Disqus - Latest Comments for cariaso

Re: Boolean Biotech

cariaso — Wed, 17 Feb 2021 01:26:26 -0000

re: GPU
https://github.com/LooseLab...
and various other commits seem to suggest CPU calling is doable.

Re: Boolean Biotech

cariaso — Wed, 17 Feb 2021 00:56:17 -0000

Can you do read-until with your setup? if not, what is the minimum setup that would be able to support
https://github.com/LooseLab...
so that you could do deep sequencing of just a few genes of interest?

Re: 23andMe finds evidence that blood type plays a role in COVID-19

cariaso — Mon, 08 Jun 2020 12:36:06 -0000

You have the genotypes necessary to distinguish people who are heterozygous at rs505922 from those who are homozygous. This is a unique advantage of the 23andMe platform, which wouldn't be possible from a typical blood test. Please do so.

Re: New – Auto Scaling for EC2 Spot Fleets

cariaso — Mon, 31 Oct 2016 10:19:23 -0000

Is this fleet autoscaling supported in cloudformation? The docs are strangely quiet, and that's a bad sign.

Re: Captchas Are Becoming Ridiculous

cariaso — Sat, 28 Jul 2012 22:01:50 -0000

A captcha costs $.00139 to break. http://www.deathbycaptcha.com

Re: Personal genomics: no longer just for rich white folks

cariaso — Sat, 30 Jul 2011 17:26:27 -0000

The 'defect' in question is http://www.snpedia.com/inde...
and the gene is http://en.wikipedia.org/wik...
and I feel it is unfair to portray the Caucasian form as a defective. Variation in this snp exists in the Yoruban population, but neither skin color was of little consequence for human survival. The ancestral form is inefficient at producing vitamin D which is essential for human survival. The migration to northern latitudes decreased solar exposure and made efficient vitamin D more valuable. Caucasians accumulated a valuable mutation for their environment. The defects here are the european descendants who decided to move to an unnatural environment and spend weekedays indoors and weekends at the beach.
http://en.wikipedia.org/wik...

Re: 23andMe DNA Test Review: It’s Right For Me But Is It Right for You?

cariaso — Fri, 03 Jun 2011 09:48:09 -0000

You can also download your raw data from
https://www.23andme.com/you...

and then use Promethease to learn more about your data
http://www.snpedia.com/inde...

Re: Threads Suck

cariaso — Mon, 17 Aug 2009 16:35:06 -0000

The "reason that I haven’t quite put my finger on yet, this feels like a very clean way to do things inside an individual program, even though it’s lame in an OS kernel". I think the applicable term is "cooperative multitasking", as linked from your wikipedia source. And it works great if you can control all of the actors (as in single program), but lousy when you have no control over rogues (an os). Every company wanted their app to demo well on a unloaded system, so they hogged all resources. The app looked great alone, but 2 or 3 such apps and you machine could crawl. A sort of tragedy of the commons played out.

The asynch/twisted model eliminates the need for polling, which is only one (albeit too common) specific application of threads. There is no one true answer. The pieces that best fit should be used, but more programmers need to learn the asynch pattern, and in many cases even the polling thread one. To walk before you run, etc.

Re: What’s scientific data all about?

cariaso — Tue, 04 Nov 2008 01:18:17 -0000

"One topic where I often disagree with people is curation. Many believe we need humans to curate data. I don’t have an answer, but don’t believe that humans scale and we will run into scale issues at some point."

Where is there is a need to choose? SNPedia looks like its for humans, but much of the content is written by external bots. It isn't a a choice between them -- software needs to do the heavy lifting AND make it easy for people to curate.

Re: Why and Why Not You May Need A Genetic Councilor

cariaso — Thu, 09 Oct 2008 08:54:48 -0000

>Computers can never provide human consolation, no matter how excellent and rational their reports.

For a standalone computer that is true. But a computer connected to the internet is capable of connecting humans to each other on the basis of shared genetics. This works equally well for paid professional geneticist counselors, PatientsLikeMe.com style communities.

>But how many people in health care today can read the following expression?
>re.search('(CAG){36,}',genome[4][3046205:3215485])
1 person. She does clinical leukemia research, occasional fashion modeling and is a certified pilot.

>Or write it?
my ($repeat) = substr($genome[4],3046205, $length) =~ /(CAG){36,}/;

>Or tell me what it means not just clinically, but biologically?
A repeat of 36 or more or 'CAG's on chromosome 4 between positions 3M and 3.2M. This reliably predicts Huntington's disease with longer occurrences having earlier age of onset.

Disclaimer: I heart Python and Woody Guthrie. "I don't want no greenback dollar"