Attention readers: This blog has moved to a new home at

Thursday, January 31, 2013

Moving day

Due to various Blogger gadgets failing and my desire to more easily cross-post to Facebook and other places, this blog is moving over to a new home at

All of this blog's contents has already been migrated, and hopefully, the move will prompt me to write more frequently. Hope to see you readers over at soon!

Saturday, February 18, 2012

Oxford Nanopore sequencer annoucements

Oxford Nanapore Technologies (ONT) announced the release of their GridION and MinION systems yesterday, which both use their nanopore sequencing technology. Luke Jostins, Nick Loman, and Keith Robison have all provided detailed commentary about this release, so I'll only offer a few of my thoughts here.

First off, the current 4% error rate (mostly in the form of deletions) isn't great, but that's almost certainly fixable prior to the production release; we should remember that the Solexa and SOLiD systems probably weren't doing much better when they were first announced either.

But most everything else about these systems looks really promising: e.g., true single molecule sequencing (no amplification needed) with reads in the tens of kilobases (kb) and promises of single reads into the 100-kb range (limited, of course, by the fragment sizes in your sample). Features like these would mean that several currently difficult informatics challenges—such as read mapping, de novo assembly, and phasing/haplotyping (if long single strand reads are achievable)—will be "solved" or at least highly simplified.

So yes, assuming that overall costs per base sequenced (including amortized capital and reagent costs) are highly competitive to the new Illumina and Ion Torrent systems, I'm willing to concede that the ONT systems could be significant "game changers". If nothing else, the types and quantity of data that such systems would make available will keep informaticists like me busy (read "employed") for a long time to come.

Thursday, February 9, 2012

Japanese food explained

From the Anthony Bourdain and Eric Ripert show at the Paramount Theatre last night: both chefs sang the praises of Japanese cuisine, citing its increasing influence in restaurants throughout America and both saying it would be the one country's food they would they restrict themselves to if forced to do so.

And why Japanese food? Because of its simplicity, its lightness (try eating rich French or Italian food for more than ten days), and its focus on the ingredients. Which lead to Bourdain providing what I thought was the best comment of the night (approximately quoted):

I think the thing that makes their porn so disturbing is the thing that makes their food so great. That is, their obsessive attention to detail.

Wednesday, January 18, 2012

And one more letter opposing SOPA/PIPA

This time, from one of my fellow graduate students:

Hello Senator Hutchison,

My name is Lindsey Wolf. I am a PhD graduate student in molecular genetics and microbiology at UT Austin. I'm also a teacher, textbook editor, and part time tutor for the UT Longhorns football team.

I'm 28 years old and did not grow up with the internet. I learned to use it in high school, but feel as though I'm on the tail end of the generation that needed to wander my college library's basement looking for a biology journal article instead of simply looking it up online.

That said, our tax dollars (I say our because I'm also a homeowner in Austin and know what that means) for science and education that pay my salary are best spent saving me time. The ease and speed of looking something up on the internet or teaching my students to do so is an invaluable skill.

Please encourage congress to appreciate the value inherent in sharing information. The country and the world need scientists and teachers like myself and we would be greatly impeded if SOPA or PIPA pass.

Thank you for your time,

Lindsey N Wolf
PhD candidate
University of Texas at Austin

Second letter in protest of SOPA and PIPA

In support of the day's protests against SOPA and PIPA, I've sent an updated version of my November letter to my representatives. I strongly urge you to contact your Congressional representatives as well—feel free to use any part or all of my letter below as needed.

Dear [CongressCritter]:

I am writing as a concerned voter in your district to once again ask you to strongly oppose the Stop Online Privacy Act (H.R.3261) and to urge your counterparts in the Senate to oppose the PROTECT IP Act (S.968).

While the Internet continues to raise legitimate questions about intellectual property rights and their enforcement, these pieces of proposed legislation are gross, heavy-handed overreactions to such concerns. In their current form, these bills would provide no meaningful protection for intellectual property rights but still threaten critical features of the Internet. Quoting from a November 18, 2011 article in "The Atlantic":

"[U]nder scrutiny, it's obvious that even a conservative accounting of [the] costs far outweigh even an optimistic assessment of [the] benefits. To sum them up, the certain costs include disrupting the business models of countless technology companies that are not in the business of piracy; handing the federal government substantial and unprecedented powers over the Internet; entrenching a guilty-until-proven-innocent attitude toward copyright infringement; making the Internet less secure for everyone; arguably infringing on the First Amendment; contravening internationally recognized Internet standards; and undermining international press freedoms and human rights."

When the bill was first announced, members of the Business Software Alliance as well as members of the Senate expressed grave concerns that such legislation would seriously harm technical innovation, stifle investment in the new ideas and businesses, and harm technology jobs crucial to future economic growth. Key computer scientists also expressed concerns that these bills would damage core components of the Internet's infrastructure and compromise cyber-security.

On January 18th, some of the web's most popular sites like Wikipedia and Reddit joined thousands of others in protesting these bills by "going dark", replacing normal content with pages asking their users to contact their Congressional representatives to stop these bills. Others like Google, Facebook, and Twitter chose not go dark, but nonetheless, continued to express their strong opposition to this legislation.

Groups across the political spectrum—including the ACLU and Electronic Frontier Foundation on the left and the Heritage Foundation and Americans for Tax Reform on the right—have also expressed their concerns about the detrimental effects these laws would have in a variety of areas.

Most importantly, as The Atlantic article notes, these bills threaten our Constitutional rights to due process and free speech. As written, they would allow sites to be blocked without affording those accused of copyright infringement their rights to answer such charges in a court of law; this sort of "guilty until proven innocent" approach to copyright law would have chilling effects. For example, under such laws, the science outreach and advocacy groups of which I am a member could find their web and social media sites taken offline due to accusations of copyright infringement while leaving them with no meaningful legal recourse to challenge such actions—even if their use of copyrighted material is protected by fair-use provisions.

Over the past few months, numerous organizations and ordinary citizens such as myself have expressed our concerns about the myriad ways that these bills will stifle innovation and our constitutional rights. In the coming days, many more will continue to do so. I hope you will take my concerns to heart and join your colleagues (among them, Representatives Issa, Paul, and Pelosi and Senators Cantwell, Moran, Paul, and Wyden) in opposing such legislation.

[Name here]