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Commits on Jun 30, 2012
@ctb kmer-percolation 27fa6ec
@ctb fix 42075a6
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+A good way to publish -- arXiv FTW
+##################################
+
+:author: C\. Titus Brown
+:tags: papers,arxiv
+:date: 2012-06-29
+:slug: science-f-yeah
+:category: science
+
+(Or, "A better way to publish bioinformatics.")
+
+We just got word that our paper, "Scaling metagenome assembly with
+probabilistic de Bruijn graphs" `[ arXiv ]
+<http://arxiv.org/abs/1112.4193>`__ `[ github ]
+<https://github.com/ged-lab/2012-paper-kmer-percolation>`__ has been
+accepted for publication in PNAS. (Yay!) I just posted the final
+version to github, and the arXiv PDF should be updated to the third
+version on Tuesday or Wednesday (July 3rd or 4th). We're very happy,
+not least because this is my first senior author paper and my grad
+student Jason Pell's first first-author paper.
+
+But we have other reasons to be happy, too.
+
+You see, back in December when we submitted the paper `(on Dec 28th,
+2011) <http://ivory.idyll.org/blog/kmer-percolation-posted.html>`__, I
+took the relatively unusual step of posting it to `arXiv
+<http://arxiv.org>`__, a preprint server. This made the paper
+available before peer review, which isn't something that we tend to do
+in bioinformatics or biology, for whatever reason.
+
+The paper didn't exactly sink like a rock, but I didn't get much in
+the way of feedback or publicity from making it available. That's OK,
+it sounds pretty esoteric -- it involves biology, computer science,
+and physics, and discusses DNA shotgun sequencing, metagenomics,
+probabilistic data structures, and percolation theory. Apart from
+being nearly impossible to review from a position of expertise (my
+group may actually be the world expert on the intersection of these
+four topics, solely because we wrote this paper), the paper seemed
+reasonably impenetrable to pretty much any audience. Oh well.
+
+Then two super neat things happened.
+
+First, about a month ago I received a request to review a paper on
+`quip <http://www.cs.washington.edu/homes/dcjones/quip/>`__, a DNA
+sequence compression package that uses probabilistic data structures.
+I was asked to review it because they cited our arXiv paper (yes, you
+can cite arXiv papers -- it's archival!) I did review the quip paper
+(it's a great paper) and I hope it appears soon. (I signed the review,
+note.)
+
+Second, about two weeks ago I heard about `Minia
+<http://minia.genouest.org/>`__, an assembler that used an extension
+of our basic idea to do really low-memory assembly of the human
+genome. What was ultra cool about this is that Rayan Chikhi, one of
+the authors, told me directly that they built off of our paper: ::
+
+ Thanks for sharing your pre-prints on arxiv, our article is a direct
+ consequence of that action!
+
+So, not only does our newly-accepted PNAS paper have two citations,
+both from *before* it was accepted, but another group has already
+extended our approach in a new direction (which looks pretty
+significant to me, BTW).
+
+This just seems to be the right way to do science, to me: minimum time
+from paper to exposure to (possible) extension.
+
+To be clear, I don't want to claim that our paper is super
+consequential (that'll wait for another blog post ;) or even that the
+Minia assembler is an amazing breakthrough that totally built off of
+our giant contribution. I just think it demonstrates a way to
+accelerate bioinformatics research -- which we should be doing, yeh?
+
+Incidentally, Cameron Neylon, the new advocacy director for PLoS, told
+me that in physics (where they've been using arXiv for 20 years or
+more) the citation count for papers peaks right around the point where
+they're *accepted* for publication -- because by then they're old hat:
+everyone has read them on arXiv already. Wow, physics and
+bioinformatics publication culture sure is different :).
+
+--titus
+
+p.s. Note that the paper is under embargo until it's formally
+published. I'm not sure what that means in the age of blogs, exactly,
+but if you're a NY Times reporter just itchin' to write a front-page
+story about our paper... please wait, okay?

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