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John C. Earls
Works at The Price Lab
Attends University of Washington
Lived in Urbana, IL
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Research Assistant, Institute for Systems Biology
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  • The Price Lab
    Research Assistant, 2010 - present
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Previously
Urbana, IL - Bloomington, IL - Princeton, IL - Colorado Springs, CO - Chicago, IL - Spring Valley, IL - Seattle, WA
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Computer Scientist, Computational Biologist, Gentleman Adventurer
Introduction
Currently, I am in your genome, analyzing its expression. Shortly, all your base pair are belong to me.
Bragging rights
I am skilled in the balloon animal arts.
Education
  • University of Washington
    Computer Science and Engineering, Ph.D., 2011 - present
  • Illinois State University
    Computer Science, BS, 2005 - 2008
  • University of Illinois at Urbana-Champaign
    Bioinformatics(Computer Science), MS, 2009 - 2011
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John C. Earls

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Wow. Science on the front page.
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Ilya Shmulevich's profile photoMax Robinson's profile photo
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Unfortunately this is a political statement--and one likely to be untrue at that--rather than a scientific/mathematical one.
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John C. Earls

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I would prefer to shutdown the NSA and our government's snooping via political action, but until that day, I feel it is my job as a citizen to make their job as difficult as possible. Very cool, free, secure email program.

The mailbox space is a paltry 100 megs, but the dual encryption, where the email is decrypted from your browser is pretty awesome.  They also have a snapchattish expiration option. More cute than useful IMHO.

https://protonmail.ch/
Secure email with absolutely no compromises, brought to you by MIT and CERN scientists. Follow us for live updates.
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John C. Earls

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I've always been a big supporter of open access publishing, but after reading Michael Eisen's latest post, I realize that I've been wrong.  Excuse me while I figure out what inconvenient results from my last study should be moved to the supplement.  Cell, here I come!!!!
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Ilya Shmulevich's profile photoJohn C. Earls's profile photo
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Me too.  The sarcasm did not come through until the end.
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John C. Earls

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Understanding The Impact of Semantic Search

It's difficult, sometimes, to explain the impact of semantic search in our world without breaking into terminology that includes Entities, Ontologies, Nodes and Edges. But, complex as the technology may be, its effects are incredibly simple to grasp. 

One of the aspects of semantic search is that it maps relationships (Edges) between people and things (Nodes) that are known to it exactly (Entities) and are grouped into closely associated clusters that have been created with a specific conceptualization and intent (Ontologies) to infer information that really means something and which no one can see. 

There are many real-life examples I could use to illustrate this but check out this one that will blow your mind: Kieran Healy, a sociology professor at Duke University, used David Hackett Fischer's (http://goo.gl/Ob95wk) account of Paul Revere's historic ride (http://goo.gl/PU2g4C) to map the relationship between him and the people who were involved in sedition (probably one of the few times I ever have the chance to use this word :) ). Without knowing anything about what any of them said to each other, what they planned or what they thought, given a little semantic search analysis King George III's 'bright young men' would have been able to proactively nip the brewing unrest in the bud, just by monitoring the communication patterns amongst all the groups concerned (sound's familiar?). What's more they could have arrested Paul Revere as "a person of interest" armed with nothing but just this evidence, interrogated him and decimated every revolutionary cell. 

Kieran has written an account of this like it's an intelligence report of the times that is a must see: http://goo.gl/mkP9L

Beyond the practical value of discovery of anything I hope you also begin to see the deeper implications of the use of semantic technologies that is part of the Web 3.0 revolution (i.e. the liberation of data). 
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John C. Earls

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Lately I have been hearing a lot about Julia and I am intrigued.  Fast, built in parallelism, python interoperability and the syntax seems reasonable.  I was thinking about investing some time in Cython, esp. after all the pain I've had with swig on my last project, but maybe that time would be better spent on Julia.  

Anyone have some experience working with Julia in a scientific context want to express an opinion? 
#Julia
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John C. Earls's profile photoBrandon Barker's profile photo
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Thanks, I saw that recently, but haven't had a chance to look at it. I've been spending most of my experimental programming time with ATS2, which I admit is more difficult to use than Julia, but more safe; I'm not yet convinced ATS2 will be the right thing for a REPL though, so I may use it with Julia. Kind of like using C++ & python together, but better in both cases :).
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John C. Earls

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Good news for Sherlock fans.
Our favorite modern-day sleuth, played by Benedict Cumberbatch, returns for season three of Sherlock on Jan. 1. The BBC tweeted the photo and message, below, early Friday, revea...
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John C. Earls

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LOL
 
Theorem: Not every tree is a pseudoforest.

(Via +Brighten Godfrey on Facebook)
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John C. Earls

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Lee is doing an AMA on reddit at 10a pacific today.  Check it out, vote it up, ask something.
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Reddit, Mozilla, Tumblr, Imgur, and over 6,000 other websites are protesting NSA surveillance. Join them.
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John C. Earls

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Yesterday was the 1st anniversary of Aaron Swartz's death.
Websites across the web are planning a massive online protest against government surevillance on February 11th, and they want you to be a part of it. Will you join them?
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John C. Earls

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Uh oh. Now they have a robot army.

novapbs (NOVA)

Google has acquired robotics company Boston Dynamics. http://t.co/8MIG0TRTUV via @nytimes



9:51 AM Dec 14th via HootSuite
http://twitter.com/novapbs/status/411916482365644800
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John C. Earls

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I need to hangout at UW more often. 
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