Wednesday, February 26, 2020

MGI Deconstructs the Sequencer

At some fancy restaurants one can get a "deconstructed dish".  As I understand it, as I don't frequent such restaurants, a deconstructed BLT would have the bread, bacon, lettuce and tomato each as their own individual item, but prepared in a novel way which highlights the strengths of each ingredient.  When I got a preview last night of Rade Drmanac's closing AGBT talk on achieving a $100 human genome (reagents price only), that was the vision I had: Drmanac and his team have created their Tx system by deconstructing the optical high throughput sequencing-by-synthesis instrument.

Saturday, February 22, 2020

CoolMPS Revealed

Having summarized MGI's announcement they are launching into the U.S. market this spring and started digging into the performance characteristics of MGI's instrument lineup, let us now turn to their BioRxiv pre-print on the CoolMPS chemistry, as it has many useful technical details.

MGI Dual Drop of CoolMPS News Ahead of AGBT

Friday morning I got excited because a preprint showed up at BioRxiv detailing the CoolMPS sequencing technology from MGI (aka BGI aka Complete Genomics).  First announced in Fall 2018, this approach sounded, well, cool.  Using fluorescently labeled antibodies specific to each reversible terminator seemed like a crazy pipe dream.  So getting a good look at it in a manuscript is an event!  But then Friday afternoon MGI had a second big pre-AGBT reveal: launch of their sequencing systems in the U.S. later this year. Below is a quick run-down of the sequencer announcement; the pre-print has many details I'm still parsing.

Thursday, February 20, 2020

A Lazy Look at The Field of Sequencing Startups

AGBT looms ahead of me next week which serves as impetus to let fly an idea I've had simmering for a while: to look at sequencing startups by a particular type of information they choose to reveal.  I'm not expecting any big announcements at AGBT from this space, though would be thrilled to be surprised.  But there is the risk of getting contaminated with some on-the-sly scuttlebutt, so better to get this done now.  By the way, in the full disclosure category, I have consulted for a few companies here and have NDAs either on my own or via employers; everything here is based on public information.

Tuesday, February 18, 2020

Skimming Seq

My last post discussed BioJulia in the face of a challenge from the new Seq programming language.  Tonight I'm going to take a bit more of a look at Seq itself and touch on both why I'm tempted to try it and why I remain reticent to do so.  I hope if any of the Seq team sees this they will regard it as some parts constructive criticism and some parts market feedback.

Thursday, February 13, 2020

A Short Master Class in Benchmarking

There's a blog post on 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.

Tuesday, February 11, 2020

Sampling Current & Future Directions in PCR Diagnostics

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 diagnostics is enormous and I don't claim to have anything near complete knowledge of it, so this should be seen as a sampler and not a comprehensive review.  Also, the usual reminder I am a paid consultant for a diagnostics company but they are neither aiming at viruses nor using PCR, so I won't discuss them -- but if you feel that shifts your priors on how I treat other companies you have the information to do so.

Saturday, February 01, 2020

A qPCR (aka RT-PCR aka rRT-PCR) Explainer

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.