Chatting Apton Acquisition with PacBio CEO Christian Henry
PacBio CEO Christian Henry chatted with me recently by teleconference on a variety of topics, but the focus was the recent PacBio acquisition of Apton Biosystems for $85M in equity.   As a regular reminder, my employer’s CEO reports in a sense to Henry, as he’s on the Board of Directors.  A particularly interesting revelation by Henry is that PacBio had its eye on Apton in late 2021, essentially as soon as they completed theOmniome acquisition announced in July 2021 that formed the foundation for their now-released Onso short read instrument.     PacBio believed then that the desktop instrument design from Omniome...
Source: Omics! Omics! - September 19, 2023 Category: Bioinformatics Authors: Keith Robison Source Type: blogs

Two More Automation Partners Join PacBio Compatible Program
A significant challenge for the long read sequencing vendors has been that short read sequencing has a decade and a half head start in evolving a tools ecosystem.   New entrants such as Singular Genomics and Element Biosciences can take the strategy of building short bridges to existing tools designed for Illumina whereas the long read players must often build anew, as tools and protocols sufficient for short reads often are lacking performance on long reads .  At J.P. Morgan in January, PacBio had announced a PacBio Compatible program to highlight products which specifically support PacBio sequencing.  This morning, tw...
Source: Omics! Omics! - September 7, 2023 Category: Bioinformatics Authors: Keith Robison Source Type: blogs

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 $110M, with $85 paid now in PacBio stock and the remaining $25M"stock and cash add-ons" according to GenomeWeb (premium/free via ex-Twitter) - so presumable based on certain milestones being met.   Read mor...
Source: Omics! Omics! - August 4, 2023 Category: Bioinformatics Authors: Keith Robison Source Type: blogs

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.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - July 31, 2023 Category: Bioinformatics Authors: Keith Robison Source Type: blogs

Price ’ s Protein Puzzle: 2023 update
One of the joys (?) of having been online for…quite some time now…is watching topics reappear every few years or so. What is the longest coherent word or phrase present in the amino acid sequence of a real protein?— Dr. Caroline Bartman (@Caroline_Bartma) July 21, 2023 Yes, it’s Price’s Protein Puzzle which I last wrote about back in 2019. The good news is that my code still runs, so I’ve updated the results of an English word search versus the UniProt Reviewed (Swiss-Prot) protein database. Just for fun I threw in a few other languages too. So what’s new? In terms of...
Source: What You're Doing Is Rather Desperate - July 26, 2023 Category: Bioinformatics Authors: nsaunders Tags: bioinformatics statistics algorithm amino acid rstats search words Source Type: blogs

The “ curse of the bye ” revisited
A while ago we looked at Geelong and the curse of the bye. And since the AFL media have outdone themselves this year with “curse of the bye” articles: see for example here, here, here and here, I decided to revisit the topic in more depth. If you like that kind of thing head over to the report at Github. It has lots of charts like this one. Executive summary: once you take into account scheduling and expected results, there’s little if any evidence for significantly more losses coming off a bye round. I doubt that will prevent the same spate of articles next season. (Source: What You're Doing Is Rather Desperate)
Source: What You're Doing Is Rather Desperate - July 10, 2023 Category: Bioinformatics Authors: nsaunders Tags: australia sport statistics afl bye rstats Source Type: blogs

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 momenta rily 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).Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - June 12, 2023 Category: Bioinformatics Authors: Keith Robison Source Type: blogs

London Calling 2023
Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - June 6, 2023 Category: Bioinformatics Authors: Keith Robison Source Type: blogs

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 beeninteresting  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.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - May 17, 2023 Category: Bioinformatics Authors: Keith Robison Source Type: blogs

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 m...
Source: Omics! Omics! - March 21, 2023 Category: Bioinformatics Authors: Keith Robison Source Type: blogs

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 mixe...
Source: Omics! Omics! - February 21, 2023 Category: Bioinformatics Authors: Keith Robison Source Type: blogs

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'...
Source: Omics! Omics! - February 5, 2023 Category: Bioinformatics Authors: Keith Robison Source Type: blogs

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.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - January 31, 2023 Category: Bioinformatics Authors: Keith Robison Source Type: blogs

Has your knowledge stopped updating?
Some years ago I read an article – I forget where – describing how our general knowledge often becomes frozen in time. Asked to name the tallest building in the world you confidently proclaim “the Sears Tower!”, because for most of your childhood that was the case – never mind that the record was surpassed long ago and it isn’t even called the Sears Tower anymore. From memory the example in the article was of a middle-aged speaker who constantly referred to a figure of 4 billion for the human population – again, because that’s what he learned in school and had never mentally ...
Source: What You're Doing Is Rather Desperate - January 27, 2023 Category: Bioinformatics Authors: nsaunders Tags: education R statistics readr read_csv rstats tidyverse Source Type: blogs

Editing metadata in trail camera images using R, magick and exiftool
I have a new hobby: camera traps, also known as trail cameras. Strapped to trees in my local bushland they sit in wait, firing automatically when triggered by a passing animal. Once in a while, something quite magical happens. The camera model I chose is the Campark T85 which for me, had the right combination of features and price point. One useful feature is the ability to transfer images and video to a phone wirelessly (albeit through a rather clunky phone app). Unfortunately, images retrieved in this way have one major flaw: an almost-complete absence of metadata. There is no GPS in the camera of course, but th...
Source: What You're Doing Is Rather Desperate - October 25, 2022 Category: Bioinformatics Authors: nsaunders Tags: environment programming statistics campark exiftool metadata photography rstats trail camera Source Type: blogs