Revisiting the RNA Tie Club

As mentioned previously, by wonderful luck I now have regular contact with Ash from the Curious Wavefunction, and he has stimulated a new burst of scientific history interest in me.  I've ripped through a bunch of scientific memoirs -- by Crick, Djerassi and Dyson -- and have learned how to summon the biographies of Wilkins and Chargaff, as well as trying to dive again into The Eighth Day of Creation.  One topic I keep stumbling across is an interesting little bit of genetic history called the RNA Tie Club, which is a story worth re-telling and re-examining

Interested in the History of Biotech Companies? Don't start with Wikipedia.

I'm generally a big fan of Wikipedia and use it often for background research.  I've gotten more active this year in editing it, particularly around biographies of scientists.  For example, this year I've made major additions or edits to the entries for Walter Gilbert and Arthur Pardee and the , created entries for Martinas Ycas, Benno Müller-Hill, Monica Riley and Helen Donis-Keller. I also stumbled my way into a campaign of major revisions to the entry on Marie Antoinette, getting sometimes into a revision war with one other editor (which we resolved with a truce).  Along the way I've gotten almost adept at writing Wikipedia references and discovered a bizarre recurrent vandalism of Wally's page in which the vandal changes his name and personal details.  Recently, I've discovered a whole category of flawed entries: those on companies in the biotechnology industry.

To Properly Assess Cancer Genomics, One Cannot Dismiss It

Through a happy series of professional events, I now get to have lunch very regularly with the author of the excellent blog The Curious Wavefunction.  If you haven't visited there, Ash not only delves into chemistry but the history of science.  In a most friendly way, he dropped a challenge on my Twitter-step that represents a long procrastinated blogging project, so I really couldn't turn it down.  And that challenge is: what has been the value of cancer genomics. Is it, as he asked, a very expensive exercise in looking for keys under the lamppost, or something far more valuable?

A Dovetail Route to Scaffolded Genomes

10X Genomics had a lot of buzz at AGBT over their approach to acquiring long range information for complex genomes via a microfluidic-assisted library preparation scheme.  Another young company, Dovetail Genomics, is starting to unveil a very different technology with similar aims.

An Impending Shakeout In Library Prep?

My ABGT teleconference-based pieces all had a theme of library preparation.  Library prep has never been as flashy as instrument performance, but is clearly critical.  A library-free sequencing technology remains a distant dream, so DNA (or RNA) must go through a series of preparative steps prior to being loaded on the sequencer.  The dominant library prep molecular biology for clonal sequencing systems consists of shearing the DNA mechanically, making flush ends with a repair mix, adding 3' runs of A and then ligating primers and finally using PCR to amplify the material.  

Mechanical shearing can be replaced with enzymatic shearing (or perhaps even chemical, though I'm unaware of chemical shearing being used in production).  For RNA of different sorts,

some upstream steps are added to convert the RNA to DNA, perhaps with a depletion at some stage of hyperabundant species such as rRNA.  This conversion may, with different levels of success, mark which strand was sense and which antisense. The transposase-based Nextera protocol represents the most drastic departure from this paradigm, enzymatically eliminating all the steps prior to PCR. 

There's Gold in Them Thar Programs

Last night was the season five finale of the Gold Rush, which I confess is one of the few television programs that I have been watching routinely near their airing schedule (the other is The Simpsons, which is a father-son bonding experience). Now, writing in a blog mostly about science that you watch something on the Discovery Channel is a bit of a bold act, given its many panderings.  The network annually features Shark Week, that has been roundly criticized for its sensationalized portrayal of these magnificent creatures.  It also features shows which purport to show individuals routinely engaged in felonies and in one case claiming to document a violent subculture in a pacifist religious community, the Amish.  I grew up near the Amish Country of Pennsylvania; if anything like that ever existed the Philadelphia papers would have had a field day.  Gold Rush itself, and a second gold show which I've developed a fondness for, Bering Sea Gold, has shortcomings that are obvious and painful.  So why am I hooked?

Can BGI Really Stir Up the Sequencing Instrument Market?

I've been asked several times recently about rumors coming out from BGI.  They've started claiming they have a super sequencer which will radically beat Illumina's offerings on both cost and accuracy. The recent 10K Genomes meeting apparently had a quick talk from BGI which led to some limited Twittering, and judging from this Mendel's Pod interview at least one person believes the buzz (though the same individual quotes a price per PacBio human genome that high by at least a factor of 25). .  The claim is that this summer at ESHG BGI will release two boxes, one a benchtop model which I haven't seen any details on, and the other claimed to offer throughput superior to a HiSeq with better accuracy.  What might be backing up these claims?

What's Been Cooking for Ion At AGBT15

Rounding out my remote coverage of platform news from AGBT, the Ion Torrent team also lent me some of their time (and at risk of sounding obsequious, I do greatly appreciate this -- vendors have almost no down time at these events) to touch on some of the topics I I wrote about in my Ion history and speculation piece.

10X Reveals Its Facets

Perhaps the heavily anticipated launch at AGBT this year is the library prep instrument for 10X Genomics.  This Bay Area startup made a huge splash at the beginning of the year by announcing a monster ($55.5M) financing.  A member of my professional network had been part of the early team and had given me very minimal hints at last year's AGBT, so I've been eagerly awaiting details for a long time. Several members of 10X's team were kind enough to chat with me by phone yesterday with the proviso that I hold off on launching this piece after their talk today at the conference (interestingly, I had crossed paths with all of them in some previous setting).  Also, they sent me some promotional materials and permitted me to post some clips from them. Now, the GemCode system is officially launched, with orders being taken now and devices planned to be delivered in early Q2.

Illumina Launches NeoPrep (#agbt15)

The 2015 AGBT conference started out today.  A few hardware makers have let me chat by phone with members of their team, since they're there and I'm not.  Tonight's dispatch is from a chat with Illumina focused on their now launched NeoPrep library preparation instrument

Can Ion Torrent Buzz Again?

In my AGBT 2015 Preview / Speculation at one point had a tightly packed (and overly long) paragraph on Ion Torrent, but I realized that this was a symptom of trying to to cram too much in too little a space -- plus I really had a lot more thoughts worth unpacking.  So here's a long form look at Ion Torrent -- with plenty of references to past AGBTs to make writing this now apropos.  One advance bit of excuse making: the historical background that follows is not intended to be a comprehensive history of Ion Torrent technology, but more of an impressionistic sketch (but as always, my worst excesses and omissions are fair game for comments!).

#AGBT2015 Preview

The annual genomics party on Gulf of Mexico beaches named AGBT runs next week, and already there have been some speculations flying.  I'd better dash something off before I'm any later to the preshow -- or more importantly before I get contaminated with embargoed information.

The MBTA Must Embrace Data!

As you may have heard, we’ve had a bit of snow in the Boston area recently.  Two storms, one the beginning of last week and one which just ended yesterday, each dumped close to a meter of snow in the area.  The two storms each had different profiles: last week’s storm featured rapid snowfall and furious winds, with the snow falling over a 24-36 hour period.  The more recent storm started on Friday afternoon, ended on Tuesday morning, with a steady fall of lazy snowflakes.  Last week a hare, this week a tortoise.  But both weeks, a paralyzed Boston from a transportation standpoint, with the MBTA mass transit system performing dismally.

Unfortunately, the main response to that failure has been a lot of political theater. GM Beverly Scott gave a press conference yesterdaythat featured the usual refrain: the system features antiquated equipment, our crews are working hard, nobody could deal with this.  In other words, a string of unquantifiable and unactionable clichés.  There's already an unhelpful murmur in the press that Scott might be fired, which would seem little fix but mostly fodder for more column inches of newspaper opinion (such as this and this)

How not to write a sequence assembly comparison paper

Lex Nederbragt flagged, via Twitter, a preprint on the F1000 site with a questionable table comparing sequencing systems.  Alas, once I looked at the paper I've gotten myself in a state where only writing up its numerous deficiencies will free my mind of it.  I've even volunteered to F1000 to review the paper, but I haven't heard anything and so I will use this space.  I'm afraid this paper fall into the small category of manuscripts that I would recommend rejection.

The preprint is titled "Advantages of distributed and parallel algorithms that leverage Cloud Computing platforms for large-scale genome assembly".  Alas, the paper doesn't attempt to deliver anything of the scope promised by that, and the abstract isn't much better.  Most papers have a certain amount of preamble and then deliver some new finding; the preamble to the paper is overlong and badly executed, and the work in the paper is far too minimal and also badly executed.

Cargo Cult Networking & Other LinkedIn Laments

LinkedIn is a social media tool I find greatly flawed, but useful.  Part of the devil's pact one makes with LinkedIn is to receive great amounts of requests from individuals who wish to grow their networks.  I have a personal guideline for such which help me weed through the requests, but last year I got a request that had me laughing -- and slightly revising that guideline.

JPM Wrap-Up:

In this final installment of a series of reactions to news coming from the J.P. Morgan Conference, I'll cover an interesting complementary technology that was announced.  But first, it might appear my prediction of no radical sequencer announcements may have been invalidated, with an announcement from BGI of plans to launch two sequencers based on Complete Genomic's technology.  Unfortunately, the only outlet that seems to have covered this is GenomeWeb, and it is in their premium (paywalled) section, so I know nothing beyond that.  It appears this was only announced around JPM and not at JPM, so I have a Clintonesque out as well.

Illumina's Expanded Lineup

In my JP Morgan predictions for sequencing platforms, I didn't do badly.  The only major player to make a platform announcement was Illumina, and they did indeed announce instruments that are not radical departures from the prior platforms.  I am kicking myself for not making more specific predictions, as the nature of the new boxes was really unsurprising and it would have been nice to nail that.

2015: Another Year of Sequencing Evolution (not Revolution)?

The J.P. Morgan Conference is firing up, and for the past few years that has meant big sequencing platform announcements -- HiSeq or Ion Proton or such.  This has stolen some of the thunder from AGBT in terms of major announcements (sadly, I won't be attending this year -- and will try not to land my self into surgery the way I did the last time I didn't attend AGBT).  I figured I'd better write this tonight before any more JPM-related sequencing instrument announcements show up, or more to my prediction, before the conference ends without any.

Druggability: An Underappreciated Issue in Translating the Human Genome Into Therapeutics

I'm sorely guilty of neglecting this space, but a recent (and now storified) Twitter conversation from Jonathan Eisen (@phylogenomics) has improbably fired me up enough to scribble something.

Reanalysis Lays Bare MinION Review's Spectacular Flaws

I will confess that when our first MinION burn-in data for lambda came in & I threw a few aligners at it (after first getting my data extractor in Julia shaken out), I was disappointed at the results.  Very few 2D reads, very few aligned reads and the alignments all short.  At this point, I sat back to wait to see what others had experienced and to think of additional bioinformatics approaches.  It never occurred to me to dash off a glorified  blog post and submit it to a journal.

Oxford Takes Some Flak, Fires Back

A huge event in the genomics community this summer has been the Oxford Nanopore MinION Access Program (MAP), which has enabled a sizable but select group of researchers to try out ONT's novel nanopore-based sequencing technology.  While results and rumors have periodically drifted out over the summer, this week saw three disclosures, one of which resulted in fireworks and action

The good, bad & missing from Bio* libraries?

As I mentioned recently, I've been exploring how I might use the emerging Julia language to solve problems.  While that requires a large amount of mental work, I see some potential gains, both in having more readable code than Perl as well as to potentially leverage a lot of high-level concepts for parallel execution that are built into the language.  But beyond the challenge of elderly canine pedagogy that I present, there is the issue that the BioJulia library is quite embryonic, with serious consideration of treating much of the existing code base as a first draft (or, that is the impression I get from skimming the Google group).  So I'm going to try to pitch in, despite my multiple handicaps.

After the New Yorker piece, what of disruptive innovation?

I don't read a lot of books aimed at the MBA crowd, but one set I have liked, and sometimes cite here, are Clayton Christensen's on inovation and disruption.  As you may have heard, a recent article in the New Yorker by Jill Lepore took a gimlet-eye view to the whole concept and raised serious questions about Christensen's methods.  This was then summarized by another author in Slate and since then Christensen has responded in part via a Business Week interview.  He's also scheduled to be interviewed on PBS this weekend, so likely there will be further developments.  Indeed, after sketching this out on the commute home I discovered a Financial Times article whose tone is very similar to what I have written below.

Dabbling with Julia

As I've remarked before, I've done significant coding in a large number of languages over the last 35-or-so years.  I don't consider myself a computer language savant; I've known folks who can pick up new languages quickly and switch between them facilely, but for me it is more difficult.  I haven't tried learning a new language in perhaps 5 years, but this week I backed into one

NGS Saves A Young Life

One of the most electrifying talks at AGBT this year was given by Joe DeRisi of UCSF, who gave a brief intro on the difficulty of diagnosing the root cause of encephalitis (as it can be autoimmune, viral, protozoal, bacterial and probably a few other causes) and then ran down a gripping case history which seemed straight out of House.

A Sunset for Draft Genomes?

The sun set during AGBT 2014 for a final time over a week ago.  The posters have long been down, and perhaps the liver enzyme levels of the attendees are now down to normal as well.  This year’s conference underscored a possibility that was suggested last year: that the era of the poorly connected, low quality draft genome is headed for the sunset as well

How will you deal with GRCh38?

I was foolishly attempting to catch up with Twitter last night during Valerie Schneider's AGBT talk last night on the new human reference, GRCh38. After all, my personal answer to my title is nothing, because this isn't a field I work in.  But Dr. Schneider is a very good speaker and I could not help but have my attention pulled in.  While clearly not the final word on a human reference, this new edition fixes many gaps, expands the coverage of highly polymorphic regions, and even models the difficult to assemble centromeres.  Better assembly, combined with emerging tools to better handle those complex regions via graph representations, means better mapping send better variant calls.

So, a significant advance, but a bit unpleasant one if you are in the space.  You now have several ugly options before you with regard to your prior data mapped to an earlier reference.

The do nothing option must appeal to some. Forgo the advantages of the new reference and just stick to the old. Perhaps start new projects on the new one, leading to a cacophony of internal tools dealing with different versions, with an ongoing risk of mismatched results. Also, cross your fingers that none of changes might be revised if analyzed against the new reference.  Perhaps this route will be rationalized as healthy procrastination until a well-vetted set of graph-aware mappers exist, but once you start putting-off it is hard to stop doing so. 

The other pole would be to embrace the new reference whole-heartedly and realign all the old data against the new reference. After burning a lot of compute cycles and storage space running in place, spend a lot of time reconciling old and new results. Then decide whether to ditch all your old alignments, or suffer an even larger storage burden.

A tempting shortcut would be to just remap alignments and variants by the known relationships between the two references. After all, the vast majority of the results will simply shift coordinates a bit, but with no other effects.  In theory, one could estimate all the map regions that are now suspect and simply realign the reads which map to those regions, plus attempt to place reads that previously failed to map. Again reconciliation of results, but on a much reduced scale.

None would seem particularly appealing options. Perhaps that latter route will be a growth industry of new tools acting on BAM, CRAM or VCF which themselves will provide a morass of competing claims of accuracy, efficiency and speed. Doesn't make me at all in a hurry to leave a cozy world of haploid genomes that are often finished by a simple pipeline!

Illumina's New Lineup

Illumina made a brace of big hardware announcements at this week's J.P. Morgan conference, and Mick Watson has done a nice job of covering them.  I'll try to cover some different points that have occurred to me after letting the news ferment -- plus Illumina made yet another announcement tonight that scotched a portion of an earlier draft of this piece.

Relearning Chemistry

An evening ritual is to inquire what homework requires assistance, and at the beginning of the year it was a science worksheet as part of an introduction to chemistry.  That, and a later project, have exposed how much rust my knowledge of chemistry has accumulated, but also have led me down the path of repairing forgotten bits and certainly learning some new stuff

Envisioning The Perfect Scaffolder

Rather than make any New Year's resolutions of my own, which I would then feel guilty about not keeping, I've decided to make one for someone else: they will write the perfect open source scaffolder.  There's a lot of scaffolders out there, both stand-alone and integrated into various assemblers, but none are quite right. 

If you are sequencing an isolated bacterium or archean and are looking for a scaffolder, except in a few rare cases, you're doing something wrong: given enough long reads from PacBio it should be possible to solve nearly every bacterial genome. But, if you're sequencing eukaryotic genomes or any metagenome (or you're unlucky or data short on a simple microbial genome), you're probably in the market for one.  I'm going to supply a list of attributes I cooked up during a long drive up the Eastern Seaboard today, without much regard for feasibility or even if some conflict with each other.

Peering Through the Flowcell Glass, Darkly

As 2013 draws to a close, I've decided to stick my neck out and make some predictions for 2014.  Perhaps I'll get lucky and a few will even come true!  After several mental experimentations on the structure, I'll settle for stepping roughly past each major player.

Assembly Could Benefit From More Circular Reasoning

It was very gratifying to get comments on my recent piece on a de novo assembly review from both a referee of the manuscript (the amazing Heng Li) as well as one of the authors of the piece (though I am truly feeling guilty I forgot to reach out to the authors).  Of course I was having my usual post-post regrets of things not written, such as the whole interesting topic of dealing with (and leveraging) uneven coverage in metagenomes and when assembling from amplified samples.  But one other thing I was reminded of is one of the minor complaints I have with assembly programs: a lack of proper handing of circular genomes.

Assembling a Review of a Review of Assembling

A review on short-read de novo genome assembly appeared recently in PLoS Computational Biology, titled "Next-Generation Sequence Assembly: Four Stages of Data Processing and Computational Challenges".  I think the review has a number of merits, but I also find a number of frustrating flaws.  I'm going to write this entry much as I would have written a referee report on it.  Unfortunately, that will mean I'll dwell a bit more on the flaws than the assets, but if you are interested in the field

Did The Biochemists of Yore Know Morse Code?

So, this piece is going to be mostly asking questions.  In one of the corners of my dream world I have a scientific historian on retainer, but in the real world my substitute is to throw some questions out and hope some knowledgeable people leave comments.  If someone I spark someone’s term paper or thesis topic, I ask only that I get an electronic draft!

Spanish Prisoner, ZX-81 or Turbo Pascal?

In  the movie The Spanish Prisoner, a brilliant inventor possesses a paranoia that "The Process" he has invented will be stolen by deceitful competitors, and everyone speaks with a highly distinctive cadence. The entire movie is suffused with deceit, starting with the title which is a notorious con scheme akin to the modern Nigerian scam. I spent last evening in some of the space in which the movie was filmed listening to a scientist in that mold (& distinctive speech) describe a process his group has invented (indeed, by lucky chance I helped him find the venue). But many remain unconvinced that Clive Brown and Oxford Nanopore are not themselves the puller of ocular wool.

Ion Previews More Accurate Polymerase, Faster Template Prep

I haven't talked about Ion Torrent for a while, because it was largely off my radar screen.  In early 2012 the PGM had been an important contributor to my early de novo genome assemblies, as it was the only fast turnaround, low cost system I could access.  But the data quality was always frustrating, with many indels, and the 200 basepair mode on the read lengths not great for assembly.  Once I could access a MiSeq, that became our dominant instrument for individual genome assembly.  We tried Ion once more with the 300 basepair chemistry, but were not particularly impressed.

Ripples from 454's Shutdown Announcment

Roche's announcement this week that they planned to shut down the 454 sequencing business in mid-2016 was not completely unexpected, as a number of rumors of shutdown had shown up on Twitter.  Most tweets on the subject fell into two categories: either just-the-facts-ma'am or jokes about the dominant error profile (which I guess you could call just the facts maaa'aaam).  But, certainly I wouldn't have thought Roche on the verge of this decision when I went to AGBT 2013 in February, as 454 had a huge suite in a prime location (just by the main conference hall entrance) and many expensive events. Now, Roche's presence in the genomics space is looking like just the recently announced deal with PacBio to market human diagnostics on that platform.

Roche Taps PacBio for Human Diagnostics

One of the two big buzzes in the genomics business world was the announcement that Roche Diagnostics has signed a major deal with Pacific Biosciences in the field of human diagnostics, which comes with a $35M upfront payment and a possible $45M in milestones, plus future sales of reagents.  PacBio stock rocketed over 70% on this news. This on the same day that cancer diagnostics company Foundation Medicine went public with a similar potent climb from their offering price; a good day for those lucky enough to have the shares (which, by the way, does not include me in any way, though Foundation shares a common venture backer with Warp Drive Bio in Third Rock Ventures).

Potential Sources of Drag on PacBio's Long Read Performance Trajectory

Over at Homolog.us there are two detailed blog entries on Pacific Biosciences entitled "End of Short Read Era?" (Part I  and Part II).  I've tweeted a number of comments on the technical aspects, but there are some more substantial thoughts reading these pieces helped me condense.

SGE Isn't For Dummies (I sort of wish it were)

Kendall Square used to have the ultimate geek book store, Quantum Books.  No fiction or graphic novels there; it was all technical books.  One could browse every O'Reilly book and many, many others.

My biggest contribution to the field of biochemistry

LinkedIn has a feature by which one can endorse other people for different fields. Periodically the system prompts me to vote yea-or-nay on a bunch of endorsements, and conversely I get regular updates as to what others have endorsed me.  It's always nice to get a vote of confidence, but sometimes I find myself wondering what it really means.

An Incomplete Guide to Asking for Help on Your De Novo Genome Project

I've been thinking about this piece for a while, because I am a frequent presence on SEQAnswers.com and often dive into questions regarding de novo sequence assembly, particularly for small genomes.  It's good to help out and a way to feel like one is contributing to a broader community, but sometimes it can be very frustrating because the seekers (SEQers?) of help do not post their questions very well.  So, it would be helpful to have a post to point them to, though I'm sure there are considerations I either haven't thought of or will fail to remember to add.  So, those can either go into the comments or a future post, or perhaps something can go in the Wiki at SEQAnswers.

But in general, think of it this way: you have some experienced hands in a field you wish to enter, who are willing to give detailed advice for free.  But, they can't give that advice unless you specify your question well, and if you don't get it right the first time they may not see (or may ignore) your second shot.

What Might Knock Illumina Off Its Perch?

The big sequencing platform news this week is Roche's announcement that they are ending their collaborations aimed at developing new sequencing technologies.  A collaboration with DNA Electronics aimed to create an Ion Torrent-like system whereas a more ambitious effort with IBM aimed to create instruments based on "DNA transistors".  As noted by Forbes' Matthew Herper in a thought-provoking piece, Illumina is sitting very high atop the sequencer market.

For What is a 454 Still Great?

I've been mulling this item ever since AGBT, but have struggled with the title.  I don't want to sound like I have a grudge against 454 ( truth is I just got some good datasets off this technology), but I do believe that they are few papers away from being stampeded.  Or perhaps not; perhaps the community is really wedded to this platform.

PacBio Back of the Envelope Numbers

Back-of-the-envelope calculations can be quite useful, but also quite dangerous.  They are meant to be quick estimates, but can't be taken too seriously.  Still, I try to get them right & deeply regret overestimating recently on Twitter the cost of a human genome on PacBio by 3X.  Twitter is particularly dangerous: tempting to fire off a note, but impossible to pack in the full calculation

Post AGBT: A Longish Item on Long Sequencing

As others have noted, a significant theme at AGBT this year was sequencing at length.  While this year lacked true bombshells, PacBio impressed many with their making single-contig bacterial genome assemblies look easy.  Moleculo had been the object of much pre-meeting excitement, and while very few additional details emerged about their process, several talks showed what could be done.  As I have discussed previously, Nabsys demonstrated their “positional sequencing” system to select invitees in a hotel suite.  Optical mapping from OpGen and BioNano Genomics featured in a few posters, but did not attract much attention.  Oxford Nanopore had no physical presence, beyond a somewhat secretive suite, but several ONT staffers were happy to reiterate their confidence that they will launch their system – when it is good and ready.

AGBT: Nabsys unveiled

In the previous post I described the Nabsys positional sequencer. Yesterday I got o see it running in their hotel suite here at AGBT13.

AGBT Preview: Nabsys

A complaint which seems to be circulating on Twitter and elsewhere is that this year’s AGBT conference on Marco Island next week doesn’t look like it will have any excitement around new platforms.  AGBT has been a traditional coming out party for platforms.  Last year it was Oxford Nanopore which created a huge buzz, and in previous years that crown has been held by Ion Torrent, Pacific Biosciences, Complete Genomics and others (including a few which seem to have gone kaput).

It is hard to argue that this year’s program is much more heavily tilted towards applications of genomics than novel genomic technologies.  Many of the genomic technology talks are updates on the evolution of existing platforms such as PacBio and Illumina (especially the Moleculo technology).  But, there will also be novel technologies.  

This past fall I had the pleasure of spending half a day with the folks at Nabsys, located a short distance from Boston in Providence RI.  Nabsys’s buildings are in a sea of drab parking lots (not to mention sheriff’s cars; a courthouse is nearby), but on the interior were quite pleasant.  I was largely wearing my “day job” hat that day, but Nabsys will be unveiling their instrument at AGBT and has given me permission to talk about what I saw (and reviewed what I've written to make sure I didn't make some dumb errors, though the content is all mine).  Of course, I will update this after I look some more at AGBT.

Matthew Yuricich: A Pre-Oscar Tribute

I'm committing myself this week to an uncommon intensity of posting.  It's AGBT week, and while I'm there I plan to be busy both here and on Twitter.  Genomics has always been the focus of this space, but once in a while I beg the readers' indulgence while I write on something else.  Just after AGBT comes the Oscars, and in the likely case I'm completely exhausted (though sitting much more comfortably than I was for last year's Oscars), I want to scribble a long-overdue tribute.  For when the montage appears of previous winners who died since the last telecast, I'll be looking for the only Oscar awardee I ever met.  The nature of his work meant that many are utterly unaware of it, but he contributed significantly to the visual spectacle of many films, including one which influenced the look of a vast number of films of the same genre that followed it.  

Moving day

I was originally going to start this with a joke alluding to one of the signature special effects of Star Trek: The Next Generation, but given the recent events in Russia it's probably in poor taste to speak lightly of flashes in the sky.  But, after much preparation, today was the day that Warp Drive Bio completed packing up, with next week ushering in our new facility.

A Short(ened) Note on Ion Torrent & High G+C

As one might guess from reading this space, I always have an itch to try new sequencing technologies or updates to existing ones.  That's generally a good thing in my position, though more than a few times I experience buyers remorse.  At least this time, I found something a bit interesting

Illumina's Blizzard

As the clear leader in the genome sequencing technology market, Illumina is often in the news.  As befitting the winter season, there's just been a blizzard of Illumina news, mostly announcements from within but also two important external ones (an excellent summary of these can be found at NextGenSeek).

Not Exactly the First Tuesday After the First Monday of November

This past presidential election was as nasty as any in recent memory, and so perhaps folks are reviewing their support for Churchill's dictum ("Democracy is the worst form of government, except all the others").  But, I make a plea now that you vote again.  I'll even extend that plea to a request that you honor a deeply held tradition in some urban political systems, which is to vote early and vote often!

In Vivo Blog follows the biotechnology industry, and now for the fifth year in a row they have a poll as to the best biotech deals in three categories: M&A, Alliance and Exit/Financing.  We've been nominated in the Exit/Financing category for our monster financing arrangement with Sanofi, which gives us a $120M runway so we don't have to worry about running out of money (a fate I don't wish to repeat ala Codon Devices).  So, please vote for us!

Okay, perhaps you'd like to objectively consider all the contenders.  The voting site has links to detailed discussions of each of the candidates, and I'm sure after reading each one that you'll be convinced we're the best, and you'll want to vote for us!

If that doesn't appeal, perhaps you like good old fashioned sibling rivalry?  At the moment, we have ground to gain on two other companies funded by Third Rock Ventures, bluebird bio and Foundation Medicine.  Both are fine companies trying to make important health care innovations.  FM was even started by our CEO, reinforcing their big brother status.  But, are any of them trying to reboot an entire sector of the industry that big Pharma nearly universally abandoned?  That sounds pretty courageous, perhaps even legendary.  So vote for us!

Sometimes a vote is strictly for an individual, but other times it makes sense to vote for a team.  We're a team worth voting for: unified in our quest, unbounded in our efforts. 

I'm Keith Robison, Principal Scientist for Computational Biology., and I approve this message.

MUSKET then FLASH, vice versa or just COPE with it?

It's gratifying to see that yesterday's The Trouble with FASTQ item gathered a number of lively comments, and there are certainly a number of branches I could (and should) take from that post.  But one item that garnered both a comment here and on Twitter was the order of operations I described

The Trouble with FASTQ

I spend a lot of time working with sequencing data, and the most common format for such data is FASTQ.  FASTQ has many things to appreciate, but FASTQ data also can be troublesome

Scribl is Neat!

Speaking of Twitter, one thing I've found it highly valuable for is discovering new tools and ideas in the bioinformatics space.  It's not a replacement for all my other methods, but I've discovered things I otherwise would have missed.  A great case in point is Scribl, which I discovered over the holiday period and vowed to try out this morning.  WOW!

BTW, I'm on Twitter

For a long while, my only interaction with Twitter was to monitor key hashtags during AGBT and ASHG.  However, I've gotten myself sucked in and am now actually contributing.  As suggested by the username OmicsOmicsBlog (archives at this link), I'm treating this primarily as an extension of this space.  So if you look you'll mostly find genomics, bioinformatics and other geeky stuff. I post more often, given that it's actually possible to author tweets on my smartphone (I once had delusions of writing blog posts there; it's really not workable). To date, I've retweeted more than I've originated.  It's certainly a challenge to compress thoughts into 140 characters.

I'm sure this has been covered elsewhere, but the 140 character limit is a weird holdover from text messaging, which itself was a weird technological cram job on the cellular voice standards.  What would Twitter be like if that limit had been higher or lower?

Why Next Gen Now?

A confession: I've considered writing this piece for a lot of years now; not quite as many as this space has existed, but many years.  Some ideas get stuck in my head, but I never force them out through my fingers.  Finally,with this one, I will pose the question: Why did "next-generation" sequencing happen when it did?

Nanopores: Fission or Fusion?

It's fall, and the foliage in New England is putting on its usual spectacular show.  What isn't showing is any of the progress in nanopore sequencing that I got caught up in last February.  Oxford Nanopore made quite a splash, and I wrote a quite breathless account based on a phone conversation with them.  Since then, other than raising some serious cash, Oxford has been quite quiet, and has neither released any data the community (or at least this blogger!) is clamoring for nor is there any sign that alpha units have been placed.  Genia was another nanopore company making noises about unveiling this year, but now they have licensed a new nanopore-based sequencing chemistry and promised boxes in 2014.   When will nanopores actually hit the market?

Does Illumina Have A Sequence Diversity Problem?

Roughly speaking, NGS sample preparation workflows can be split into two basic classes of workflows.  Complete molecule workflows are currently suitable for microRNAs and other small fragments at the moment, but attempt to capture the entire molecule.  With luck, long read technologies will someday make these the standard.  Fragment workflows are the workhorse, and take input material (RNA, DNA) and convert them into a library of fragments representing (or directly from) the original material. 

BGI Gobbles Complete Genomics

An email this morning alerted me that BGI Shenzhen is acquiring Complete Genomics.  I hadn't been following Complete's business very carefully and had missed (or forgotten about) their quarterly report in August warning that they were dangerously low on cash and had engaged a firm to look at strategic alternatives.  If you are holding Complete Shares (with the wonderful ticker symbol GNOM), you'll get $3.15 cash for each for them.  If you were unfortunate enough to buy them at the top, that's over $11 a share in capital loss to put on next year's tax returns.  I'm not one to watch stock prices closely.  Buy-and-hold an index fund is my primary investment strategy; A Random Walk on Wall Street is the best route to sound sleeping and good returns.  I've never held any GNOM stock.

Shameless cancer quacks

A news item meant to shock its readers caught my eye, but in the end I was shocked and sickened in a way that I think lay far beyond the writer's intent.  The writer's tale is of a desperate family of a cancer-stricken teenager being taken advantage of by a fame-seeking hoaxer; the tale I read is of a desperate family of a cancer-stricken teenager being fleeced by cancer quacks.

Is Cambridge Almost Full?

If you tour around the extended Kendall Square area of Cambridge, you'll find a number of large construction sites.  Various projects for Pfizer, Biogen, Novartis and more speculative projects are consuming most of the large surface parking lots in the area, and many that are yet untouched (such as the one next to Starbase Athenaeum)  are marked out for development.  There are a number of single story buildings, such as the bank by the Kendall T-stop, which seem likely to also become such sites.  However, on the outskirts of Cambridge just such a proposal has kicked up a serious hornet's nest, and one that suggests that the biotech (and tech) real estate boom here may soon hit a serious wall.

Farewell to a Giant Leaper

When I was a boy, a nearly annual occurrence was a trip to Kentucky to my maternal grandparents' house.  My biological grandmother died when I was quite young, but there would be many visits to see my grandfather.  I enjoyed them greatly, but of course he is now long gone.  So I have a few regrets, and mostly I wish I had thought to ask him a few questions.

Owning a Sequencer is NOT a Prerequisite for Sequencing!

Besides the little cancer genomics piece yesterday, another genomics paper getting quite a bit of popular press attention is the nice work from the NIH tracking down a deadly outbreak of drug-resistant Klebsiella pneumoniae, with 11 of 18 infected patients dying.  Rapid genome sequencing provided a much higher level of detail for tracing the outbreak than older methods, even distinguishing isolates taken from different sites on the same patient.

The Perils of the Too Small Gene Panel

The newswires are alive with summaries of an item in Science Express which, discounting the supplementary material, isn't much bigger than the news articles describing it.  It's a nice piece showing the relevance of cancer genomics, but there's also a backstory fleshed out in the news items which is interesting.

The gist of the paper is this: a trial of everolimus, an MTOR inhibitor, in bladder cancer did not go well; very few patients showed benefit.  But, one patient did spectacularly well.  So the researchers performed whole genome sequencing and found inactivating mutations in the well-studied tumor suppressors TSC1 and NF2.  Screening 13 more bladder tumors with a panel of cancer-specific genes found 3 more cases of inactivating mutations in TSC1, plus one patient with a missense mutation of unknown significance.  In the trial, patients with TSC1 mutations stayed on trial longer than patients without the mutations.  

My first reaction was "this all makes sense" -- TSC1 and NF2 are genes which immediately suggested themselves as TOR-related. 

What's interesting from the news items is a suggestion that the original patient had been sequenced for a limited number of genes around mTOR, and that this did not include TSC1 or NF2.  Of course, the problem when doing a limited screen is picking who to include, and from my 2 second analysis on the train I would have included TSC1 and NF2.  But, that could be much easier said than done.  They are attractive, since they are tumor suppressors known to be mutated in cancer, but so are other genes in the neighborhood (such  as TSC2 or PTEN).  There are activating mutations known in the neighborhood as well, such as PI3K or various AKT family members.  Presumably it was a PCR-based (quite likely Sanger) method, in which case it can be challenging to target every exon both because you may have an "exon budget" (number of exons to be amplified) and some exons are nightmarish to amplify.  

I think the case illustrates one reason whole genome or whole exome sequence are by far the best strategies in a case such as this.  The potential payoff in understanding is huge, as you have one strong outlier patient.  The number of patients are small (though, admittedly, this is probably one success pulled from many dry holes).  Plus, these days the cost of WGS/WES is probably not much more than targeted PCR, given the costs of developing good PCR assays.  

The other potential advantage of WGS/WES, over even broad cancer-specific gene panels, for a case such as this, is that the field can change.  New oncogenes and tumor suppressors are identified periodically, perhaps even in the time period between when a panel is designed and it is used.  In a research setting to understand the basis of a clinical trial anomaly, it's particularly valuable to explore all corners, because what might not make sense today might become clear tomorrow.

Jackalopes & Guest Posts

Recently, the topic of jackalopes showed up at work.  Anyone who has toured the American West has probably come across postcards of these curious beasts, with the bodies of jackrabbits but antelope-like horns.  Even out East, at some frequency reports of these creatures appear stochastically.

An unconvincing case to X-out algebra

I had a bit of a long commute yesterday, driving from south-central New Jersey up to Starbase Cambridge.  In general it's a dull ride, having been done too often.  Still, it was the perfect time to absorb the magnificence of a George Washington Bridge crossing, followed by a great sunrise-lit view  from the loop ramp onto the Henry Hudson Parkway, and similar snippets of the Palisades also glowing in the early sun.  But, much of the time I was flipping through radio stations.  Due to this, I caught the tail end of a NPR interview with Andrew Hacker, who wrote a recent NY Times opinion piece calling for algebra to be removed from the required high school curriculum in the U.S., which has garnered letters both for and against.

Complete Genomics Goes Long

In Nature this week (as an open access article!) is a report from Complete Genomics and collaborators describing CG's new "Long Fragment Read" (LFR) technology for generating long range sequence information and haplotypes.  Technically, there is a lot of cool stuff -- but excitement for many (such as myself) must be balanced against CG's business model of sequencing only human genomes

Qiagen Buys A Sequencer

Today's news (take your pick of Bio-IT or GenomeWeb for original stories) is that Qiagen has bought out Intelligent Biosystems (IBS), the company in nearby Waltham developing a platform using sequencing-by-synthesis chemistry licensed from Columbia University

Out Damned Spot Instance! Out I say!

A piece of advice for anyone in the bioinformatics world: get working knowledge of the Amazon EC2 cloud computing system.  Now, there is a lot of controversy over whether EC2 (or other cloud services) eliminate the need for a mongo local compute resource, but even if you like doing things at home there are multiple niches that Amazon can fill.  It can be your experiment sandbox, which can be quickly shut down if something goes haywire.  It can be overflow capacity, dealing with a sudden surge of compLocationute need.  It can also be a reserve for if your main system is experiencing hardware issues.  Or it can be a neutral zone for collaborating with someone outside your organization's walls.  Or it can be where you do your consulting work (approved, of course!) that is independent of your organization (or between organizations).  Or anything else; it's there and it's likely at some point you could use it, if not now then in the future.  Better yet, you can get your feet wet with their Free Tier of services, which of course is a hook to try to get you to consume more.

Don't be scared off by the wide array of different services Amazon offers.  You certainly need to understand only a few to get started, and many are really intended for e-commerce sites and the like.  I've probably used less than half a dozen services from the menu, though I'm sure there are a few more I could use profitably.

One catch with EC2 is that you are going to do a lot of low level UNIX systems administration, something I've generally avoided in my career.  I've been able to because I usually have a few UNIX gurus close enough by to do all that, and besides it's been in their job description and not mine!  The few times I have dabbled have been mixed.  At Harvard I once burned a day getting a printer back on the network, but was compensated by that lab's PI with a gift certificate for yummy bread.  On the other hand, at one of my employers I succeeded in disabling my server, which could only be restore by re-installing the OS.  Again, one reason to consider Amazon for a sandbox!

What do I mean by low level?  Well, with the nice web GUI you fire up a machine.  Note that any disk attached to that machine by default is (a) too tiny for real work and (b) will go away when you kill the machine.   If you want big, persistent storage you need to create an "EBS Volume".  With the GUI you create the volume and then attach it to the machine, but at that point it is useless.  Using low level UNIX commands you need to now format the drive, create an attach point, mount the drive and set the permissions.  If you want password-less SSH between nodes, that's a few more configuration file tweaks.  Not rocket science, but tedious to do time after time.

A past colleague and friend of mine recently let me know about STAR::Cluster, and this free software is amazing.  It automates not only the UNIX toil and trouble I found tedious, but other low level stuff I hadn't gotten around to yet.  For example, every EBS volume in the cluster is NFS-mounted to all the nodes, which is critical for some operations (though other tools, such as MIRA, are positively allergic to such setups, as the extra IO traffic kills performance).  Plus, your cluster comes loaded with useful cluster tools such as OpenMPI and the Sun Grid Engine job queuing system.

Each of these is useful for bioinformatics.  For example, OpenMPI is the framework for the nifty Ray assembler.  Ray can handle your really big de novo assembly jobs, as it allows you to spread the job out across multiple nodes.  In contrast, on Amazon you are very limited by tools such as Velvet because they can work in the memory of only a single machine, and the biggest machines at Amazon aren't very big (about 68Gb).  Celera Assembler can use the Grid Engine, which is pretty much essential with that assembler. Furthermore, under Amazon's pricing model to get big memory you must rent a lot of cores, and for a single core tool that's a bit of a waste.

So for now, I'm loving STAR::Cluster but forsaking spot clusters.  That is, until I figure out a way to divine the correct bidding strategy, which may require the services of a cauldron and some eye of newt.

STAR::Cluster has mostly behaved for me, but I have had a few hiccups in which nodes didn't quite come up as planned.  I don't know why, and in one case I reverted to doing the low level work to fix it (indeed, I finally learned how to NFS mount a volume).  In the other case, I couldn't figure out a solution and had to kill the damaged nodes.  Still, most times everything has gone as planned.

However, STAR::Cluster also tempts you with spot instances, which have not been productive for me.  Amazon's pricing is a 3-dimensional grid: where is the machine, what is its capability and which pricing scheme.  On the where side, most times you probably just want cheap, which tends to mean one of the US sites (their Asian sites are definitely about 10% more expensive to use).  It is useful to stay in one location, as only when EBS volumes are in the same zone as a compute instance can you attach (and then mount) that volume on that machine.

As noted above, capability spans a number of machine classes.  I tend to go for two of them.  The 32-bit instances are cheap (about the cost of a newspaper per day) and useful for maintaining a permanent presence for uploading & downloading files, but are under-powered for much else.  At the other end, I tend to use the premium-priced high-memory quadruple extra large instance, because this gets the most compute power and memory for the standard instances, which tends to be needed for the projects I'm offloading to Amazon like huge short read assembly or mapping efforts.  I haven't tried out the cluster compute instances yet, which are even pricier but may yield higher performance (faster networking and power) nor have I tried the GPU instances; both are likely in my future.

After these, Amazon offers three pricing schemes.  On demand instances are simple to use: you fire one up and pay for each hour you use it; make it go away and the meter stops turning (rounding up to the next hour, of course).  If you are using the system heavily, then a reserved instance involves an upfront payment but a lower per-hour cost.  Catch is, for each instance you want simultaneously you'll need to reserve another one.  The third scheme is interesting but can easily scorch your fingers: spot instances.

A spot instance is charged the current market rate for an instance of that type.  Much of the time, it's half the cost of an on demand instance, and when you have a cluster of big instances running at $45/day per node, that's not trivial.  However, you put in a bid for the maximum price you are willing to pay.  Should the spot price exceed that price, your instance can die instantly with no warning.  You can browse the prior history of a spot instance in your selected zone and get some idea, but so far I've been very unlucky.  Despite putting in spot prices well above the apparent previous price spike, new price spikes have bumped off my instances.

The big problem for me is that none of my applications can tolerate croaking in mid-operation.  Apparently there is a way to do this with Grid Engine, and apparently Ray can work off Grid Engine and probably Celera Assembler can be restarted automatically, but I'm not yet to the point of understanding how to do these.  So, having a cluster die late in a process is an expensive disaster, with the clock completely reset.  So, after multiple misadventures I've sworn off spot instances for now, which is probably costing the company significant dollars but now I'm not losing sleep -- and those aborted runs weren't free.

So STAR::Cluster lets you boil your data without a lot of toil and trouble

States Funding Companies: Always a Bad Idea

The annual BIO meeting will be in Boston next week, so the media is looking a little bit more at our sector.  Today's Globe has an Op-Ed from Geoff MacKay, the CEO of Organogenesis, titled "Keeping Mass in biotech race" (or, online, "Fueling the next wave of biotech growth" .  Reading it, I've been kicked out of my posting inertia, as it touts exactly the sort of strategies which I believe are mistakes, with recent events nearby providing evidence.

MacKay's lead-in is that Massachusetts has a thriving biotech industry and that this contributes in important ways to the economy of the state.  No argument there.  He goes on to describe how other states and countries are eagerly trying to lure companies away, which is certainly true.

When BIO Nebraska offers convention-goers Omaha steak tips at the end of a long day, or when BIOTECanada supplies Tim Horton’s doughnuts and coffee for thousands at breakfast, they are not just showcasing their hospitality. They are firing the opening salvo in an aggressive marketing campaign that may include strong financial incentives, tax breaks, lower labor costs, and, in some cases, a fairly convincing argument about quality of life benefits outside of our state.

MacKay knows this well, because as he continues his own company was heavily recruited a number of years ago, and only when Massachusetts laid out a package of financial incentives did Organogenesis commit to stay.

Now, I do not believe I'm a Mass biotech snob, and there are certainly many companies that do very well outside hub areas such as Boston, the Bay Area or the D.C. Metro area.  But, my suspicion is that many of those companies do well because they grew organically in their location, and I also believe there are many real costs to a business in operating outside of the hubs.  For some companies, the benefits outweigh the negatives, but that is even less likely if you move to such an environment.

A key advantage of being in a hub is a supply of experienced staff.  Biotech has its ups-and-downs, but because there are so many companies in the Boston area there are lots of folks who are looking for positions.  When you are the hiring manager, that means you can look carefully for the right fit yet find someone relatively quickly.  Big tech hubs like Boston also mean that there are more opportunities for spouses and life partners who are technically oriented, and while that doesn't describe my situation it does seem that an awful lot of senior biotech folks share their lives with other senior biotech folks.

I'm also suspicious that many CEO's know all this, and simply rationally play states against each other to their company's benefit.  However, there are plenty of examples of CEO's who aren't so sophisticated, with the former management of BiogenIdec serving as one data point.  A few years ago someone had the brilliant idea of moving the non-R&D folks outside the Cambridge headquarters to the tony town of Weston, which happened to be where the then-CEO lived.  Those who had to live with this decision rapidly discovered the sheer inefficiency of it, as while the organization chart might have shown a clean split the reality is that communication must flow throughout an organization, and communication is often most effective face-to-face.

As far as incentives, there is a danger that Massachusetts politicians will soon forget the recent blow-up of 38 Studios (indeed, I thought about titling this "38 Reasons States Shouldn't Bribe Companies to Stay", but who's going to read something that threatens you with 38 bullet points?).  Curt Schilling started and ended his major league baseball career in Boston, and played a key role in the 2004 drive to a World Series victory, most memorably while playing with a jury-rigged ankle repair that visibly bled during the playoffs.  At the tail end of his career, he became known both for loudly espousing a free-market approach to the economy (he was even mentioned as a possible candidate for political office) and for a deep interest in sophisticated video games.

Schilling founded a company which ended up being named for his uniform number, 38 Studios.  The goal was to produce a new generation of online multi-person video games.  After starting in Massachusetts, he successfully wangled a $75M loan guarantee from Rhode Island on the condition that the company move there and create a set number of jobs.  Amazingly, Massachusetts officials refused to make a sweeter offer.  38 Studios' first game arrived this past winter and was greeted with critical praise but relatively modest sales.  More importantly, in the meantime the governor's chair in Rhode Island switched from someone who had spearheaded the deal to someone who publicly opposed it.

This spring, it all blew up rather spectacularly.  Rhode Island realized that 38 Studios was in serious trouble, and was asking for an advance on some additional tax credits (which it could in turn sell).  Governor Lincoln Chafee, was clearly not in favor of further aid, though did consider it.  38 was also due to make a payment on one of the loans, and looked like it might miss and default on the loan.  To much fanfare, the company delivered a check for the amount -- but it soon came out that they had tried to quietly tell RI not to cash it immediately, because it would bounce!  Later, it would come out that the company hadn't been making payroll for several weeks.

The whole incident underscored multiple points of why governments should not be directly funding businesses.  Schilling had a passion for the business, but no experience.  A good VC (I'm not claiming these are universal or common, but this is my experience) would help guide the company; politicians are completely wrong in this goal.  Schilling would later complain that Chafee's dire pronouncements on the company had killed a potential financing deal, but one of the Business 101 lessons apparently never taught to #38 by his agent is that if you don't have contractual control over who says what, then anybody can say anything.  In any case, if public money is at risk then the governor is ethically obligated to speak up.

The state also had no business investing so much in a single risky company.  Just the financials looked ugly; 38's next game was at least a year from delivery and they were carrying hundreds of employees.  Given media reports, it seems not unlikely that 38 Studios was going to go $150M-$200M in the hole to develop the game, which could only be justified by absolutely chart-topping game sales.  RI was effectively also help fund economic activity in other states, as 38 Studios had acquired other companies along the way.

Massachusetts can't be smug about 38 Studios, as it bet a similar outsized amount in a green energy company called Evergreen Solar, which also went bust. Solyndra in California has been a national example.

If the pols really feel they must spend, there are good ways to spend that money.  Unfortunately, that spending is much more spread out and doesn't quickly generate a bunch of jobs which can be claimed to be the direct result of the legislation.  Of course, many such jobs really aren't -- many would have been created already.

One core area in need of investment is transportation.  The MBTA system is creaking along due to deferred maintenance and delayed rolling stock replacement, and probably needs billions of dollars.  A recent Globe front page graph showed clearly that MBTA ridership growth continues at a steady clip, but there hasn't been service growth to match.  Indeed, due to equipment shortages that spacing of trains on several lines is growing.  After the T, there is the expansion of the Hubway bicycle system beyond the small core region served now.  If you never use the T or Hubway, just remember that riders on these systems would probably be in cars competing with you on the roads.

Housing continues to be expensive in the Boston area for a variety of reasons.  While some of this is deliberate and chosen (such as towns wanting to manage their population densities), there are many opportunities for government to foster housing development in ways that will encounter little resistance.  Cleaning up brownfields and streamlining permitting processes are obvious ones.

There's also the local environment.  Workplaces are more appealing when they are near parks, restaurants and other amenities.  The Globe today also had an item on the conversion of individual parking spots to miniature parks, and idea that has a lot of merit as long as it isn't overdone.  Exploring ways to add more food and entertaining options, ranging from expanded night hours, additional liquor licenses for very small trendy bars and food truck zones, these are all the obvious purview of government.

Finally, there is that issue of training.  The area's premier universities and colleges play a key role in providing scientists, and many of the existing companies groom new executives.  Where the state should play a role is fostering training programs at the high school and community college level to prepare a healthy cadre of research technicians, which during the boom years at the end of the last century were in short supply.  Many of the skills that go into such training, such as keeping meticulous records, following procedures to the letter and learning how to capture and report data, all are valuable in non-biotech fields.

Perhaps that is my overall theme.  If government wishes to enhance the biotech industry, or the robotics industry, or the computer services industry or the myriad of other exciting sectors in the local economy, the wrong way is to try to throw money at individual industries or companies.  Targeted tax breaks and loan guarantees are rarely deployed well, are often timed badly, and benefit few outside those targeted.  Broad improvements to the transportation, park and educational infrastructures will pay dividends for every industry and all of the citizenry.  Let gullible states throw their money away luring a few gullible companies; invest instead in across-the-board improvements which will both boost the current crop of companies as well as enable new exciting industries that don't even exist yet.

The Challenges of Sequencer Comparison

I've slipped back into a lack of posting again.  Some of it is a residual from my recovery this spring from surgery (physical therapy can really be draining), and a lot is due to being really busy in the day job (finding highly rare substances like dilithium is not easy), but in the end those are incomplete explanations.  What should be really embarrassing is that I got access to Nick Loman and colleagues' comparison of benchtop sequencers several days before it published, and here it is weeks later and I'm finally getting around to covering it.

Thank You, Mrs. Woodrow

Tonight I will continue the recent trend of punching these out on some magical date.  Now, I usually have some sorry excuses for my erratic writing, but for once I actually have something bordering on reasonable.  Just after writing about Oxford Nanopore, my confidence in my skiing skills exceeded my actual skills, resulting in my femur taking on my tibia.  Here for sure, size matters, and the tibia lost horribly..

Announcing the Omics! Omics! Sequencer Evaluation Program

A serious issue which has been raised often both by myself and commenters is the challenge of properly evaluating sequencer performance prior to widespread commercial availability of a platform.  A number of roads have been frequently taken, but each have their issues.  Data generated by a company is always met with suspicion.  Alpha releases are often to academics connected to a company, which has the advantage that they are likely the most passionate about proving its worth, but the downside these users may not be viewed as fully objective.  Beta (or early release) sites are often less connected to a company, but by the time they publish their results through peer-reviewed journals it is long since commercial launch.  Conferences such as Marco Island help shorten the cycle time, but not entirely.  Early users are sometimes also suspected of having agreements which give the platform makers the power to squash bad data.   So how can a manufacturer gain "street cred" for their instrument

An Oscar Night Request

I've tried pretty hard to keep this blog focused on all the omics, but occasionally take the license to stray to my other interests, primarily one of them.  Tonight is the Oscars, and I have a plea for the movie industry.  Now, I realize the overlap between readership of this space and the big wigs in Hollywood is tiny, but perhaps a friend-of-a-cousin-of-a-spouse-of-a-sibling of a reader can make a difference.  It is this simple: you have less than two years to get off your rears and launch a Blu-Ray 30th anniversary edition of an Oscar-winning picture.

Why Oxford Nanopore Needs to Release Some Data Pronto (Besides Bailing Me Out)

Last week's piece on Oxford Nanopore got a lot of attention and a lot of comments, which to me is the true mark of success in this space (discounting the higher than normal spam attempts).  A couple of folks were kind enough to tweet a link (now captured in Nick Loman's wonderful tweet archives for AGBT 2012), and it was also picked up by Matthew Herper at Forbes, Dan Kobolt at MassGenomics and others (apologies for all I haven't shouted out).  It also can't be denied that some of those comments felt I had been too generous / gullible with Oxford Nanopore

Oxford Nanopore Doesn't Disappoint

Oxford Nanopore's AGBT presentation should have just finished up, so the embargo is off.  Oxford was kind enough to chat with me last night and to share their press release in advance; on the call were CTO Clive Brown, SAB member Ewan Birney and Director of Communications Zoe McDougall.  A real challenge posed by Oxford's news is trying to write about it without slipping into clichéd techspeak about what they will be releasing later this year ("second half").

2012: Enter the Nanopores?

This summer will make it twenty years since I first heard of the concept of nanopore sequencing.  A very affable post-doc in George Church's lab was starting some experiments in the concept.  Unbeknownst to any of us, another group at Harvard in the Biolabs (Dan Branton's) was also working on a nanopore sequencing technology.  In the time since then, the field has generated many papers and much speculation, but no workable sequencer.  I had started joking a few years ago that nanopores were the monorails of sequencing: always the technology of the future.  To be a bit more fair, nanopores had started to resemble nuclear fusion, a tantalizing vision always just out of technological reach.

Does Illlmina Also Have A Homopolymer Problem?

One of the most widely-publicized error modes with Ion Torrent and 454 sequencing has been the challenge of correctly counting the number of bases in homopolymer runs.  Because these chemistries use non-terminating nucleotides, polymerase is free to add as many as possible.  Unfortunately, the signal linearity breaks down, making it difficult to correctly count.  Ion Torrent today released a note on homopolymers, but rather than plowing this well-trod ground it goes for a less publicized problem: Illumina having a more specific challenge in this department.  The note is available on the Ion Community, free registration required.

Roche Guns For Illumina

Due to a business dinner & general exhaustion, I turned in early last night & was caught unaware this morning of the big news: Roche is making a hostile takeover bid for Illumina.  Ugh!

Sequencing Technology Fireworks

I actually awoke today expecting an exciting press release, but I sure wasn't prepared for the big announcements from Ion and Illumina.  Not that they were totally unexpected, but there's a huge difference between speculation and announced products (which, of course, are hugely different from ones you can actually buy!)

Ion Torrent Pairs: To What End?

Ion Torrent quietly released a set of paired end datasets over the holiday break.  This is a bit embarassing for me, as in my last post on Ion I stated the platform "will probably never have paired ends" and in fact Ion had already announced the protocol.  Oy!  I also missed their mate pair protocol being released, though the document itself is another victim of Ion's incredibly counterproductive security policy.  If you don't own a PGM, you can't access the document -- never mind if you are trying to plan for a potential buy or are preparing a library for a friend/collaborator to run.  

Year's End

I hoped this year to push myself to blog more frequently and regularly.  Clearly I did better than some years, but not up to the standard I had hoped for.  I've also realized that I missed noting some significant personal milestones.

Reflecting on a Year of Ion Torrent

Ion Torrent released three more datasets this morning, all generated on their 318 chip.  One's from E.coli but two are human genomic samples.  With approximately 1.2Gbp of raw data coming from these 318 chips (fron around 6 million quality filtered reads per chip), they are starting to move up the food chain in human genomics from pure amplicon sequencing to more complex small targeted resequencing efforts.

Fitting Out

One of the attractions of my new shop was the possibility to see a biotech company built from the ground up.  Each of my previous companies had been a long-standing concern by the time I got there; even Codon Devices had a year plus under its belt and some equipment already mothballed.  The new venture moved into its first lab space last week, and as you can see from the picture all we have at the moment there are bare walls.

MiSeq Made Easy?

The first computer I ever tried to program was built from a kit by my brother and father.  The DATAC-1000 was a single-board machine, with that single printed circuit board about the area of a large laptop (image on page 9). Sporting a grand 1K of RAM, it was a grand machine.  User input-output was entirely through a set of binary touchpads and LEDs, though a cassette tape interface enabled storing and reading programs.  If I helped any with it, I might have sorted the resistors since I had just learned the color code.  The machine sported the same processor as some other machines of the time, such as the KIM-1 and the PET and even something called an Apple.

Thinking Outside the Box or Just Plain Nuts?

Please take the title in the spirit it is intended: as a bit lighthearted. Seeing the object pictured and reading the accompanying blog post from one of Jonathan Eisen's graduate students.  It's an unusual solution to a common problem, and gave me a good chuckle.

Boston's Boris Bikes

When I discovered that my new gig would temporarily in Boston, I realized I had an opportunity to try out Boston's new bikeshare program. Started this summer, Hubway consists of racks of bikes in public places which can be used for short hops around town. I like my folding bike, but on some rush hour trains it is very hard to find space for it, especially with some train conductors who are more interested in giving dirty looks than serving their passengers. Plus, it's now quite dark on the last leg of my commute, and even if I had some really slick lights I don't like riding even short distances in the dark.

Transitions

I went to an Infinity going-away lunch last week. We head off to some favorite local restaurant and order a modest (but delicious) meal on the company dime. The departee makes an impromptu speech, there are goodbyes and handshakes and usually a number of pleas to stay, both fictitious and heartfelt. Those staying wonder what could lure someone away from the very safe and green pastures of the company. I've been to many such lunches with Millennium and Infinity; with Codon the lunches tended to be group affairs as people were laid off in batches.

Illumina Calls for a Flag on the Play

Continuing my sports analogies, but switching games, in my coverage of the benchtop sequencer war today.  Alas, I can't refer to instant replay, as the usual set of procrastination excuses has resulted in this being filed very late after I was made aware of it (first by a comment in the blog, then by a friendly chap from Illumina alerting me).  In any case, Illumina has responded to Ion Torrent's claims on long reads and overestimated MiSeq quality, and mostly done so by crying "Foul!".

Genetic Education:

   A study by the American Society of Human Genetics (ASHG) is published today suggesting that few U.S. states have adequate standards in place for genetics education.  I forgot to ask for a link to the article that would go live post-embargo, but it should be on the website of the journal (CBE Life Sciences Education)

Will Max-Seq Gain Traction?

      At the beginning of the month, I had dinner with J Adams from Azco Biotech and some friends/colleagues of his and talked over the Max-Seq.   And yes, I did let them pick up the bill -- J wouldn't let me pay for myself.  In Sequence did a nice piece on it the next week, so again I've blown an opportunity to scoop them.  Then somehow, between vacations and other distractions, this piece was stuck in blogger limbo.  But, there are some details I don't see there and some color I think worth adding.

Wishing I Had Been A Referee: A Renaissance for Tagamet?

Back from vacation & watching another wave of Hurricane Irene soak the area (curiously, the windiest times so far seem to be breaks in the rain).  August has not seen much attention paid to this space (indeed, I have one piece that has gestated nearly the whole month), so time to put the shoulder to the wheel.

 

Just before my vacation, a pair of papers showed up in Science Translational Medicine which describe two attempts at drug re-positioning by transcriptional profiling.  The key concept is to take expression profiles for diseases and try to find drugs which appear to generate the opposite transcriptional pattern, with the theory that the drug could nudge the disease pattern back to a normal state.  This is an idea which has been kicking around for a while, and at one time was the focus of a number of companies.  One was even trying to re-position a drug I have a small connection to (MLNM developed it from a target I spotted in an EST library), but I believe that is a dead effort.  One challenge in tracking this field is that it is rarely obvious what happened in the end; did a drug fail to pan out or did the backers just run out of cash?

Names in Collision

I will claim that I saw this coming, in that I've toyed with the basic skeleton of this post before.  But, I hadn't gotten around to it -- but how could I miss this opportunity.  On a mailing list devoted to SAM, someone asked about a related topic to SAM, and one of the experts on the board replied with an electronic head-scratching

Ion Throws A Long Punch At MiSeq

The benchtop sequencer wars are heating up!  Illumina and Life are engaged in a fierce war of pamphlets and datasets to convince the world that they have the edge.  I won't attempt to give a complete play-by-play, but hit on the latest developments, which includes Ion releasing a dataset of 250+ bp reads.

How Many Toes Does Ion Have Left?

I've previously complained about Ion Torrent's bungling and secrecy when it comes to educating their current and potential future users about key technical information.  I've recently come across yet another botch, one that underscores that attempting to control information in the Internet age only serves to distract from the goal of ensuring access to correct information.

Tschuess, Shuttle!

Clearly with a week having passed since touchdown, my farewell to the space shuttle program is grossly overdue.  I actually missed watching the event live, as I was off on a camping trip in some beautiful New Hampshire woods.  

Atop of the usual excuses, it's been a bit hard to figure out what I could write that was different than so much that has been written.  It would seem that every major media outlet opined on the subject, and most did a decent job in hitting the key points. 

Ion's Gaggle of New Accessory Products

     Ion Torrent had a press release announcing a number of new components to the platform, as well as shipping of the 316 chip and a drop in price of the original 314 chip to $99 (alas, the announcement was not synchronized with updating the online store, so no details could be checked -- such as the price of the 316 chips).

PacBio's Foray Against the German E.coli Outbreak

    I recently remarked that it was surprising that PacBio had not jumped on the German E.coli outbreak strain, given CEO Eric Schadt's professed interest in biosurveillance.  Dr. Schadt was kind enough to spend a half hour discussing the topic with me last week, in the wake of PacBio releasing de novo assemblies of this strain and 11 other pathogenic E.coli strains (6 having never previously been sequenced) on the PacBio DevNet website. Dr. Schadt also has a detailed blog post on the project.

    In both the blog post and our conversation yesterday he explained why PacBio wasn't in the forefront of this effort but still decided to jump in. Dr. Schadt was certainly aware of the outbreak; he was in Germany at a conference when the public alarm was building. But initially, the company was trying to stay focused on the commercial launch of their instrument. However, after seeing the first public assembly come out at several thousand contigs, they consulted some academic collaborators and decided to run their own sequencing, with a goal of providing a much less fragmented assembly.  The initial thought was a hybrid assembly containing both PacBio and short read data, but after another group generated a high quality short read assembly the emphasis switched to a PacBio-only assembly.

     Sequencing proceeded rapidly, as before; about 2 days from receipt of the samples to generation of data for assembly.  Three machines were enlisted, using current generation SMRTcells but with pre-release polymerase and protocols (these are scheduled to go to customers by year's end). A number of eye-popping statistics are shown: mean mappable reads of 2.5-3Kb, 5% of the reads at 6-7Kb or greater and one herculean read of almost 23Kb!  Yield from the SMRTcells was variable, ranging from a mean per sample of 13K to 55K (overall mean of 26K).  Raw accuracy was still about 85%.

     For the German strain, both a large insert library and a small insert circular consensus library were sequenced.  One challenge that the PacBio team ran into is rapidly generating a DNA population of defined size which is bigger than about 9Kb.  The populations must have a restricted size range, or else the smaller fragments are preferentially loaded into the zero mode waveguides where the sequencing actually takes place.  Due to this, the value of the monster reads was diminished.  Indeed, Schadt sees this leading to PacBio's inability to drive their data to a single contig (the main chromosome is broken into 33 contigs); there simply weren't reads able to bridge some very large repeat elements.  This also is why they didn't use the strobe sequencing mode, which generates islands of sequence separated by statistically-defined gaps.  Given that so many of the reads were approaching the size of the inserts, strobing wouldn't do much good.

    Not very far back, I presented a somewhat bearish case for PacBio.  Do the latest results change this? As much as I love the technology and the idea of long reads, I'm still concerned that too many scientists will see these as a nice-to-have and not a must have.  Dr. Schadt mentioned they are working on projects to demonstrate PacBio sequencing of much larger (100+Mb) genomes, which is an important start.  Still, it may be that few labs will see the incremental value of long PacBio reads as not important enough, or that they simply don't need to invest in a machine but instead rent some of the existing capacity (I know of two service providers offering the system).  As PacBio pushes the reads longer and longer (imagine if 5% of the reads were 20+Kb!) it will offer advantages for closing long gaps.  For example, PacBio should require relatively little DNA for library construction, whereas some of the competing mate-pair techniques are notorious for being very inefficient at converting input DNA to usable fragments (as well as creating some level of noise from chimeras generated in ligation steps).