PubMed retractions report has moved
A brief message for anyone who uses my PubMed retractions report. It’s no longer available at RPubs; instead, you will find it here at Github. Github pages hosting is great, once you figure out that docs/ corresponds to your web root :)
Now I really must update the code and try to make it more interesting than a bunch of bar charts. (Source: What You're Doing Is Rather Desperate)
Source: What You're Doing Is Rather Desperate - May 23, 2018 Category: Bioinformatics Authors: nsaunders Tags: R statistics github pmretract pubmed retraction rstats Source Type: blogs
Miscellaneous & Disorderly Thoughts on the Eve of London Calling
It's the night before London Calling. I hope to post Thursday, but an after-meeting report won ’t be until nest week - I must dash on Friday fir a slightly insane/exhilarating routing to meet my family in Florida for the holiday weekend. Exhilarating as I will have a layover in one of the ancient capitals of Europe, Lisbon, which I’ve never visited. Insane, because it’s a 12 hour overni ght layover. Anyway, between the challenge of covering Oxford Nanopore's expanding reach of products and applications and being sleep-addled from taking the redeye flight I'm going to throw out a bunch of thoughts without ...
Source: Omics! Omics! - May 23, 2018 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Should PentaSaturn Buy An iSeq: A Hypothetical Scenario Illustrating Platform Picking
Editorial note: I wrote this in early January, then planned to slot it in after some other items. Thenlife knocked me upside the head, then AGBT came along and then it was forgotten. Once I remember it, I fretted it had gone stale. But I had put a lot of effort into it and really nothing has changed with regard to iSeq, other than it should be shipping now. Besides, this week is London Calling and so having an Illumina-centric piece could be a bit of useful balance. So, f or your consideration:Some of the online discussion around this January's iSeq announcement, springingfrom my piece or elsewhere, explores ...
Source: Omics! Omics! - May 22, 2018 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
50% bananas
Today in “blog posts that have spent two years in the draft folder” – “Humans are 50% banana.”
“Humans are 50% banana.”
Perhaps you have heard this statement, or one like it. It seems to be widely-quoted. As an example it’s hard to go past this article from UK tabloid The Mirror which, in addition to the banana, also informs us that “the entire internet weighs about the same as one large strawberry”. I don’t even know where to begin with that one.
A couple of years ago whilst between jobs and with time on my hands, I thought I’d go in search of the sou...
Source: What You're Doing Is Rather Desperate - May 9, 2018 Category: Bioinformatics Authors: nsaunders Tags: genomics humour banana human myths Source Type: blogs
PromethION Racing: A Call To The Post
I was at a get-together yesterday for bioinformatics folks associated with Third Rock Ventures companies at a local pub. The organizer, who I've known for a number of years, was introducing me with the pleasant"Keith writes a nice blog" -- but then the barb"but he hasn't posted in a while".Ouch! But it hurts because it's true; too many excuses to not write and far too many half-baked ideas and interviews that should be out (or worse, a nearly complete post). Since it is May, which in the U.S. is bookended by iconic racing events, I'd like to trot out an idea that has been idling f...
Source: Omics! Omics! - May 3, 2018 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Mission Bio Launches Custom Panels
Back in OctoberI covered the launch ofMission Bio's single cell platform, Tapestri. Tapestri is a microfluidic platform which encapsulates cells and sets of barcoded primers into droplets, lyses the cells within the droplets and executes PCR on the released DNA. Mission initially targeted hematologic cells, since they do not require disaggregation, and offered a standard panel of primes. Around the time of AGBT, Mission launched a custom panel option and took the time to sit down with me. Now with AACR, Mission has announced placing Tapestri at multiple major cancer centers: the NCI, Mt. Sinai, MD Anderson, Me...
Source: Omics! Omics! - April 16, 2018 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
A Small Rampage Over STAT's Movie Piece
A movie opened this weekend which, by all prior evidence and new reviews, is unbelievably silly but destined to rake in the bucks. Rampage is very loosely - as if it could be another way - based on avideo arcade game. The original game ’s backstory had a mysterious ray transforming people into monsters, but the movie has changed that to CRISPR. So STAT had a piece which, to my great disappointment, gave the movie ’s science a near pass in a piece featuring two writers chatting . . (Note: this post has mild spoilers, though if you've seen the trailers they give almost all of this away).Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - April 14, 2018 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Moving from RPubs to Github documents
If you still follow my Twitter feed – I pity you, as it’s been rather boring of late. Consisting largely of Github commit messages, many including the words “knit to github document”.
Here’s why. RPubs, an early offering from RStudio, has been a great platform for easy and free publishing of HTML documents generated from RMarkdown and written in RStudio. That said, it’s always been very basic (e.g. no way to organise documents by content, tags). There’s been no real development of the platform for several years and of late, I’ve noticed it’s become less reliable. Bugs, ...
Source: What You're Doing Is Rather Desperate - April 4, 2018 Category: Bioinformatics Authors: nsaunders Tags: R statistics this blog github markdown publlishing reports rpubs Source Type: blogs
A Most Unfortunate Sequencing Error
If you are in the sequencing business, you'd like to get things right. But sequencing is a form of measurement and measurement has error. No matter how diligent and committed you are, sometimes the data doesn't break your way. Mick Watson has aset of posts and apreprint illustrating quality issues in many deposited bacterial genomes. Some of those are bad luck and some of those are from complacency. Some errors radically affect biological interpretation and some don't. I'm going to detail here one of the worst cases of bad luck I've seen, where relatively small errors sat undetected for ove...
Source: Omics! Omics! - March 21, 2018 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Farewell then, PubMed Commons
PubMed Commons, the NCBI’s experiment in comments for PubMed articles, has been discontinued. Thoroughly too, with all traces of it expunged from the NCBI website.
Last time I wrote about the service, I concluded “all it needs now is more active users, more comments per user and a real API.” None of those things happened. Result: “NIH has decided that the low level of participation does not warrant continued investment in the project, particularly given the availability of other commenting venues.”
NLM also write that “all comments are archived on our FTP site.” A CSV file is avail...
Source: What You're Doing Is Rather Desperate - March 15, 2018 Category: Bioinformatics Authors: nsaunders Tags: R statistics comments pubmed commons rstats Source Type: blogs
A Morning Visit to SeqLL
I've written in the past aboutSeqLL, the company which purchased all of the hard assets from Helicos after the latter's demise. At the end of last year, CEO Elizabeth Reczek invited me to stop by for a visit and so I spent a morning having a frank discussion with Dr. Reczek and Director of Sales Lee Dalton and also was treated to a tour of their facilities.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - March 6, 2018 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
PromethION: Straining at the Starting Gate
Due to the usual time conflicts, I've only watched bits-and-pieces of the Winter Olympics from South Korea. Which is unfortunate, as I do enjoy observing many of these events as so many combine grace, power and finesse. In the various timed events, the competitors can be seen tightly wound, ready to spring out at the crack of the start. Increasingly, that is how Oxford Nanopore's PromethION looks: a superb performer ready to bolt away.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - February 25, 2018 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
AGBT: It Ain't Over'til the Tattoo Wears Off
AGBT officially ended on Thursday night with a space-themed party, but I have a bunch of notes from interviews with company representatives and even a few notes from sessions. So be prepared for a string of further AGBT reports. This dispatch will have some overall thoughts as well as some notes on the possible return of AGBT to Marco Island next year. I also want to mention two good AGBT 2018 summaries, onefrom Dale Yuzuki and another fromDecibio's Stephane Budel.newly appliedRead more » (Source: Omics! Omics!)
Source: Omics! Omics! - February 18, 2018 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
AGBT: Twist Biosciences Launches Sequence Capture Product
Twist Biosciences today launched a new product into the sequence capture space. CEO Emily Leproust was presenting to the Gold Sponsor workshop as I started writing this, but she also sat down with me yesterday to preview thenew offering for targeted sequencing.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - February 14, 2018 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
AGBT: BioNano Launches New Labeling Approach
AS AGBT opened, optical mapping companyBioNano Genomics announced a new scheme for labeling genomic DNA inputs which substantially improves performance. Sven Bocklandt from the company sat down with me yesterday to walk through the new Direct LabelingRead more » (Source: Omics! Omics!)
Source: Omics! Omics! - February 14, 2018 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
