Kon Tiki

like all forms of information, archetypes have a half-life. the memes that reify archetypes also have a half-life. so archetypes can die if no new memes are created which instantiate the archetype, and the existing archetypal memes stop being used in culture (death). one of the most popular archetypes of our time, and perhaps of all time, is that of the hero’s journey. briefly stated, the hero’s journey is a story where the protagonist heeds the “call to adventure”, and leaves the safety of his comfortable everyday surroundings, and journeys out into unknown.
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literary freeware

Bruce Sterling bruces@well.com Literary Freeware – Not For Commercial Use Game conference speech: “The Wonderful Power of Storytelling” From the Computer Game Developers Conference, March 1991, San Jose CA Thank you very much for that introduction. I’d like to thank the conference committee for their hospitality and kindness – all the cola you can drink – and mind you those were genuine twinkies too, none of those newfangled “Twinkies Lite” we’ve been seeing too much of lately.
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seasons in the automata

on buying a farm

From Cato the Elder’s De Agricultura: When you are thinking of acquiring a farm, keep in mind these points: that you be not over-eager in buying nor spare your pains in examining, and that you consider it not sufficient to go over it once. However often you go, a good piece of land will please you more at each visit. Notice how the neighbours keep up their places; if the district is good, they should be well kept.
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BioWordCount: An Intro To Bioinformatics on Apache Spark

Previously on archetyp.al, I demonstrated a bioinformatics use for Hadoop MapReduce. The idea was to build on the ubiquitous word count example, but using a problem which is at least somewhat relevant to bioinformatics. So I read in a VCF file and parsed out the reference and the variant bases, and collected an overall count of the mutation spectrum. So here we are, back at it with an Apache Spark version of the demo.
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BioWordCount: A Brief Introduction to Hadoop For The Bioinformatics Practitioner

Many people who do bioinformatics (the field seems to have settled on “bioinformatician”, but I like “bioinformaticist” better) find themselves dealing with large data sets and long running processes, arranged in myriad pipelines. In our time, this inevitably demands distributed computing. Life innovated during the Cambrian explosion by going from single cells to colonies of cells. Life found a way to distribute and parallelize its processes. In order for us to properly focus our analytical microscopes on life, we imitate life in this strategy and distribute our processes across multiple CPU’s.
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FDA, 23andme, and Innovation

I’m neither a doctor nor a lawyer, so consider my opinions appropriately. I began my career as a software developer at the Genome Institute (TGI) at Washington University in St.Louis. I didn’t set out to get into bioinformatics, it just happened that it was the most interesting problem to work on in St.Louis at the time I was getting my degree in computer science. So I set about learning the craft of software development and the field of bioinformatics at the same time.
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gypsies and jet-setters: Bruce Sterling at 2006 SXSW

This is the first Bruce Sterling talk that I encountered. Now I’m an inveterate Sterlingite, but at the time, 2006, I had only barely crossed intellectual paths with Sterling. I downloaded it with some long dead, precambrian cousin of google reader that lived in the swamps and estuaries of windows computers and survived by allowing the user to view RSS feeds on his desktop. Then pushed it to my equally antediluvian, single purpose device, an Archos mp3 player.
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textruder

Textruder is the next installment in a long line of one-dimensional cellular automata implementations on various platforms and various media. This adventure begins like so many, on the command line. The inspiration for this project came from reading one of Stephen Wolfram’s papers on cellular automata. The original output of the programs testing the concepts of cellular automata was not graphical in the sense of directly mapping each cell to a pixel or block of pixels.
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convert your 23andme raw data into VCF format

A week ago I received my results from 23andme.com. Aside from the obvious points of interest, health risks, heritage, neanderthal composition, etc., I was also interested in getting my own data in raw format. While 23andme does provide a way to download your “raw” data, they are not really providing raw data. One cannot access the image data from the microarray sequencer that they used. What they do provide is formatted as follows:
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