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Omics! Omics! 02/13/2020 22:39
There's a that is well worth reading, even if you don't use Julia or I'd argue if you don't actually program. It looks at an issue of performance that was raised with BioJulia and with fierce but respectful passion examines the critique and explores just why BioJulia didn't perform well in the comparison. In the end, this triggers a code review and a huge speed increase in the problematic areas -- which will widely benefit BioJulia users.
Omics! Omics! 02/11/2020 22:06
My qPCR explainer seems to have done relatively well, though it took some refinement after readers caught a number of errors. The most embarrassing of those is that I got my PCR ramp units upside down, so instead of 4 seconds or so per degree C it's degrees C per second so my times were off by a factor of 16! Ouch! Despite that miscue, I'm here going to explore some of the variants on PCR that are out there, including some that are being employed searching for the newly renamed COVID-19 virus. Included here are some of my own speculations and musings, so as always remember I'm someone who thinks about these things and sometimes talks other people into running them, but I haven't set up a PCR in 8 years. Also, the field of PCR variations for.
Omics! Omics! 02/01/2020 21:55
I've gotten in a number of Twitter threads and seen a lot of Quora questions about the qPCR test for the Wuhan coronavirus that I realized would really be best handled by writing an explainer. I'm intending it for financial types, reporters and anyone from the lay public interested in learning a bit more. For most regular readers of this blog, there won't be anything new to you. If you'd check me for accuracy, I'd be grateful but perhaps many will skip over this one. That also means I going to try to resist my usual urges to make lighthearted references to popular culture; they're a good way to be confusing.
Omics! Omics! 01/30/2020 22:53
A notion dawned on me when I was mentally planning g, but I decided to put off fleshing it out until a later date. After a bit of procrastination plus a crush of other ideas, here it is: Oxford Nanopore flowcell lineup has been a bit complicated for a while, but it's probably going to get worse. There's always been serious issues with the current level of complexity and it's hard to believe this will do anything but escalate.
Omics! Omics! 01/27/2020 22:31
Homopolymeric sequences have never been easy for any sequencing platform, but single molecule sequencers struggle the most with this. Oxford Nanopore has made remarkable strides in both raw an consensus accuracy via chemistry and software improvements, but still is challenged by systematic problems with homopolymers. The R10 series of pores is intended to significantly improve performance by having a longer narrow region to interact with more bases, and at the Nanopore Community Meeting there were several slides touting improved performance. Nanopore's slides have an X-axis that goes to 8. By happy circumstance, around that time we generated a large dataset on R10 and got results very similar to ONT's. Plus there's a available from Mads Alb.
Omics! Omics! 01/26/2020 19:55
I've made a few references recently to TELL-Seq, both in (I missed a key business development in their raising $18M in October; I stand by the science comments and fear that the fund raise buys them about a year of time) and on . Now to actually dig into that technology -- a bit late given the , but better late than never. So put on your , conjure up the image of and key up the , because here I go.
Omics! Omics! 01/23/2020 22:38
When playing with the structure of this piece in my mind, it occurred to me that Norman Maclean's apply just as well to biotechnology companies. It is also interesting that thoughts about fishing are often carried on in dialogue form where Hope and Fear -- or, many times, two Fears -- try to outweigh each other. The executive team at may well be gripped by this situation, as they are faced with two great perils: their finances and their markets.
Omics! Omics! 01/22/2020 19:51
Once in a while I get the thrill of someone sending me a really good tip - that surge that comes with knowing that I know something that most people don't. That rush of knowing that soon I'll get to spill the beans. It's great, even if it upends my widely disseminated opinions. Even if a moment later I realize that if I had thought harder I would have unearthed the nugget on my own. All of which is the case here -- my tea leaf reading that indicated that Genia is no more -- well, that interpretation is no more. Because I got a hot and verifiable tip that Genia is very much still an active project at Roche. And the verification is how I could I found this independently.
Omics! Omics! 01/19/2020 20:06
10X Genomics original product was a kit for generating linked reads from genomic DNA. The idea had been kicking around for a while, partitioning long DNA into compartments and generating tagged libraries from each compartment. This enabled both genome assembly and haplotyping from very small amounts of DNA. When first reviewing 10X's slides from J.P. Morgan I had this thought "where's the genome kits" but then forgot to include it in my write-up. Now I'm even more chagrined to discover that the explanation had been posted days before the conference: 10X has told their customers that their genome library kits are in the process of being discontinued.
Omics! Omics! 01/17/2020 10:19
Time to close out J.P. Morgan season with a grab bag of kvetches and kibbitzing on multiple 'omics companies that presented. Much of this has been stimulated by Twitter discussions, with particular credit going to Varro Analytics and Albert Vilella. While I've never been to J.P. Morgan physically and am skeptical I'll ever go, reviewing all this is a great prep for AGBT -- which I'm happy to be returning to this year for it's last Marco Island appearance for many years (forever?).
Omics! Omics! 01/14/2020 22:16
Genapsys' CEO. and delivered an expansive vision of where the company is going both this year an the long term. This includes planned commercial launch of the 144M chip this year, an aggressive expansion into international markets and another round of "pre-IPO" financing.
Omics! Omics! 01/13/2020 22:25
Illumina presented this morning at the J.P. Morgan Healthcare Conference (, & ). For us sequencing geeks, the biggest news is the launch of a pair of new sequencers -- but not where either myself or Shawn Baker anticipated. Rather than doing something about the low end of their line () or replacing the MiSeq as , Illumina perceived a need for desktop instruments to span the range between the existing NextSeq 550 and the NovaSeq and has christened the new instruments NextSeq 1000 and NextSeq 2000. They also come with some slick new technologies embedded.
Omics! Omics! 01/12/2020 13:41
According to both the FTC and CMA, Illumina holds a nearly complete monopoly on the sequencing market, with other players (Ion Torrent, Oxford Nanopore) holding on to toehold niches. Illumina has held that position for an extended period, so what might upset it? I'm going to explore the case that they may have some serious inroads at the bottom of their line.
Omics! Omics! 01/09/2020 22:24
I've had some people asking, either privately or via Twitter, what might come from Illumina next week at JP Morgan (8:30 am PST on Monday). I have another post in the works (ideally going out not long after this one) on one aspect of their business, but then I thought of something else. Something in the great tradition of proposing a plan while being quite unaware of all the critical details that the plan relies on!
Omics! Omics! 01/05/2020 22:52
If you haven't seen Ford v Ferrari ( or Le Mans '66 in parts of Europe), I strongly suggest you do so if it is still in a local theater. I'm neither a gearhead nor a fan of watching automobile races, but while the movie is centered on an attempt to win the 1966 24 Hours at Le Mans, there is so much more going on. Designer Carroll Shelby (Matt Damon) must not only project manage a difficult task, but also deal with unreliable allies (as one wag put it, the biggest villain in the title isn't Ferrari) and a cantankerous star driver named Ken Miles (Christian Bale). One touching aspect of the movie is the portrayal of Miles' relationship with his young son, an audience proxy who idolizes but sees all sides of his father.
Omics! Omics! 01/02/2020 20:31
I had planned to post this morning a "preview of 2020" piece I had drafted in my head on the ski slopes the previous two days, but never got around to actually committing it to bits and bytes. that the Pacific Biosciences acquisition from Illumina is officially dead means the first item of that piece is mostly going uncaptured.
Omics! Omics! 12/26/2019 13:55
A theme of the 2019 Nanopore Community Meeting in New York was the long and short of nanopore sequencing. While the public sparring with Illumina/PacBio over the definitions of sequencing types wasn't explicitly discussed, certainly ONT wants to make sure that people understand they don't intend to ignore applications that are naturally short reads. I've been slowly trying to get this summary to gel for awhile, with the usual distractions this time of year of some trips, planning for holidays and a bout with a virus. Plus general procrastination. I'm just going to cover Clive's talk; there were some really spectacular presentations (including one by someone who remarked that they hoped their upcoming thesis committee meeting would go well!

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