Friday, August 04, 2023

Apton (Super) Resolution to Be Acquired Fulfilled by PacBio

Wednesday night brought the news that Pacific Biosciences has both officially launched their Onso desktop short read sequencer and bought technology for a high throughput version of it by acquiring Apton Biosystems.  Apton had been developing their own short read chemistry and an instrument based on super0resolution imaging to go with it and was apparently relatively close to launch.  PacBio got Apton for 110ドルM, with 85ドル paid now in PacBio stock and the remaining 25ドルM "stock and cash add-ons" according to GenomeWeb (premium/free via ex-Twitter) - so presumable based on certain milestones being met.  

Monday, July 31, 2023

Overheard in a Thai Restaurant

An amusing incident happened on the Sunday of Memorial Day weekend that is a reminder that even when there are no walls the walls in the Boston area can have biotech-tuned ears.  Oh, and a funny quirk of fate that I swear I'm not making up.

Monday, June 12, 2023

Illumina: Where Was the Board?

Sunday brought news that Francis deSouza had resigned as CEO of Illumina.  It at first might have seemed he had survived the boardroom challenge from activist investor Carl Icahn, losing only one ally - Board Chairman John Thompson.  But that apparently effectively made him a lame duck, and he is now leaving immediately -- leaving no one at the helm of Illumina momentarily but also eliminating any interference from deSouza with the installation of his successor.  If you have access to STAT+, Matt Herper's commentary is very informative (I'd expect nothing less).

Wednesday, May 17, 2023

Called Back To London Again

After a too long pandemic-induced hiatus, I'm in the UK for this year's edition of London Calling.  I talked myself out of going last year well in advance, which would have been interesting as my rapid tests were still coming up positive about the time I would have needed to fly from Boston over the Atlantic.  And while I've been watching remotely, I've been dismal over the past year in actually writing anything about it.  Which was foolish on my part as ONT has been going through an interesting transition.

Tuesday, March 21, 2023

Thoughts on Unexpected Sequences Found In COVID mRNA Vaccines

Writing this piece is not easy, not only because the topic matter is completely in controversies around SARS-CoV-2 and the vaccines for it, but because the data was generated by someone whose outspoken opinions on any COVID-19 public health topic are nearly always ones I find myself in opposition to.  Someone who periodically lobs my way personal attacks on my ethics.  It doesn't help that these results will be certainly misused to attempt to undermine public confidence in the vaccines, or that this post will probably attract a lot of commentary that I don't wish to address because of the adage that generating misinformation takes far less energy than rationally correcting it.  But, data is data and in the end I believe that whatever our differences, the data generator is not someone who would construct a hoax.  And in any case, the results can be checked, so if somehow it were a vicious hoax that could be exposed.  And importantly, I feel that what has been found should be discussed, as no advanced technology is ever perfect - these results I feel suggest new standards for the design and implementation of mRNA therapeutics.

Tuesday, February 21, 2023

Is Illumina Delivering the MVP of Long Reads?

At AGBT last week Illumina released additional details on their still incubating Complete Long Reads (CLR) product (formerly known as Infinity) but is still holding back both some interesting technical information as well as exact performance specifications.  Illumina is already floating some of their marketing messages, which in some cases are dependent on some of those still-in-flux specifications and some of the claims may not withstand careful scrutiny.  And Illumina continues to make statements that irritate anyone with deep technical knowledge of the long read space.  The reaction by attendees was definitely mixed - one long read aficionado even offered me a very spicy title suggestion for this entry.  Alas, I can't use it, as it would be a bit of an inside joke based on a portion of a presentation that the presenter asked not be tweeted.  So instead you get the above title,  which may not be what you think. 

Sunday, February 05, 2023

What's AGBT Like?

AGBT begins in less than 24 hours, and the signs are everywhere here at the Diplomat Resort in Hollywood Florida.  I arrived Friday with family, and the count of old friends I've chatted with is steadily climbing.  If you somehow forgot about the meeting, the insides of the elevator doors will remind you. This is the fifth time I've attended in person, plus heavy monitoring of about twice as many via Twitter.  It's one of the premier events of the genomics conference schedule, and if you haven't been it's certainly fair to ask why?  Or whether you would want to go to a future edition?  So I'll try to capture what makes AGBT so irresistible to many but also why it just might not be your cup of tea

Tuesday, January 31, 2023

AGBT 2023 Is Nearly Upon Us!

AGBT is less than a week away in Hollywood Florida - and I've been letting everything else get ahead of writing anything here.  The JP Morgan Conference at the beginning of this month didn't have major fireworks from the sequencing vendors, but did have some news.

Tuesday, October 25, 2022

PacBio Revio: Same Footprint, 80% The Time, 15X The HiFi!

PacBio has been rolling out announcements around the ASHG meeting and now delivers a huge one: the next generation SMRT instrument “Revio” will roll out next spring and it’s a big step up in throughput. With Revio’s 15X boost in per-run throughput over Sequel IIe, PacBio is touting this as 30X HIFi genomes for under 1ドルK sequencing consumables per genome. 

Wednesday, October 19, 2022

Better Than FizzBuzz: First Bioinformatics Problem in an Erratic Series of Indeterminant Length

Periodically in my work or during writing this blog I come across computational problems that have the aspects of making, at least in my mind, very good teaching problems.  Some of the characteristics are that the basic problem is relatively simple to explain, the skills required are reusable on other problems, the concepts are germane to other problems and that the posed problem can be expanded in steps to something much richer.  Such problems might even be the nucleus of undergraduate or even high school bioinformatics projects, though with the recent news of a high schooler sequencing his dead pet angelfish's genome the bar for high school projects has leapt a few notches! In contrast to a programming problem that doesn't fit these, I'm going to tag such posts as "Better than FizzBuzz".

Thursday, October 06, 2022

General Inception Aims to Ignite New Company Formation

A week ago, a company calling itself General Inception emerged from stealth as a new concept, which they call an “Igniter company”, to promote the formation of new life sciences company.  As described to me in a phone conversation with General Inception CEO Paul Conley, General Inception provides a range of science and business expertise and support to enable embryonic ideas to condense into functional startups.  


The igniter metaphor Conley offered me is the spark plug of a car: it is required to start the engine and continues to provide a key part of the functioning whole.  Conley extended this to say that General Inception plans to go for the ride, but let the scientific founders occupy the driver’s seat.  But another ignition metaphor occurred to me, the skill of turning a tiny spark from flint and steel into a raging campfire.  Without careful nurturing, most tiny sparks will never ignite a blaze; only with careful and staged addition of oxygen and fuel does this reliably occur.


General Inception is not a fund, Conley stressed, but structured as a corporation. The ultimate goal is to make systematic and reproducible the generally artisanal craft of discovering and nurturing new ideas – as well as sometimes terminating efforts early that do not appear successful.  


So what does General Inception offer?  First, some of the boring business functions such as quotidian finance functions such as paying bills.  Also a wide range of expertise, from access to technical experts in a diverse set of biological disciplines to persons familiar with estimating markets and development paths. General Inception has lined up Contract Research Organizations and Contract Manufacturing Organizations, but not just as contract partners – General Inception has “meaningful” equity stakes and perhaps board seats in these companies.  A key goal of General Inception is to identify key experiments which can be run quickly at these partners to test project concepts.  This might be simply reproducing results from an academic lab or perhaps running a key experiment to de-risk the project.  An example of a CRO partner is Triple Ring Technologies, which offers company incubator services and facilities both in the San Francisco Bay and Boston areas.


Interestingly, General Inception is casting a very wide net.  Any life science concept is potentially a target: therapeutics, diagnostics, tool companies, agriculture, synthetic biology or whatever else is centered around biotechnology.  Within the company there are defined practice areas: Tools & Diagnostics; Cell Engineering & Synthetic Biology; Therapeutics.  But these are intended not to be siloed fiefdoms but rather foci which overlap each other and reinforce each other. After all, so many technologies are converging - a diagnostic may require synthetic biology or a therapeutic cell engineering.  Conley believes human health will continue to grow – but non-health life sciences might grow even faster and overtake healthcare in terms of total economic value, so he is positioning the company to support company formation in all areas.


In terms of geography, not only are they scouring US labs but also in Europe.  In the latter case, the companies that emerge might have R&D remaining in Europe but commercial operations headquartered in the US.  Conley says the venture environment in Europe remains more conservative than the US, so General Inception can make a particularly large impact in Europe by helping ideas cross “the valley of death” to where a venture firm is comfortable investing in it.


Not only is General Inception stalking the halls of academia, but they are also talking to existing companies about dormant assets that might find new life in a startup. And General Inception hopes to form long-term relationships with innovators; having an idea fail early won’t be held as a demerit against the academic.  


In terms of deal structures, General Inception looks to set themselves up as a founder, with founder’s common stock.  Generally they would be funding companies at the seed or pre-see stage, perhaps taking the place of angel investors or “friends and family” investments.  Venture capital firms often demand preferred stock, which gives them first rights to the financial carcass of failed ventures - General Inception will be taking the same risk as scientific founders of not getting anything from liquidated companies.  


General Inception itself has raised 60ドルM from a set of venture capital firms. Their goal is to reach a steady state in which around 25 companies are seeded and graduated annually. General Inception also sees itself as evolving to an information business – with a large experience base of startups they hope to glean new insights into predicting what ideas work and finding the best company structures to maximize the chance of success.  Venture firms that invest in General Inception will have early access to companies incubated by the company.  Conley has been piloting the company since February 2020, refining the approach and the set of expert resources which General Inception can draw on


In my career I’ve interacted with startups in a variety of contexts - as a potential employee or consultant, an actual employee or consultant and as a potential or actual partner.  I’ve also daydreamed a rough business plan or two.  I will be the first to proffer that this is hardly a comprehensive exposure to the variety of ways that companies are seeded.  Thinking back on experiences such as Warp Drive, I can see the value of quick proof-of-concept experiments to either validate a company or simply nip off an idea that is unlikely to ever bear fruit – but I also know how complicated it can be to identify such experiments or assemble all the components to perform such an experiment.  So I’m intrigued by General Inception and wish them well, though I reserve a certain amount of skepticism that starting new companies will ever be anything other than artisanal.


Monday, October 03, 2022

Illumina Roadmap Part 2: Infinity Becomes Illumina Complete Long Reads

The Only Thing Clear About Infinity Is It Is Now Complete Long Reads. 
Illumina told us a new name for Infinity -- Illumina Complete Long Reads -- and an initial pair of products, but didn't reveal anything new about the underlying tech.  They threw out a number of claims, but very vague ones.  Particularly confusing is that it "isn't synthetic reads".  If not, then what is it?  

Wednesday, September 21, 2022

Notes From Coffee With MGI

A couple of weeks ago  I sat down for coffee with a pair of MGI representatives - American Region CEO Yongwei Zhang and Director, Global Business Development Damon Zhang. Since I hadn’t been at AGBT 2022 (my 2023 application already filed!). Yongwei and I had planned to try to catch up the next time he was in Boston area, so I braved our current subway issues (not one, but two major lines shut for extended maintenance!) and covered a range of topics.

Tuesday, August 23, 2022

SRA Entries Should Not Ever Disappear Into Thin Air

I ran into an annoying problem last night and was quite steamed, but had the discipline to wait until morning to vent publicly about it.  Now I'm more in a morose mood on the subject, not furious but still quite frustrated. The quick version of what happened is I'm belatedly trying to go through some nicely documented reproducible analysis code to explore some concerns I have with the analysis, and the code is working on an SRA entry -- and that SRA entry is the entire point of the analysis. And that SRA entry which I know once existed now doesn't - other than this code and the preprint to go with it, it's as though it never existed -- which is terrible.  And I'm irritated with everyone who contributed to that terrible result, starting with NCBI

Tuesday, August 16, 2022

Supply Stall Slows Singular

Singular Genomics reported earnings last week and delivered an unpleasant surprise: inability of suppliers to make timely deliveries of key (but unspecified) hardware components have slowed G4 instrument production to a very slow crawl.  Given the lively competition in the desktop short read space, this is a serious setback for Singular's commercial launch.  

Thursday, June 23, 2022

AGBT 2022: Overhanging Questions

AGBT broke up a couple of weeks ago and I've failed to write anything here so far.  It was frustrating not attending, but not registering for a meeting in February seemed prudent given the pattern of COVID waves - I hadn't considered (nor would have wanted to bank on) AGBT organizers reacting so well and rescheduling the meeting.  It sounds like a number of attendees did catch the virus at the meeting -- though I'm presumably still quite protected by my infection a month earlier.  Anyways, I'm going to organize this around one to two questions that hover in my head for the different sequencing providers.  AGBT also had a strong spatial angle, but I feel ill-equipped to cover that in the absence of being on the scene -- I don't work with spatial data and so don't have a deep feel for it.  As always, please flag me here or on Twitter or by email for any errors I made -- or any juicy sequencing company gossip you wish to share!

Wednesday, June 08, 2022

Admin: Feedburner to Follow.it Switch

A bit over a year ago Google made one of their dreaded announcements that they would be slowly killing off one of their acquisitions, in this case FeedBurner.  Well over a thousand of you have been using FeedBurner to follow me via email.  Follow.it has a wonderful free plan that can take over all of the previous functionality and I could just import the old subscription list
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