Sequencing Technology Outlook, January 2017
Another year of blogging is upon us! Since theJ.P. Morgan Conference starts a week from today and then before long it's time forAGBT. So if one is going to prognosticate, then there's no time to lose, as announcements could start flying at any time.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - January 1, 2017 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
A Change of Direction
In this post: a brief summary of what I got up to, work-wise, in 2016 and my plans for a rather different 2017. The short version: it’s goodbye bioinformatics and hello educational data science!
It feels as though 2016 was a challenging year for many people in various ways. My year was no exception. I spent the first 6 months working as a data scientist for a healthcare technology startup. It was a new, different and very enjoyable experience. However, a change in the focus of their business resulted in my redundancy mid-way through the year.
I took some time out, then began applying for jobs. I received a lot of su...
Source: What You're Doing Is Rather Desperate - January 1, 2017 Category: Bioinformatics Authors: nsaunders Tags: career education personal cese nsw Source Type: blogs
Evidence for a limit to effective peer review
I missed it first time around but apparently, back in October, Nature published a somewhat-controversial article: Evidence for a limit to human lifespan. It came to my attention in a recent tweet:
Just wow https://t.co/fupXIOAC43 pic.twitter.com/vsxT3VyTg6
— Nick Loman (@pathogenomenick) December 11, 2016
The source: a fact-check article from Dutch news organisation NRC titled “Nature article is wrong about 115 year limit on human lifespan“. NRC seem rather interested in this research article. They have published another more recent critique of the work, titled “Statistical problems, but not enou...
Source: What You're Doing Is Rather Desperate - December 18, 2016 Category: Bioinformatics Authors: nsaunders Tags: publications R statistics human longevity peer review Source Type: blogs
Sequencer Archaeology
One of the frustrating side effects of outsourcing all your sequencing is that lack of connection to the actual machines. Rarely have I gotten to visit sequencing labs, and the only time I've seen one with the cover open waswhen a Polonator was being shown off at a conference. So it was a lot of fun to watch an almost hour-long YouTube video that Lex Nederbragt had pointed out in which someone who likes to disassemble complicated electronics performs his craft on a 454 FLX.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - December 17, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Roche Abruptly Breaks Off PacBio Partnership
This morning was a solid block of meetings, but in a pause I checked my phone and saw the shocking headline: Roche Diagnostics hadsuddenly terminated their partnership with Pacific Biosciencesto commercialize the Sequel instrument for clinical applications. Based on the few things I've read and a conversation with Bio-IT World's Allison Profitt, I've formed a few ideas, but certainly still find this a bit mystifying. Perhaps the first part of next year, with the JP Morgan Conference and AGBT, will see Roche revealing a bit more about why they decided to break up with their partner. Particularly when Roche h...
Source: Omics! Omics! - December 14, 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
An Analysis of Contributions to PubMed Commons
I recently saw a tweet floating by which included a link to some recent statistics from PubMed Commons, the NCBI service for commenting on scientific articles in PubMed. Perhaps it was this post at their blog. So I thought now would be a good time to write some code to analyse PubMed Commons data.
The tl;dr version: here’s the Github repository and the RPubs report.
For further details and some charts, read on.
Currently, there is no access to PubMed Commons data via the NCBI Entrez API aside from a PubMed search filter to return articles that have comments. However, a Google search for “pubmed commons apiR...
Source: What You're Doing Is Rather Desperate - December 1, 2016 Category: Bioinformatics Authors: nsaunders Tags: publications R statistics comments ncbi pubmed commons 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
Putting data on maps using R: easier than ever
New Zealand earthquake density 2010 – November 2016Using R to add data to maps has been pretty straightforward for a few years now. That said, it seems easier than ever to do things like use map APIs (e.g. Google, Open Street Map), overlay quite complex data visualisations (e.g. “heatmap-style” densities) and even generate animations.
A couple of key R packages in this space: ggmap and gganimate. To illustrate, I’ve used data from the recent New Zealand earthquake to generate some static maps and an animation. Here’s the Github repository and a report published at RPubs. Thanks to Florian Tesc...
Source: What You're Doing Is Rather Desperate - November 24, 2016 Category: Bioinformatics Authors: nsaunders Tags: R statistics earthquakes ggplot2 maps new zealand visualisation 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
