Florence Nightingale ’ s “ rose charts ” (and others) in ggplot2
It’s been a while. I hope you are all well. Shall we make some charts?
About this time last year, one of my life-long dreams came true when I was told that I could work from home indefinitely. One effect of this – I won’t say downside – is that I don’t get through as many podcast episodes as I used to. Only a select few podcasts make the cut, and one of those is 99% Invisible.
I first heard Florence Nightingale and her Geeks Declare War on Death, an episode of the Cautionary Tales podcast, premiered as a special episode of 99% Invisible. It discusses Nightingale’s work as a stat...
Source: What You're Doing Is Rather Desperate - March 16, 2021 Category: Bioinformatics Authors: nsaunders Tags: R statistics crimea florence nightingale ggplot2 podcast polar area rstats Source Type: blogs
AGBT21: VizGen Unveils MERSCOPE
More spatial profiling news coming in from AGBT -- Harvard spin-out VizGen is launching in the U.S. an instrument implementing MERFISH technology.  This sub-$300K instrument will initially enable panels of up to 500 genes to be profiled, with plans to expand that capacity to 1000. Users either pick from a menu of pre-designed panels or select genes using a Gene Panel Design Tool and VizGen would proceed to manufacturing the panel in around two weeks. VizGen CEO Terry Lo and Senior Director of Marketing Brittany Auclair were kind enough to give me a preview last Friday.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - March 2, 2021 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
AGBT21: Rebus Esper for Spatial Sees Things You Wouldn't Believe
My predictionthat spatial would be a hot topic at AGBT was easy to make knowing I was sitting on embargoed news in the spatial space.  This morningRebus Biosystems announced the launch of the Rebus Esper system for wide field spatial profiling of gene panels with subcellular resolution.  Rebus is promising that this instrument will offer true walkaway automation from fluidics through imaging, and data processing, requiring only one hour of hands-on time.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - March 1, 2021 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
AGBT21: A Few Pre-Conference Mutterings
Getting some miscellanea out before AGBT21 starts later this morningRead more » (Source: Omics! Omics!)
Source: Omics! Omics! - March 1, 2021 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
AGBT21: The LabRoots Presentation Platform is an Unmitigated Disaster
Rant isON! I've been having an utterly miserable experience with the LabRoots conference software that AGBT is using for their virtual meeting.  This year has exposed many of us to a wide variety of teleconference and virtual meeting software and many of the glitches are small and hard to pin down. Or matters of personal preference (though if you don't share mine, you are simply wrong!).  But now on two major platforms I've come across major issues with LabRootsRead more » (Source: Omics! Omics!)
Source: Omics! Omics! - March 1, 2021 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
AGBT 2021: A Spatial Foundation
I'll call it now -- the big buzz at this year's AGBT will be around spatial profiling.  Trust me, it's not just a hunch.  The two current players in the field -- nanoString and 10X Genomics -- both have significant presence in the virtual conference. Don't be surprised to see more players on the field -- just sayin'Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - February 28, 2021 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
PacBio With SoftBank's $900M: How Might TheyWork?
Pacific Biosciences continued its roll of successful business development, snagging $900M from Japan's SoftBank two weeks ago.  Combined with a recent secondary stock offering and a major deal with Invitae, PacBio has gone from their self-proclaimed near-derelict status during the Illumina acquisition attempt saga to rolling in cash.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - February 27, 2021 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
More Details on 10X's Sample Profiling Trident
10X Genomics had an online event Wednesday called Xperience (as far as I could tell no Jimmy Hendrix music was used, a missed opportunity!) to lay out their development roadmap. Â This largely paralleled thepresentation given at J.P. Morgan, but there were a few new bits and of course much more technical detail to whet the appetites of scientists -- and judging from a number of very positive tweets I saw today they were successful in that goal. Some of the 10X management was kind enough to walk me through the deck earlier this week as well as permission to borrow images from it, so this summary is based on that as well as...
Source: Omics! Omics! - February 26, 2021 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Could I See Myself at J.P. Morgan?
There's a question that others pop my way pretty much every year around J.P. Morgan: would I ever attend myself? Â I'll confess it never occurred to me before I was asked, but that isn't necessarily a deal breaker. Â I foolishly didn't attend AGBT until 2013 when Alexis Borisy (then CEO of Warp Drive) suggested I go -- I think it was mostly because he thought it was a good investment and probably only secondarily to keep me off the ski slopes for a week -- I shattered my knee just after AGBT 2012 ended. Â It's an interesting but complex question which I will answer one way here, but freely admit that...
Source: Omics! Omics! - February 9, 2021 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Why I Hated One Genapsys Slide
I claimed in my Miscellanea piece that I was one post away from being done with J.P. Morgan -- oops, forgot I had drafted a minor screed on data display which I'll push out before the last piece - particularly since I hinted I would be taking Genapsys to task on this subject.  Unexpectedly good timing too: maybenew Genapsys CEO Jason Myer'sfirst big initiative can be to fix this plot!Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - February 8, 2021 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
J.P. Morgan: Miscellania
Before J.P. Morgan is truly a month ago I should clean up some loose ends as a penultimate post driven by this year's virtual conference (the last post isn't exactly time sensitive).  In contrast to the single company focused items that preceded it, this is a grab bag of minor observations and notes.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - February 6, 2021 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
J.P.Morgan: NanoString
Almost done with my J.P. Morgan summaries -- this will be the last focused on a specific company: nanoString.   They wish to emphasize that they are becoming the company for spatial analysis of DNA, RNA and proteins in biological samples. They also want us to differentiate that space into two segments: profiling and imaging. Profiling gathers spatial information from regions of multiple cells; imagin g in their lingo covers spatial techniques with single cell or subcellular localization. In both cases nanoString is betting heavily on oligo-tagged antibodies to enable deep multiplexing of protein detection to be inte...
Source: Omics! Omics! - January 28, 2021 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
J.P. Morgan: Genapsys
Genapsys' J.P. Morgan presentation by CEO Hesaam Esfandyarpour focused on their story of delivering a compact sequencer based on electronic detection that offers low capital, low cost sequencing.  There were two bits of specific product news, but mostly general painting of a rosy picture.  Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - January 25, 2021 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
J.P. Morgan: PacBio
PacBio CEO Christian Henry ’s presentation at J.P. Morgan wasn't rich in technical specifics. But he gave a very bullish portrait of a company aiming for the stars.  A conflict reminder: he’s a member of the Board of the Strain Factory that employs me, though I haven’t yet had the pleasure of meeting him.The biggest news is a broad partnership with Invitae four clinical human genome sequencing. The only specific here is that this is not the whole enchilada; platform development will take place both within the Invitae collaboration and outside it. What might that development be?Between Henry ’s comments in the...
Source: Omics! Omics! - January 19, 2021 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
J.P. Morgan: 10X Genomics
As I attempt to collate various incomplete thoughts about the J.P. Morgan presentations I have read and listened to from genomics instrument shops, one thing stands out about 10X Genomics: they actually announced new gadgets and kits! I should thank the company for supplying the slides after I snarked on Twitter about how they weren't archived in the J.P. Morgan webcast -- but now it is there.  So either my eyes failed again or I had a personal IT failure (I think the website doesn't like iOS and I may have forgotten that).  The slides were presented by CEO Serge SaxonovRead more » (Source: Omics! Omics!)
Source: Omics! Omics! - January 16, 2021 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
