Let's Stop Talking Consensus Accuracy
A common approach for comparing sequencing platforms and assemblies is to report the consensus accuracy, just as for the platforms themselves the raw read accuracy is often reported. I'm going to go on record with my opinion that stating these as"99.9% accurate" is a terrible habit which must be kicked, as it interferes with proper comparisons.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - December 13, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Siddhartha Mukherjee's The Gene, An Intimate History & the Crafting of Scientific Stories
Back in 2011, I read andreviewed Dr. Siddhartha Mukherjee's book on the history of cancer therapy, The Emperor of All Maladies. I liked the book, but as is my character I also listed some criticisms. It was a very pleasant surprise to one day discover an email from Dr. Mukherjee engaging me on my points. A real author, writing me! Fast forward to this fall, and I had some inexplicable inertia to reading his new book, The Gene, An Intimate History. This time he drove the process forward, asking if I'd like to read and review the book and if so could his publisher send me a copy? Wow! Having just fini...
Source: Omics! Omics! - December 8, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Reversible Terminators: Not Just For Sequencing
Reversible terminator nucleotides lie at the heart of sequencing-by-synthesis systems such as Illumina. These nucleotides in their original state cannot be extended, terminating DNA polymerization. But with the correct chemical treatment, the block is removed and polymerization can continue. A recent paper moves the concept from sequencing to making large single mutation libraries. The authors have apparently also applied for a patent (according to the Conflicts of Interest statement accompanying the paper), though that does not turn up on Google.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - December 5, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Oxford Nanopore New York City Meeting, Day 2
The second and final day of Oxford Nanopore's New York User Meeting ran today. I've again been mining tweets, since I wasn't on site. Oxford itself hasposted a summary of Day 1, which has the enormous benefit of the author being present! I'll make a few quick summaries. The tweets for today can be found in two semi-thematic Storify entries: one givesgeneral coverage and of ONT's demos, whereas the other coversONT's technical talks and talks by users.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - December 1, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Oxford Nanopore New York City Meeting, Day 1
Oxford Nanopore officially kicked off its Community Meeting in New York City today; a training session took place yesterday. Already there have been several interesting announcements and presentations, including a new prototype sample prep gadget, a new basecaller which improves homopolymer calling, a read-both-strands approach that isn't 2D sequencing and details on multiple human genomes run on MinION. A reminder: I'm working only from tweets; I'm not at the meeting.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - November 30, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Is PromethION a Strategic Error?
Be prepared for another burst of Oxford Nanopore coverage; their annual Community Meeting in New York City begins on Thursday (perhaps while you are reading this). I won't be attending; only so many absences from the day job are ultimately feasible each year, and I've long since hit the limit. Hopefully some prolific tweeters will keep everyone updated, and I can summarize from there.As with most posts on Oxford Nanopore, mypiece on the closure of the Illumina litigationcaptured some comments; I think it is reasonable to expect more on thepiece on the opening of litigation by Pacific Biosciences. How you perc...
Source: Omics! Omics! - November 29, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Revisiting Mendel
Inyesterday's post, I flagged a small factual error in Siddhartha Mukerherjee's The Gene. I really liked Mukherjee's prior history of cancer,The Emperor of All Maladies, and was thrilled when Dr. Mukherjee wrote a thoughtful response to the criticisms I did make. So it was another happy moment recently when he asked me if I'd like a copy of the book so I could review it. I'm only about a third through the book, but it is definitely worth reading (why did I wait so long? no good reason). Since I like it, when I get to a full review I'll probably be mostly in"this is what I would have sug...
Source: Omics! Omics! - November 28, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Nostalgic for Fly's Eyes
Kumar Thangdu's mission of prodding me has contributed to a bout of nostalgia for one of my graduate student rotation projects. He asked in a tweet how I'd allocate funds if I was given stewardship of a billions in grant money. If you want to get some big results but are willing to be very patient, then a great way way to invest is in model organisms. As a rotation student at Harvard, I spent several months pushingDrosophila melanogaster, the not-so-humble fruit fly.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - November 27, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
RNA-Sensing USB Stick: Promise Despite the Hype
Earlier this month the newsfeeds were abuzz over a new USB-stick style nucleic acid testing device. Based on technology from the United Kingdom firm DNA Electronics, this device is intended to make testing for infectious diseases portable and inexpensive. Since the pulse of news was triggered by a publication in a journal, I dove in to see where things really stand. The device is interesting, but alas the paper describes a prototype far from ready to deploy. Also interesting to ponder is how this device might stack up against other devices emer ging for the portable diagnostics marker, such as Oxford Nanopore's M...
Source: Omics! Omics! - November 22, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
News from Old Neighborhoods
Five years ago, the initial band of scientists at my current employer had just moved from the offices of our venture capitalist sponsor, Third Rock Ventures, into lab space in Cambridge sublet from Blueprint Medicines. The Athenaeum Building is a large brick-faced building which once held the publishing house by that name. Eleven Biotherapeutics was trying to engineer new immune-modulating proteins, initially focusing on a treatment to dry eye. Some of their IP I understand was pulled from the wreckage of C odon Devices. Also on the floor was Verastem, a company spun out of work from Robert Weinberg and Eric Lande...
Source: Omics! Omics! - November 20, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Will Liquid Handling Robots Ever Join the 21st Century?
In the course of this blog, there are many topics I've thought about writing that I haven't touched. Sometimes it is due to the problem of the topic being too revealing to what I am working on, sometimes it is because I'm not satisfied with the result, but far too often I procrastinate so long that it no longer seems fresh. Or I'll just do it another time when the moment is right, which it never is. But a recent Twitter exchange reminded me of a long-suppressed lament on some expensive, finicky and problematic -- but very useful -- denizens of a modern lab: liquid handling robots.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - November 19, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
HGP Counterfactuals, Part 7: Wrapping Up
It's been interesting revisiting a bunch of now ancient history of the Human Genome Project with the goal of exploring other possibilities. Istarted by considering the entire concept of alternative histories, then reviewed theconstruction of physical maps,strategies which were considered for sequencing the clones comprising the minimum spanning map of the genome and theactual sequencing technologies employed, then considered scenarios in whichno HGP is launched or the project is given a much smaller budget andforced to focus on technology development. Tonight, I'll close this out by trying to summarize some of ...
Source: Omics! Omics! - November 16, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
HGP Counterfactuals, Part 6: Ax Sharpening Only
Atthe beginning of this series, I promised two alternative histories on the Human Genome Project. Yesterday I explored a timeline in which opponents of the HGP successfully kept it from ever being funded. Today, I'll try to imagine what would have happened if the project had been funded only to develop new sequencing technology. One warning: as part of this I will show the most reviled plot in genomics, but to make something other than the usual point.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - November 15, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
HGP Counterfactuals, Part 5: HGP Stifled
Okay, enough procrastination. I've outlinedthe general idea of counterfactuals and then obsessively detailedthe generation of physical maps,planning the sequencing of BAC clones and therapid winnowing of sequencing technologies during the early stages of the genome project. Time for a main act: what if the public Human Genome Project never happened?Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - November 14, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
HGP Counterfactuals, Part 4: Sequencing Tech Landscape Circa 1992
In thisseries leading to a pair of Human Genome Project alternative histories, I've been warming up with a trio of analyses of the technology landscape. At first I couldn't decide on the order to post these in, but then it was clear to me: a progression of scale fromphysical maps of the genome tohow to organize the sequencing of the BACs, and now to the actual sequencing technologies which were in play. In particular, how there was a very rapid evolution from 1992 (when I first was deeply exposed to this angle by attending Hilton Head) to 1997 (when I defended, but also the outcome was clear). In this time pe...
Source: Omics! Omics! - November 13, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
