complex combination appears to control appetite
UK-based scientists say they have identified the brain circuits that control how much we eat.

The Nature study, by University College London and King's College London, could aid development of new obesity drugs.

Using brain scans, the teams showed the appetite-regulating hormone peptide YY (PYY) produces a more complex pattern of activity in the brain than thought.

It targets not only the primitive areas controlling basic hunger urges, but also the pleasure and reward centres.

Understanding which brain regions control eating in different environmental conditions may help us to develop more targeted treatments for people with weight problems
Dr Rachel Batterham

PYY is released from the gut into the bloodstream after eating and signals to the brain that food has been eaten.

A nasal spray containing the hormone is currently being trialled to see if it can be used to tackle obesity.

Studies on animals suggest it regulates appetite by acting in primitive parts of the brain such as the hypothalamus and brainstem.

The latest study showed that the same was true in humans.

But the hormone was also found to act in the cortico-limbic regions that determine the pleasure sensations associated with eating food.

The biggest effect of all was found in an area called the orbitofrontal cortex (OFC) - a region thought to make overall sense of the pleasure sensation.

The researchers found that the greater the change in activity in that area, the less the volunteers ate.

Drip tests

Eight normal-weight men took part in the study. After 14 hours without food, they were given a drip of either PYY or a placebo for 100 minutes while their brains were scanned using an MRI machine.

Thirty minutes later they were offered an unlimited meal.

Each volunteer was tested twice, a week apart, once with PYY and once with the placebo.

PYY infusion reduced subsequent average calorific intake by 25%.

Researcher Dr Rachel Batterham, who is funded by the Medical Research Council, said: "In the food-deprived state, brain activity within the hypothalamus predicted how much food the subjects ate.

"However, in the presence of increased PYY levels mimicking a meal, there was a switch in the circuits controlling eating so that brain activity within the orbitofrontal cortex now predicted feeding behaviour."

The researchers hope a greater understanding of how appetite is controlled could help tackle the obesity crisis - 23% of the adult UK population is classified as obese.

Dr Batterham said: "Understanding which brain regions control eating in different environmental conditions may help us to develop more targeted treatments for people with weight problems.

"Further research is now needed to investigate whether underweight and overweight people have abnormalities in these circuits."

Dr Ian Campbell, medical director of the charity Weight Concern, said weight control was not as simple as just counting calories.

He said: "Understanding the way we perceive food, develop the feeling of satiety, and our emotional relationship with food are key to helping an individual to regain control

"What this study seems to do is shed new light on one of the reasons why it's so difficult - more than just a behavioural issue, there may well be complex hormones that influence both the way we think and feel about the food we eat."



Please, please, no more car insurance ads

I _don't_ have a car. I _don't_ have a driving license. The amount of car insurance ads is unbearable!!!




Here's two nifty recipies for using a debugger at rumtime:

At any arbitrary moment. Perhaps you've got some process that's long running and you occasionally want to stop it, examine its contents and then tell it to continue. Presumably you'd do the moral equivalent of Enbugger->unimport to remove the debugger.

$SIG{USR1} = \ &start_debugger;
sub start_debugger {
require Enbugger;

Start the debugger on exception.

$SIG{__DIE__} = sub { require Enbugger; Enbugger->import };


perl debugger tip

a neat little Perl debugger hook that can be placed in code for automatic breakpoints.

Instead of stepping through code until all the modules are loaded, and then continuing to a line number or a specific method in a module , you can continue to a pre-defined breakpoint. To add such a breakpoint use :

$DB::single = 2;

Here’s some explanatory text on it from Programming Perl:

You can exert a little control over the Perl debugger from within your Perl program itself. You might do this, for example, to set an automatic breakpoint at a certain subroutine whenever a particular program is run under the debugger. From your own Perl code, however, you can transfer control back to the debugger using the following statement, which is harmless if the debugger is not running:

$DB::single = 1;

If you set $DB::single to 2, it’s equivalent to the n command, whereas a value of 1 emulates the s command. The $DB::trace variable should be set to 1 to simulate the t command.


Charlie Boone -- Global mapping of genetic and chemical-genetic interactions in yeast
Synthetic lethality or unlinked non-complementation - two mutations fail to complement and yet do not map to the same locus.

World canavinine crisis... :p

S. pombe biology is better than yeast for high-throughput (HTP) genetic interaction analysis

HTP Quantitative Cell Biology

bni1 synthetic lethality -- a highly complex network of 50 genes

8 SGA screens -- 291 interactions -- 204 genes

1000 genes - ways to kill the cell when ko a gene
100,000 ways when ko two genes

Interactions occur amongst functionally related genes
Genetic Network is a Small World Network

Scoring Genetic Interactions Quantitatively -- linear regression model for colony size -- doublings per hour

syntethic lethals VS pairs of genes whose products are in the same nonessential complex/pathway

Molecular Barcodes Tag Deletion Strains -- barcodes for each mutant: 20bp oligo pairs -- stitching PCR -- drug hypersensitivity screen -- barcode chip


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