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Wednesday, February 29, 2012
gethostbyname command line
[View/Post Comments] [Digg] [Del.icio.us] [Stumble] Thursday, February 23, 2012
Google Scholar Bookmarklet
[View/Post Comments] [Digg] [Del.icio.us] [Stumble] Friday, February 17, 2012
As predicted 6 months ago, and again last week, Oxford Nanopore is shaking up the industry. Pacbio, Complete Genomics, Life technologies and others are all seeing their stocks drop 5% on the news that sequencing a genome just got 10x cheaper.
[View/Post Comments] [Digg] [Del.icio.us] [Stumble] Monday, January 30, 2012
Church-Turing thesis and strings
And as new features are added, the problem of writing out and reading files slowly becomes most of what that program does - until the program resembles an actual Turing machine: ploddingly scribbling and reading things from an infinite tape which, because of flooding in Thailand, is infintely expensive. [View/Post Comments] [Digg] [Del.icio.us] [Stumble] Monday, January 23, 2012
Embed Tab Size Info in Source Text
The sig must be in the first or last 128 bytes of a file (so reading the sig is faster) The syntax could be something like: open paren or brace, % or # sign, open paren or brace, the word "tab" then a ':', then anything except a closing/matching paren or brace, then a percent and then another closing paren/brace. [(\[][%#][(\[]tab:[^\)]*[%#][(\[] Examples: C++ [View/Post Comments] [Digg] [Del.icio.us] [Stumble] Friday, December 23, 2011
Uncovering significant miRNA species with RNA-seq
[View/Post Comments] [Digg] [Del.icio.us] [Stumble] Monday, December 19, 2011
Xenograft & Contamination Filter
[View/Post Comments] [Digg] [Del.icio.us] [Stumble] Friday, October 21, 2011
Connecticut Martin
It had never been enough. Even though idle wealthy housewies had long since taken up the pen and written libraries of wisdom and humour, and the girls hanging out at the tattoo parlors had discovered the zen of automotive engineering. Even though the unemployed had long ago sought out physics texts and wrangled secrets of a new energy density theory, it still hadn't been enough. The question remained... what were we working for? The crowd at the coffee shop, from here, seemed angry, but as Martin walked closer he could see familiar faces, sternly triumphant. [View/Post Comments] [Digg] [Del.icio.us] [Stumble] Friday, October 14, 2011
Non "allelic" variation - thinking out loud
(Later Note: I wrote this before I knew what it's called. The term most people use is "Somatic Mosaicism". Apparently this is a pretty well researched topic... so I can go back to all the biologists that looked at me like I was crazy and tell them .... hmm.) Here's a link to a good article on the topic: Original rant below... But let's assume 30 is our number. It's nice and small. And it's good to have a lower-bound. That is only the set of variants that went into the "first cell" (fertilized egg) of an organism. When that egg divides, half the organism has another, different, set of mutations. So 100% of the organism has 30 de-novo mutations and 50% of the organism will have *another* 30 de-novo mutations (30 new ones in that 50%, plus 30 original). But wait, there's more. When those 2 cells divide in half again, you now get 60 new mutations, 30 from each cell. These 60 will be detectible at the "25%" level ... IE: 25% of the final organism will have them. High-throughput sequencing can readily detect variation at the "1%" admixture level. That is, commonly detect variation when as little as 1% of the cells have that variation. So how much variation can we expect, based on a low de-novo mutation rate, detectible at the 1% level? 100%->30, 50% ->30, 25% ->60, 12.5% ->120, 7.25% ->240, 3.12% ->480, 1.6% -> 960 So we can expect about 1000 de-novo variants in a healthy individual, or 32 times the mutation rate. But what if the somatic mutation rate is higher, say, 3000 variants per replication? This may be the case in some organ development. Thus, at the 1% level, would that be 96000 non-inherited detectable variants. I would call that my "upper bound". In real pileup data... I see around 30% "non-allelic" variation. So if, say, you've got 15000 SNPS (a reasonable number), we would expect 5000 "background" snps.....putting the mutation rate at "156.25" (5000/32). That's smack in the middle of the e-coli based estimate. Lots of variant callers filter these out.... but I'm interested in them... i think they may be a lot more important than people think. [View/Post Comments] [Digg] [Del.icio.us] [Stumble] Friday, September 30, 2011
Looks fun. Seems like it would be cool to play against other players... but they are rarely there. The developer needs to link-in to Armor or Kongregate or Facebook or some other PVP network.
There's probably a market for that... build a PVP portal so that lesser known games that are still fun can have a base of players.
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