csbio (biocs tumbled)

Today’s visualization idea: use the Fibonacci sequence to...

Wed, 20 Feb 2013 11:26:26 +0100

Today’s visualization idea: use the Fibonacci sequence to generate breaks for a heatmap with a huge spread of values (which are minus-log10-pvalues).

A small utility for repeatedly running grep on the same file

Wed, 05 Jan 2011 09:24:56 +0100

A small utility for repeatedly running grep on the same file

"If you disagree, I’d appreciate either a reference or an implementation; thanks ;)"

Mon, 20 Sep 2010 09:23:50 +0200

“If you disagree, I’d appreciate either a reference or an implementation; thanks ;)”

- Daily Life in an Ivory Basement: Assembly is hard because it’s not decomposable

"If you are not paying for it, you’re not the customer; you’re the product being sold."

Mon, 13 Sep 2010 10:17:04 +0200

“If you are not paying for it, you’re not the customer; you’re the product being sold.”

- User-driven discontent | MetaFilter

"Furthermore, for many [E. Coli] cells the only source of some proteins is those that are inherited..."

Fri, 30 Jul 2010 10:19:51 +0200

“Furthermore, for many [E. Coli] cells the only source of some proteins is those that are inherited from the mother cell, as mRNA is produced relatively rarely (see the figure). This results in unequal inheritance of the limited number of molecules of a given protein during cell division (8, 10), a phenomenon that also occurs in mammalian cells (11).”

- E. coli, What a Noisy Bug — Tyagi 329 (5991): 518 — Science

AP Exclusive: Scuba Diving in the Gulf Oil Spill (via...

Thu, 10 Jun 2010 17:02:07 +0200

AP Exclusive: Scuba Diving in the Gulf Oil Spill (via AssociatedPress)

What happens when you flip a starfish wrong side up. Starfish...

Thu, 03 Jun 2010 22:48:14 +0200

What happens when you flip a starfish wrong side up. Starfish won’t be amused, but what it’ll do is awesome. Thanks Evolution for these wonders.

Newick TreeVisitor cheat sheet

Mon, 31 May 2010 10:45:00 +0200

pre_visit_tree(t) — callback called before exploring (sub-)tree t.

post_visit_tree(t) — callback called after exploring (sub-)tree t.

pre_visit_edge(src, bo,le, dst) — callback called before exploring an edge. Here src is the source node and dst is the destination node, bo is the bootstrap support of the edge and le is the length of the edge.

post_visit_edge(src, bo,le, dst) — callback called before exploring an edge. Here src is the source node and dst is the destination node, bo is the bootstrap support of the edge and le is the length of the edge.

visit_leaf(l) — callback called when exploring leaf l.

(From the Newick source)

I’ll see your oil spill and raise you a genetic...

Thu, 27 May 2010 09:04:59 +0200

I’ll see your oil spill and raise you a genetic bottleneck : bioephemera — more ecology-themed trading cards at Phylo

With the addition of a few branches, the STRING/STITCH source...

Thu, 20 May 2010 13:56:05 +0200

With the addition of a few branches, the STRING/STITCH source code repository is starting to look like a railroad network :-/

"We hypothesize that the presence of a rare codon, marked by the synonymous polymorphism, affects the..."

Tue, 11 May 2010 11:30:26 +0200

“We hypothesize that the presence of a rare codon, marked by the synonymous polymorphism, affects the timing of cotranslational folding and insertion of P-gp into the membrane, thereby altering the structure of substrate and inhibitor interaction sites.”

- A “silent” polymorphism in the MDR1 gene changes substrate specificity [Science. 2007] - PubMed result

FORA.tv - Sage Commons: Josh Sommer, Chordoma Foundation via...

Mon, 10 May 2010 13:26:00 +0200

FORA.tv - Sage Commons: Josh Sommer, Chordoma Foundation via Cameron Neylon / Deepak Singh : “The one video every life scientist should watch”

Python for Chemistry

Tue, 04 May 2010 14:10:01 +0200

Python for Chemistry:

slides from a talk by Noel O’Boyle

OpenStreetMap data is on your train - OpenGeoData

Fri, 23 Apr 2010 14:38:14 +0200

OpenStreetMap data is on your train - OpenGeoData

Functional share policy: SGE tries to give everyone the same...

Wed, 21 Apr 2010 11:19:45 +0200

Functional share policy: SGE tries to give everyone the same share of the cluster without any compensations for users who use the cluster in bursts (via gridengine.info)

Share Tree policy: past usage is taken into account for...

Wed, 21 Apr 2010 11:18:00 +0200

Share Tree policy: past usage is taken into account for assigning the current priorities (via gridengine.info)

Bentham: nobody has acess anyway, so the icon on PubMed says:...

Fri, 26 Mar 2010 16:02:37 +0100

Bentham: nobody has acess anyway, so the icon on PubMed says: “Full-Text Article Inquiry”

"LG Electronics [fridges] were found to contain an illegal device that activates an energy-saving..."

Thu, 18 Mar 2010 10:26:16 +0100

“LG Electronics [fridges] were found to contain an illegal device that activates an energy-saving mode when it detects room conditions similar to those in a test laboratory.”

- LG fridges: life’s not so good

"Here’s my point: businesses don’t get to pick the timetable for when their preferred model takes a..."

Thu, 11 Mar 2010 18:00:34 +0100

“Here’s my point: businesses don’t get to pick the timetable for when their preferred model takes a permanent dirt nap.”

- kung fu grippe Entitled to Care

"Somehow a highly-trained group of scientists at the start of the 20th century knew less about scurvy..."

Thu, 11 Mar 2010 11:14:15 +0100

“Somehow a highly-trained group of scientists at the start of the 20th century knew less about scurvy than the average sea captain in Napoleonic times.”

- Scott and Scurvy