A computational biologist's personal views on new technologies & publications on genomics & proteomics and their impact on drug discovery
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 $1K 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".
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