JP Morgan: Illumina
Illumina presented at J.P. Morgan on Monday, reminding us that they aren't just a sequencing instrument company but an interlocking set of businesses focused on genomics. CEO Francis deSouza spent much of his time discussing the Grail acquisition and some of the other ways in which Illumina is pushing rapidly to become an essential part of clinical medicine, but there was one slide on future improvements to sequencing technology and a few on the lineup of existing sequencers. Reminder: I'm working off public sources, as during the day we work closely with Illumina and they even sunk some serious cash into my emp...
Source: Omics! Omics! - January 14, 2021 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
J.P. Morgan 2021
TheJ.P. Morgan Healthcare Conference has started this morning in virtual form, so I'd really better get this draft cleaned up and out (indeed, Roche is presenting as I hurriedly type, though about pharma not diagnostics). 2021 already feels like a darker continuation of 2020, between the appalling putsch attempt in my nation's center of government last Wednesday and the still buggy roll-out of the coronavirus vaccine. As I noted in my piece on the Oxford Nanopore Community Meeting, the many disruptions of 2020 make grading the progress of companies essentially impossible: many were disrupted by lockdowns, sup...
Source: Omics! Omics! - January 11, 2021 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Advent of Code vs. FizzBuzz
A bunch of coding types at the Strain Factory participated inThe Advent of Code, a clever 24-day set of programming challenges that runs each year before Christmas. Each day a new two=part programming challenge was posted. Technically it is a speed contest, but you won't find me on the public leaderboard as I'm not nearly quick enough to ever rate a point there. One of my major official activities last month was contributing towards screening candidates for three different computational positions, one of which we threw open to general data science experience. As a result, I've been thinking far too ...
Source: Omics! Omics! - January 3, 2021 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Peri-New Year Nanopore Playing
Ever since the community meeting I've been toying with an idea, then never quite trying to code it. So on New Year's Eve I started getting the dataset together and reducing it to a bunch of dataframes, and today I pushed that a bit further and started graphing some of it. It's very much a rough project -- some of the dataframes have some issues I'm still chasing down with redundant data not being initially collapsed, but I think the data is accurate. I also think I have my conventions consistent -- at one point confused myself into inverting the labels on the plots! In other words, ApG would be ...
Source: Omics! Omics! - January 2, 2021 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Nanopore Community Meeting: Progress Despite the Pandemic
I realized a few Oxford Nanopore announcements too late that I should have tried to log all their predictions with a date made so I could track carefully any delays or quiet disappearances from the new feature lineup. If I had done that, this year would have presented an even worse conundrum: how do you score progress in a year of constant disruptions? Like many companies in the sequencing field, at least some of that disruption has been a diversion of attention and resources to fighting the pandemic. For ONT that is largely supporting the ARTIC viral genome sequencing and also developing LamPORE diagnostics.Read mo...
Source: Omics! Omics! - December 18, 2020 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
BGI Floats Idea of Tape-Based Sequencer
I reported on the AGBT 2020 final talk a few centuries ago -- or at least it seems like that given how quickly the world went to hell just after that -- by BGI in which Rade Drmanac showed off a system whichI described as a deconstructed sequencer -- an integrated set of plate handling robots, liquid handlers and imagers which dipped the slides into reservoirs of reagents instead of flowing them through a flowcell. Now BGI has apreprint on BioRxiv which takes this idea a bit further, changing out the reagent tanks for a polymer film on which a thin layer of reagent is distributed, which is then pressed gently against th...
Source: Omics! Omics! - December 13, 2020 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
PacBio's Renewed Energy
When confronted by antitrust regulators last year, the core thesis of Illumina and Pacific Biosciences was that PacBio could not survive as an independent company. After giving up on the merger, PacBio decided to dispute their own thesis -- and seem to be succeeding so far. As highlighted at their recent"Global Summit" meeting, they have a new CEO, new financing and a burnished product offering.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - November 30, 2020 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Bioinformatics Exercise: Gene-Specific Ser Codon Usage
I saw aprovocative abstract in PNAS about the usage of serine codons in E.coli that triggered the"this could make an interesting student exercise" (for my prior effort, see:Exercise: A Sequence Signature for Transcription-Translation Coupling in Bacteria?). The paper is behind a paywall (though a relatively cheap one at $10) so I haven't actually read the paper, but the purposes here that isn't really a problem -- I'm not going to critique the paper, but just use the concept as a springboard.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - November 19, 2020 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Bionano Genomics: A Belated Update
Back before I can remember -- as in January of this year -- I wrote a piece on the challenging situation of BioNano Genomics. I got an important detail wrong in that piece, missing some important fundraising, but in general from the point-of-view I took I thought it was a decent piece, meant to convey the challenge of a really amazing technology having its original market disappear. Some commenters took strong excepti on to the piece and suggested I had not-so-pure motives for writing it. They're wrong -- but at AGBT I got a chance to learn more about the company's new direction and how I hadn't been loo...
Source: Omics! Omics! - November 14, 2020 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
10X Triples Down on Spatial Analysis
10X Genomics last week announced the purchase of ReadCoor, a company that unveiled its 3D spatial sequencing instrument back at AGBT, paying $350 to acquire the Cambridge MA company. This follows quickly on the heels of 10X purchasing Swedishin situ sequencing company CartaNA for another $41M. 10X already had the Visium spatial transcriptomics product on the market. So now 10X has three different technologies in the spatial profiling space.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - October 12, 2020 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Keeping an Index on a Subtle Difference in Illumina Chemistries
I like to pretend in this space that I catch all the little details of the different sequencing platforms. Well, at least over time I try to do that. But ego aside, that is often a mark not made. A bit of a year ago I discovered that there's a small difference across the Illumina family that is completely separate from how clusters are generated (Bridge Amplification randomly arrayed or Exclusion Amplification in nanowells) or the wavelengths of light used in the fluorescence microscopy (now blue on the newest NextSeqs, with superresolution microscopy coming soon) or 4 color vs. 2 color vs. 1-color (well, rea...
Source: Omics! Omics! - September 29, 2020 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Self-Assessing My Python
I've been programming 90+% in Python now for over a year and a half -- when I joined the Strain Factory I vowed to finally make the break from Perl. Partly this was disgust with so often finding libraries I wanted to be missing or broken, and partly it was recognizing that the Factory is primarily a Python shop and I would have the most impact if I worked in thelingua franca.I was first exposed to Python back at Codon Devices, but there was a strong C# faction there and I fell in love with that language, so my primary dabbling in Python was learning enough to glue the key Python code into my C# with IronPython. I...
Source: Omics! Omics! - August 30, 2020 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Two Pandemic-Related Programming Problems
I will offer here two bioinformatics programming problems which I think are interesting, useful and should be approachable by an advanced undergraduate. For a variety of reasons I've been thinking a lot of about skill levels and how to assess them. One key reason is we have two open slots in our group, so I'm plowing through CVs and engaging in the usual hiring funnel struggle -- how do you winnow CVs to phone screens and then down to interviews? We also thought we might, but now won't, bring on a one year intern. But I'm also trying to take a look at my own skill set with a critical eye. Plus I...
Source: Omics! Omics! - July 23, 2020 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Virtual London Calling, Veritably Late, Part II: Platform Development
Last time, I covered Oxford NanoporeLamPORE COVID-19 detection scheme. London Calling was over a week ago, so the chance to scribble before its all old news is rapidly shrinking. As noted yesterday, Clive Brown didn't speak here but instead will broadcast at some future date; it was left to his top technical lieutenants to cover the developments in the platform which have happened since the Community Meeting in New York back in early December. I've tried to hit the highlights here, but don't claim to be comprehensive.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - June 28, 2020 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Virtual London Calling, Veritably Late Copy: Part I, LamPORE
London Calling was last week, held online due to the pandemic. My plans to attend in person were one of a myriad of travel arrangements upended by the calamity, though that is utterly trivial in comparison to the tragedy of so many lost lives, damaged survivors and economic ruin. Attending remotely also made it harder to ignore my work duties, which are at a crescendo (well, not really: it's been this intense for months). But all the talks are available online, so I have stolen some time to review the Oxford Nanopore technology announcements. There wasn't a Clive Brown talk; apparently he will deliver a b...
Source: Omics! Omics! - June 23, 2020 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
