Metabolic Whac-a-Mole
Derek Lowe summarized a really cool paper back in October. I've been meaning to grab a copy, but discovered recently that the MIT library no longer has an easy way for outsiders to slip in an use their subscriptions. So I'm working off his summary, but since this is mostly an excuse for flights of genetic fantasy actually reading the paper would probably just hinder me!Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - January 28, 2019 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
2019 Tech Speculations: Oxford Nanopore
As promised in the last post, I'm segregating out Oxford Nanopore. Admittedly I tend to cover them relatively closely -- though I never seem to quite finish writing up their conferences -- but at the moment ONT is the only major player in the U.S. research sequencing marketnot being run out of (or about to be run out of) Illumina HQ. And I'll be very to the point: ONT has a lot of balls in the air and irons in the fire, but from my point-of-view what matters most is rapid and regular progress on the accuracy front.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - January 25, 2019 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
2019 Sequencing Tech Speculations: Will We Actually See New Entrants?
An astute reader caught a sentence fragment about MGI inlast night's Illumina JPM roundup -- the unfortunate evidence of a a mental battle over whether to put any further comments on MGI in an Illumina-centric post. So now I'll sweep that bit into a general post about not-Illumina (and not-Oxford, that will go in yet another).Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - January 15, 2019 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Illumina JPM Talk
Illumina CEO Francis deSouza delivered his J.P. Morgan Healthcare Conference talk (webcast audio,slides&Q&A audio) a week ago. I can claim that some ofmy speculations came true -- just the most boring and obvious ones. Overall, the presentation was the talk of a confident market leader. Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - January 14, 2019 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
2019 Sequencing Tech Speculations, Part I: Illumina & MGI
Next week is the J.P. Morgan Healthcare Conference. It's striking this year the paucity of companies in the genomics space -- Illumina on Mondayat 6:00 EST and MGI on Wednesday at 5:30 EST and Nanostring at 6:30 EST on Wednesday. Perhaps NVIDIA will say something interesting about their forays into healthcare, such as providing the chops for real time nanopore basecalling, on Thursday at 11:30 EST. There's also some nice polls from Albert Viella on TwitterWhat would you like@illumina to announce at#JMP2019 ?https://t.co/TDn5J0glhi part 2— Albert Vilella (@AlbertVilella)January 5, 2019and some more Twitter s...
Source: Omics! Omics! - January 6, 2019 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
2019 Resolutions
2019 is upon us; I'm hoping it will be a bit less eventful than 2018. It wasn't all bad -- I took two trips that delivered scenery I have only right to see once in a lifetime -- but it was essentially bookended bylosing my father anda revolution in my workplace. Mixed in there is the bittersweet pride of seeing one's offspring graduate from high school and proceed on to college.New Year's resolutions are notoriously difficult to keep -- one is fighting entrenched behaviors -- but bringing in some external pressure might help. So I'll make my two resolutions for the year very public: that I post...
Source: Omics! Omics! - January 3, 2019 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
An Unfortunate Master Class in Poor Plotting
I hope my admiration for Pacific Biosciences intellectual acumen was clearin my post on the acquisition by Illumina, because now I'm going to be a rabid crab over awebinar they aired yesterday. I take telling scientific stories seriously and an important part of telling such stories is displaying data well. I'm a perfectionist in this department by intention, but not always by execution -- I'm constantly reanalyzing my plots and diagrams for errors and cringing when I find them. The webinar is trying to extol the value of the latest developments in the SMRT platform, but the data graphs often actively f...
Source: Omics! Omics! - December 13, 2018 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Flappie vs. Albacore via Counterr
I'm going to go through some analysis of Oxford Nanopore basecalling, running some quick comparisons using afreely-available tool called counterr which was announced at the Nanopore Community Meeting two weeks ago. Counterr was developed byDay Zero Diagnostics, a startup I advise -- though in announcing yet again my COI I will stress I don't get paid to help give away software! This is just a small bit of analysis; nothing as comprehensive asRyan Wick's ongoing analysis with a ready-to-submit preprint masquerading as a README file.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - December 12, 2018 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Nanopore Community Meeting 2018: The Clive Report
Given it's late and I just dashed through a classic San Francisco downpour, I'm going to mostly stick to covering Clive Brown's talk tonight. Within it there were a number of announcements, and for anyone following this space I get to point out things I've proposed in the past that are moving to fruition as well as recent statements I made that were quite erroneous.Also note that tweets during his talk have been collected by ONT into aTwitter MomentRead more » (Source: Omics! Omics!)
Source: Omics! Omics! - November 29, 2018 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Extracting data from news articles: Australian pollution by postcode
The recent ABC News article Australia’s pollution mapped by postcode reveals nation’s dirty truth is interesting. It contains a searchable table, which is useful if you want to look up your own suburb. However, I was left wanting more: specifically, the raw data and some nice maps.
So here’s how I got them, using R.
The full details are in this Github repository. There you’ll find the code to generate this report.
Essentially, the procedure goes like this:
Use rvest to create a data frame from the data table in the online article
Clean and pre-process the data using dplyr
Join the pollution data w...
Source: What You're Doing Is Rather Desperate - November 28, 2018 Category: Bioinformatics Authors: nsaunders Tags: australia environment statistics geospatial maps pollution rstats Source Type: blogs
A Few Things Before Nanopore Community Meeting Begins
Nanopore Community Meeting begins within the hour. San Francisco is spectacular as ever -- Alcatraz Island disappearing into the fog as I fiddled with camera settings, the spectacular Bay Bridge spans are visible from the the breakfast area and I even got to see some notable locals on my walk over from the hotelIf this crowd doesn ’t get a move on, they’re going to miss#nanoporeconf breakfastpic.twitter.com/rFwfGdQTit— Keith Robison (@OmicsOmicsBlog)November 28, 2018Hans Jansen was kind enough to remind me by tweet of a couple of missed topics inmy preview piece. So let's cover them!.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - November 28, 2018 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Nanopore Community Meeting 2018 Preview
Okay, now that I'mdone venting -- for now -- about ONT's customer service experience (well, almost done -- they sent me the same damn letter they sent my colleague -- why were they several hours apart???) -- let's move on to the Nanopore Community Meeting. Technically it started today with the training session, but I'm not heading out until tonight. At the first one of these in NYC Oxford tried to avoid making any announcements, but they seem to now like having two major focus times a year sometimes supplemented with Clive Brown webinars in between. Here are someRead more » (Source: Omics! Omics!)
Source: Omics! Omics! - November 27, 2018 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
How Not Do Think Like A Customer: Examples from ONT and AMZN
I'd planned today to use some downtime to write up a preview of the Nanopore Community Meeting which I am attending tomorrow and Thursday. I might still do that, but the same organization just engaged in the sort of customer engagement that drives me batty (yeah, twisting the lion's tail before entering their den -- smart move or what?) and it reminded me of another lousy experience I had recently with avery prominent company: Amazon.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - November 27, 2018 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Using OSX? Compiling an R package from source? Issues with ‘ -fopenmp ’ ? Try this.
You can file this one under “I may have the very specific solution if you’re having exactly the same problem.”
So: if you’re running some R code and you see a warning like this:
Warning message:
In checkMatrixPackageVersion() : Package version inconsistency detected.
TMB was built with Matrix version 1.2.14
Current Matrix version is 1.2.15
Please re-install 'TMB' from source using
install.packages('TMB', type = 'source') or ask CRAN for a binary
version of 'TMB' matching CRAN's 'Matrix' package
And installation of TMB from source fails like this:
install.packages("TMB", type = "source")
clang: ...
Source: What You're Doing Is Rather Desperate - November 18, 2018 Category: Bioinformatics Authors: nsaunders Tags: programming statistics compiler llvm osx Source Type: blogs
We do not wish to share
The article Cytotoxic T cells modulate inflammation and endogenous opioid analgesia in chronic arthritis contains a statement that I don’t recall seeing before:
Availability of data and materials
We do not wish to share our data at this moment.
This seems odd for an open-access article, published by a “big on open-access” publisher:
How is this possible @BioMedCentral ??https://t.co/cgmLq8Weay
— Mick Watson (@BioMickWatson) November 15, 2018
However, according to the BMC policy on open data:
Question: Do authors need to publish more data than they publish already?
Response: We are not requiring ...
Source: What You're Doing Is Rather Desperate - November 15, 2018 Category: Bioinformatics Authors: nsaunders Tags: open access publications biomed central Source Type: blogs
