Thursday, December 31, 2015

Closing the books on 2015

The last line of Perl has been written, the last SQL select executed. As 2015 draws to a close, I want to extend a thank you to everyone who has read this blog, commented on it here or over on Twitter, followed me on Twitter, engaged me on Twitter, or any of the other myriad of ways that suggest that what I write and tweet is of interest to others. It is very rewarding to know that others find this space engaging, and I hope to continue to earn your attention and time.

So long 2015.  I mustered a bit more resolve this year than previous years, hitting the 5th most number of posts for a full year (which should make it the median). 2016 promises to be an exciting year in the sequencing and genomics arena and I will try to both up the frequency and reduce the variance in the frequency of these posts -- ideally while improving the quality.  Will I succeed -- only you, the reader, can score the quality aspect.

Loose 2015 Threads #2: Thanks for the help with bootstrap values

I owe a belated thank you to everyone who responded to my post on my muddled thinking around phylogenetic tree bootstrap values.  I think I'm straightened out now and even dare to think I can explain this to someone else. 

Wednesday, December 30, 2015

Loose 2015 threads #1: MiSeq 2x300 Issues

Before 2015 ends, I'd like to tie up two loose threads.  In doing so, I'll deviate slightly from my usual pattern and publish two posts in a day; I could have lumped them together but instead I'll split.  First up, a belated explanation, prompted by a comment, of my mention of issues with the MiSeq 2x300 reagents and a bit more on my confusion with regard to bootstrap values.

Monday, December 28, 2015

Thoughts on the Synthetic Biology of Seveneves

Neal Stephenson's Seveneves is a sprawling space novel of truly epic ambition and scope, which I enjoyed thoroughly.  I'm not going to review it or give a detailed plot summary, but there are aspects related to the biology angles which interest me enough to scribble -- which means I must reveal some key plot points.  I've grown increasingly sensitive to spoilers and (yo Charles Schulz's ghost: thanks for wrecking Citizen Kane for me at a young age!) for myself prefer to go into a major book or movie as cold as possible.  So, if you haven't read the book and were planning to do so, please don't jump beyond the jump break.  If you do, don't blame me for any reveals!

Friday, December 11, 2015

MinION and Time-to-Result

Peripatetic blogger Dale Yuzuki posed a question on my last piece which I'll answer with a separate post because it crystallizes for me what makes the Oxford Nanopore platform so different for a large number of counting-type assays.  Dale's question was on Zev William's talk on pre-implantation screening and the number of reads required.

Monday, December 07, 2015

MinION Community Meeting 2015: Reflections & Wrap-Up

I spent the end of last week at the New York Genome Center for Oxford Nanopore's MinION Community Meeting 2015.  Since the family joined me for the weekend, I let my thoughts simmer for a wrap-up.  Plus I've been spending time scrutinizing the complementary "pen" for a USB connection and sample port, with no luck.  Wisely, I've given up on that -- so I can start the same process with the "notepad".  I've also finally stopped looking over my shoulder for a pitchfork-and-torch crowd after my numerous Twitter miscues, ranging from omitting speakers' names and affiliations to various mutations of the official hashtag (when I remembered any hashtag).  For a slightly better synthesis of the Twitter stream, see my Storify.

Monday, November 30, 2015

Admitting to Ignorance on Interpreting Bootstrap Values

Okay, one of the points of this space has always been to crowdsource the project of educating myself, which also means on of the underlying principles is that I sometimes need to admit ignorance in a very public manner.  After staring at a lot of phylogenetic trees, I've sufficiently unglued my confidence in my deep understanding of the principals (beyond coming just plain unglued) of confidence / bootstrap values.  Despite trying a number of sites and reviews and threads on the Net, I can't quite find a detangling of the particular mental knot I've tied, so I'm throwing out the problem for group help.

Tuesday, November 24, 2015

Well, that was brief!

BGI news today is that they are jettisoning the Revolocity large sequencing system, announced all the way back in June.  Along with the product abandonment, 40% of the ex-Complete Genomics group in the Bay Area is being laid off, with remaining staff focusing on the desktop BGISEQ-500 sequencer.

Monday, November 16, 2015

Do Demons Dream of Phylogeny Packages?

Miserable day today  - spent my entire day wrestling with bad formats and flaky tools and trying to bull my way past them, leading to many a mad expostulation. The whole day down in the pit, with the pendulum of multiple deadlines swinging just over my head. The MBTA released new schedules that muck with my routines.  And the then to top it off, Mick Watson writes a piece titled "The Five Habits of Bad Bioinformaticians" that cuts far too close to home.  So I arrived home in a foul mood, my senses unpleasantly heightened to every sound.

Wednesday, November 04, 2015

Comments on "The use and misuse of supplementary material in science publications"

Mihai Pop and Steven Salzberg have an opinion piece in BMC Bioinformatics titled "Use and mis-use of supplementary material in science publications", examining issues arising from the ever growing data supplements accompanying papers, particularly in high-profile journals with strict article length limits.  Pop & Salzberg make a number of important points, but there are some topics they didn't cover that I think are also worth treatment.

Saturday, October 31, 2015

HelicosTech Back on the Dance Floor?

It's Halloween, and as is my habit I fired up Saint-Saëns, As death tunes up his violin in a graveyard, the dead residents live again and dance with abandon, until the rooster (oboe) crows in the dawn. In a similar vein, a pre-print on bioRxiv has demonstrated new life in the Helicos single molecule sequencing platform, though while the platform stopped being commercially distributed (and Helicos went bankrupt just under 3 years ago), a scrappy little company called SeqLL has kept up a service business.  A new Chinese company called Direct Genomics, with two Helicos founders onboard, plans to commercialize the new version of the technology.

Tuesday, October 27, 2015

BGI Launches the BGISEQ-500

This weekend brought the formal launch of the BGISEQ-500 desktop sequencing instrument from BGI (though deliveries won't begin until early next year).  Utilizing the ex-Complete Genomics ligation technology also used in the Revolocity system, the instrument appears to sport a price similar to the Illumina NextSeq but offers throughput somewhere running from a NextSeq up to the low end of a HiSeq. Two flowcells can be run at a time (apparently in sync with each other, unlike QIAGEN's long-delayed machine), with a small and large versions of the flowcells.  There's some ambiguity on questions such as the precise read length, though it is very short compared the the typical Illumina offerings.  Dale Yuzuki has a nice write-up (complete with a picture next to the box) based on attending the International Congress of Genomics 100 where it was unveiled.  One of these days I should wangle my way to that conference -- not only would the genomics be fascinating, but China holds a special allure -- or more specifically, Ailuropoda, for our household.

Wednesday, October 21, 2015

Concepts for Better Sequencer Calibration

Last week's release of the MARC data for the Oxford Nanopore MinION rebooted a train of thought I've had around DNA samples used as standards.  Ideally, standards would meet a number of criteria, though some of these may be inherently in conflict and there are issues of practicality. But as a whole, the standards used for molecular technologies are often short of ideals in ways which could be addressed, as I will attempt to argue here.  While many of my comments will be placed directly around MinION, many apply to other platforms -- as would solutions I have been contemplating.

Tuesday, October 20, 2015

Dovetail Takes Flight

Back in March I covered the unveiling of Dovetail Genomics' approach to scaffolding genomes via deriving long distance constraints from reconstituted chromatin.  This morning the company announced full access to their genome sequencing and scaffolding service.   Founder Ed Green and CEO Todd Dickinson chatted with me by phone last night about this launch.

Dovetail's offering is a complete service for sequencing or scaffolding large animal or plant genomes.  Users can choose from a menu of service components, which can range from scaffolding an existing short read assembly for around $10K to a complete genome sequencing and scaffolding for around $40K, with a turnaround in either case of 6-8 weeks and scaffold sizes on the order of chromosome arms.  

Since the beta program opened in the spring, Dovetail has worked to streamline both their wet lab and informatics protocols as they completed over 45 different customer projects.  Of particular note is that the input DNA requirements are down from 5-10 10ug to 1-2ug.  However, the Dovetail team agreed with my comment from before that with their current markets, de novo sequencing and structural variant calling on known genomes, input DNA has not been a serious constraint.  They do believe they can substantially reduce the requirements further, perhaps to a few hundred nanograms.

While the service offerings can include users supplying their own high molecular weight DNA, Dovetail prefers to perform the extractions in house.  The logic here is simpler: results are critically dependent on the size of the input DNA.  As a result, Dovetail has spent great effort becoming expert in extracting DNA from a wide variety of different species and sample types, as well as using pulsed-field gel electrophoresis for DNA quality control  

Dovetail is currently offering their Chicago technology only as a service, which has obvious advantages.  Anyone who has attempted technology transfer will know how difficult it can be to make a process consistently repeatable at multiple sites, not to mention the variances that can easily creep in due to the vagaries of shipping.  Aspects of this can be seen in the recently released MARC data for Oxford Nanopore.  For users, a pure service offering means no learning curve and no equipment purchases; just turn over some biomass to Dovetail and wait for a high quality genome to be returned.

That doesn't mean kits aren't in on the horizon; Dovetail does plan to offer them at some future point.  Also in future plans is expanding the service offerings to include metagenomes and haplotype calling. In the nearer term, a publication describing the scaffolding of a human sample (NA12878) and the American Alligator genome, which Dovetail has discussed in the past, is "well along" the publication pipeline.  While the current offering is based on Illumina sequencing technology, Dovetail emphasizes that the technology itself is platform-agnostic.  In a similar vein, when asked about how Dovetail differentiates themselves from the growing swarm of long range technologies, including Oxford Nanopore, PacBio Sequel, BioNano Genomics, and the now-launched 10X GemCode, their team praised the field  as full of exciting technologies, but emphasized that they offer the ability to scaffold complex genomes very fast with no specialized equipment and no new techniques to learn..

Personally, a pure service offering is very attractive, since that means not having to find internal resources to learn the new technology and then execute on it. I checked with Dovetail, and while I don't have $40K burning a hole in my pocket, if I did I could grab something out of the garden or from the local seafood market, I really could have a complex genome scaffold of my very own in about two months.  That's an exciting vision, and perhaps will be a major force in the sunsetting of science's tolerance for highly fragmented draft genomes.

Monday, October 19, 2015

MARC spots the Ox(ford)

Last week's end brought the initial report from MARC, the MinION Analysis and Reference Consortium, detailing a body of experiments intended to benchmark the performance and consistency of the Oxford Nanopore MinION sequencing device.   The MARC paper is also the inaugural research article in F1000's new channel for nanopore papers.

Thursday, October 01, 2015

PacBio Sequel: Smaller Box, Bigger Bang

Boy, am I regretting taking a vacation from online due to being engrossed in A Canticle for Leibowitz.  Between last night and this morning, my neglect of my Twitter feed meant a colleague tipped me to the new PacBio machine with "what's this Sequel I keep hearing about from PacBio".  So a lot of folks had a huge jump and covered it pretty well, including Keith Bradnam, Mick Watson, and James Hadfield.  Long rumored, the new instrument costs about half as much (but that's still $350K), takes up much less floor space (and doesn't need any reinforced floors) yet the new flowcells deliver about 6 7 times as many reads than the older ones.  WOW!

Thursday, September 24, 2015

Farewell Nabsys

A bit over a week ago brought news that mapping instrument hopeful Nabsys had ceased operations.  As a veteran of one failed biotech, I have a lot of sympathy for the team there. Plus, I knew a bunch of folks at the Providence RI firm.  Nabsys's signle molecule mapping technology was a wonder -- what single molecule technology isn't? Already stories are emerging of a disgruntled founder who wants to buy up the intellectual property and give it another go. It is easy to admire that stick-to-it spirit; it's a lot harder to find a rational reason to believe that such a revival will be any more successful.

Thursday, September 17, 2015

How Do You Differentiate Archea and Bacteria in the First Week of High School Biology???

I have a long standing interest in biology education -- I seriously considered it as at least a career to explore -- but now I really have skin in the game.  TNG just executed a schedule move that will defer his biology this year to the second half of the term, but I also have a niece who is taking AP Biology at her STEM high school.  Even in his short time in biology class, TNG has succeeded in asking for homework help that has me scratching my head.

Wednesday, September 09, 2015

Freely & Unrepentantly Confessing to Heresy

Keith Bradnam reported a huge influx of traffic for a recent post -- not surprising, since he labeled it NSFW (Not Safe For WorK).  And yes, despite my skepticism that it would be truly offensive, I'll confess I checked it with phone, not my work laptop.

Tuesday, September 01, 2015

Ion's S5

The Ion Torrent team rolled out a new sequencer line this morning, the S5.  The S5, whose impending release had been tipped on the internet by the leak of a manual, arrives in two models, the standard and the XL, which differ only by on-board computing power and not sequencing metrics.   As has been the trend, Ion's focus is entirely on focused sequencing, and the new lineup emphasizes making targeted sequencing with AmpliSeq and other approaches fast and simple.

Wednesday, August 26, 2015

The Road to Hell is Paved with Bioinformatics Formats

If you really want to raise a bioinformaticist's blood pressure, loudly declare your new tool generates output in brand new data formats.  This leads to the frequent observation that a large fraction of bioinformatics work is simply converting formats. It is probably consensus that the field is awash in too many formats, though it is equally clear that we can't agree on which should survive.  Between some recent news and a Twitter thread on the subject that erupted last night, there was a bunch of fodder for me to collect in a Storify -- and to lay out my own idiosyncratic views.

Monday, August 24, 2015

Do Helix's Numbers Work?

A number of efforts in the consumer genomics space have been attempted in the past, with 23andMe appearing to make limited headway and Knome not much at all.  I haven't been able to get any investment interest in my own concept, though perhaps that's because it was tongue-in-cheek (or tongue held out while panting).  Last week brought a big splash, with a new company Helix launching with $100M and three major players as backers: Illumina, LabCorp and the Mayo Clinic

Friday, July 10, 2015

Clinical Metagenomics Pipelines: Revisiting & Reflecting

When I set out to start this blog nearly over eight years ago, I set myself a number of goals.  One goal was to take some risks -- not crazy risks but to not just play it safe.  But counterbalancing that goal was one to be open, accurate and honest. My piece last week on clinical metagenomics pipelines had a fair amount of attention, and resulted in an ongoing electronic conversation with one of the key parties.  In the course of this, there are now parts of that piece I wish I had handled differently. Some other important topics have been raised, and I would like to cover here.

Thursday, July 02, 2015

Leaky clinical metagenomics pipelines are a very serious issue

Update: Some significant issues with the tone of this post are discussed in a follow-up.

I am a firm believer that the practice of science is the result of contingency; we do not necessarily have the best scientific culture possible but rather one which has evolved over time driven by chance, necessity and human nature.  We should never hesitate to re-examine the way science is actually practiced, and that particularly holds true for how we analyze data and publish results.  A re-analysis of a prominent Lancet paper has just come out in F1000, and this work by Steven Salzberg and colleagues illustrates a number of significant issues that slipped past the conventional peer review publishing practice

Tuesday, June 30, 2015

June 2015: Busting Out All Over with Genomics Technology

This month I again entered the prime of my life, though next year my programming brother points out that next year I (and the first Apollo manned missions) hit the big 30.  Beyond my personal milestone, it's been a busy last couple of weeks on the genomics technology front. Despite a lack of conferences or other traditional venues, big news has poured out from Pacific Biosciences, BioNano Genomics, Genapsys, BGI (which had another announcement earlier in the month), 10X Genomics and a pair from Oxford Nanopore.

Monday, June 08, 2015

BGI Unveils a Sequencing Factory to Go

When I was in George Church's lab, he submitted a grant proposal (which, alas, was not funded) for a sequencing factory to generate one megabase of data per day.  In those days that was an ambitious goal, and the plan would have truly been on a factory scale, with a large workforce and an assembly line of stages to yield the final product of data.

Tuesday, May 26, 2015

Is Illumina Serious About an Alternate Chemistry for the Rapid Amplicon Market?

Back in January, at the end of my post on Illumina's new machine lineup I speculated whether Illumina might see a niche for a lower cost, lower throughput sequencing system that would slot below the MiSeq in their lineup.  Such an instrument, I posited, might go after applications in biosurveilance and diagnostics where relatively small amounts of data are needed quickly. I speculated that perhaps a smaller instrument with less expensive optics could compete in this arena, which is heating up due to Oxford Nanopore and the growing acceptance of DNA-based diagnostics.  As luck would have it, a few days later Molly He, Mostafa Ronaghi and colleagues at Illumina actually published a proof-of-concept paper for just such an instrument.  Unlike many sequencing technology PoC papers, this one demonstrates feasibility of reading actual templates (phiX rides again!). 

Wednesday, May 20, 2015

London Calling Wrap-Up

The second, and final, day of Oxford Nanopore's London Calling conference concluded last Friday -- and I'm behind on writing it up.  Some of that was due to travel (and the wrong power supply going on the trip) and post-trip exhaustion, but failing to finish this last night was pure slacking. That route was shut down when one reader asked when I'd get things done.  Anyway, I again organized the activity into a storify story as I did for the first day of the conference. I'm going to go into less detail on individual presentations below and instead engage in the vice of far-ranging speculation.

Friday, May 15, 2015

London Calling Day 1: Highlights

Oxford Nanopore's London Calling conference kicked off today; I've Storified a large collection of Tweets from it, covering today up through about dinner.  I'll summarize some highlights below

Wednesday, May 13, 2015

Oxford Nanopore's London Calling: Pre-meeting speculation

Oxford Nanopore's London Calling confab starts up in a matter of hours.  Alas, several issues scotched my plans to attend (not only does it promise to be an exciting conference, but I simply love exploring London on foot).  It is worth emphasizing that the MinION devices and consumbables have been out in the wild for not quite 11 months at this time.  In that time, Oxford has dealt with a wide variety of technical and logistical headaches. While performance is still variable, many MAP participants are forging forward and the available tools for nanopore data continue to grow.  London Calling will likely bring a burst of new announcements; Oxford's Clive Brown has been giving talks recently but has promised that exciting stuff has been reserved for the confab.  Below is a set of semi-informed speculations calling out likely happenings, mostly based on Clive's recent presentations and tweets.

PacBio's New Sample Prep Plan: Too Late to the Dance?

Pacific Biosciences had a string of announcements around its earnings release last week.  Of particular interest is a collaboration with RainDance to develop a new sample preparation system for generating long synthetic reads from minuscule inputs.  If some of that sounds familiar, the loose outline in the press release suggests an approach similar to that of 10X.  But is this proposed system arriving too late to the party?

Monday, April 27, 2015

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

Monday, April 13, 2015

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 YcasBenno Müller-HillMonica 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.

Tuesday, March 31, 2015

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?

Tuesday, March 10, 2015

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.

Monday, March 09, 2015

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. 

Saturday, March 07, 2015

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?

Wednesday, March 04, 2015

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?

Saturday, February 28, 2015

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.

Friday, February 27, 2015

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.

Wednesday, February 25, 2015

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

Sunday, February 22, 2015

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!).

Saturday, February 21, 2015

#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.

Wednesday, February 11, 2015

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)

Saturday, February 07, 2015

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.

Monday, January 19, 2015

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.

Sunday, January 18, 2015

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.

Wednesday, January 14, 2015

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.

Monday, January 12, 2015

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.