Nice graphic? Are they taking the p …
Yes, it started with a tweet:
Nice graphic on urine components via https://t.co/sfuXNB02sF pic.twitter.com/vhVLahQ8su
— Metabolomics (@metabolomics) January 31, 2017
By what measure is this a “nice graphic”? First, the JPEG itself is low-quality. Second, it contains spelling and numerical errors (more on that later). And third…do I have to spell this out…those are 3D pie charts.
Can it be fixed?
So far as I know, there isn’t a tool to generate data by extracting labels from images, so I sat down and typed in the numbers manually. Here they are for download. The top and bottom pie cha...
Source: What You're Doing Is Rather Desperate - February 4, 2017 Category: Bioinformatics Authors: nsaunders Tags: R statistics charts data visualisation Source Type: blogs
The real meaning of spurious correlations
Like many data nerds, I’m a big fan of Tyler Vigen’s Spurious Correlations, a humourous illustration of the old adage “correlation does not equal causation”. Technically, I suppose it should be called “spurious interpretations” since the correlations themselves are quite real, but then good marketing is everything.
There is, however, a more formal definition of the term spurious correlation or more specifically, as the excellent Wikipedia page is now titled, spurious correlation of ratios. It describes the following situation:
You take a bunch of measurements X1, X2, X3…
And a second ...
Source: What You're Doing Is Rather Desperate - February 2, 2017 Category: Bioinformatics Authors: nsaunders Tags: R statistics causation correlation proportionality ratios Source Type: blogs
Could Hermione Tackle MinION Yield Variability?
A bit of a foray into Oxford Nanopore land again. By replacing a bench bumbler with someone competent, we've seen some success with our MinION at Starbase. Highly variable yields though. I've done some looking and discovered this isn't a unique experience. And now Oxford is suggesting that software upgrades alone will give MinION about another 50% boost in yield; it will be interesting to see what this does for variability. Finally, I have a notion of some of the sources of variability and an idea for a troubleshooting toolRead more » (Source: Omics! Omics!)
Source: Omics! Omics! - February 1, 2017 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Taking steps (in XML)
So the votes are in:
Your established blog is mostly about your work. Your work changes. Do you continue at the current blog or start a new one?
— Neil Saunders (@neilfws) January 23, 2017
I thank you, kind readers. So here’s the plan: (1) keep blogging here as frequently as possible (perhaps monthly), (2) on more general “how to do cool stuff with data and R” topics, (3) which may still include biology from time to time. Sounds OK? Good.
So: let’s use R to analyse data from the iOS Health app.
I own an iPhone. It comes with a Health app installed by default. Not being a big user of mobile...
Source: What You're Doing Is Rather Desperate - February 1, 2017 Category: Bioinformatics Authors: nsaunders Tags: personal statistics this blog health iOS parsing xml Source Type: blogs
Illumina Drops NeoPrep
At the2015 AGBT meeting, Illumina launched the NeoPrep, a ~$40K instrument to automate the preparation of up to 16 sequencing libraries at a time, using a technology called electrowetting microfludics. Now news comes that Illumina is dropping the NeoPrep, halting sales immediately and allowing existing users about a year of reagents. What happened and how does it impact genomics?Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - January 31, 2017 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
On The International Nature of American Biotech
I'll spend two hours in project meetings tomorrow. Around the table will be a group of scientists who are all at the top of the game and among the best in the world at what they do. We will be trying to push forward new antibiotics to save lives. Yes, we are also trying to be rewarded monetarily with it, but we all share a mission to improve humanity by finding new drugs for important medical needs.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - January 30, 2017 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Perl: The Bad Habit I Can't Quite Kick
TULIP is a new assembler for long, error-rich reads such as from nanopore. I was a bit stunned to see that TULIP is written in Perl; I was starting to wonder how many holdouts like me there were. Which led to this exchange on Twitter@hans_j_jansen@github as someone who can't quite kick the habit, I both applaud&grimace with your use of Perl for leading edge bfx— Keith Robison (@OmicsOmicsBlog)January 23, 2017@hans_j_jansen@OmicsOmicsBlog@github if it ain't broken...#perlforever— Roger Pettett (@zerojinx)January 24, 2017Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - January 26, 2017 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Notes on a Conversation with 10X
I've been remiss in writing up a piece on 10X Genomics based on a phone discussion last week with Michael Schnall-Levin (VP Computational Biology and Applications) and Anup Parikh (Director, Product Marketing). I always appreciate companies reaching out to me and spending time to educate me on their products and plans, and this was a very interesting and enjoyable conversation.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - January 23, 2017 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Bio-Rad Sips Up RainDance
Monday evening brought news that Bio-Rad has further consolidated its grip on the droplet microfluidics space by acquiring RainDance Technologies for an undisclosed price. Bio-Rad had previously acquired droplet digital PCR company QuantaLifeback in October of 2011 and targeted sequencing company GnuBio in April of 2014. While the droplet digital PCR has been marketed for many years now, the GnuBio effort had gone relatively quiet since the acquisition. However, Bio-Radannounced the JP Morgan conference that this technology will be launched as OncoDrop late this year.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - January 16, 2017 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
State of the lab 4 – the one before the four year review
It has been 4 years since I started as a group leader at the EMBL-EBI (see past yearly reports –1,2 and3). This year the group composition has been mostly stable, with the exception of interns that have rotated through the group. We had Bruno Ariano (twitter) visiting us for 6 months working on a project to build an improved functional interaction network for Plasmodium. Matteo Martinis has joined the group for a few months and is working with David Ochoa on comparing in-vivoeffects of kinase inhibitors with their knownin-vitro kinase inhibition effects. Finally, Areeb Jawed has joined Cristina and Bede, for some mo...
Source: Evolution of Cellular Networks - January 13, 2017 Category: Cytology Tags: state of the lab Source Type: blogs
Illumina Unveils HiSeq Successor NovaSeq
At today's J.P. Morgan Healthcare Conference Illumina made a number of small announcements -- some new partnerships, Firefly on track for launch later this year, launch of the single cell workflow partnered with Bio-Rad. Then CEO Francis deSouza dropped the big news: a new high-end sequencer architecture to ultimately replace all of the HiSeq instruments. It sounds like an interesting evolution of the Illumina product line, but unfortunately too many headlines and tweets have focused on a distant goal of $100 hu man genomes. Worse, not only did some commentators misconstrue the announcement as delivering on $100 ...
Source: Omics! Omics! - January 8, 2017 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Pondering What Is Lost In Teaching Translation
I'm good at acquiring distractions, and a relatively new one is Quora. This site allows users to ask questions which are then answered by members of the community. I lurk in a number of fields, but have answered a few questions related to genomics and related fields of biology. Tackling a question last night required re-learning some details I was disappointed I had forgotten. In researching to regain that knowledge, I skimmed a number of study guides online, which leads to this post.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - January 7, 2017 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
#JPM17 Genomics and Synthetic Biology Companies
With the2017 J.P. Morgan Conference in Healthcare (#JPM17)starting Monday, I and others have engaged in early reporting or speculation. I've tried to compile a list of presenting companies in the genomics, informatics and synthetic biology tool spaces, but these were filtered quickly from a long list of presenting companies so I may have missed some -- please leave comments and I can add. Also, some of the big conglomerates could speak on these topics but might ignore them, so no promises. For example, Roche has their pharmaceutical CEO speaking, so we may not hear anything about thePacBio breakup orGenia lawsuit...
Source: Omics! Omics! - January 6, 2017 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Two Pore Guys Previews Handheld Nanopore Analyte Sensor Ahead of J.P. Morgan Conference
2017 is certainly shaping up to be a big year for nanopore news. I touched on Oxford Nanopore's very full plate in my speculation about sequencing platforms and we already know of two different legal actions which will be progressing,PacBio vs. Oxford Nanopore andUniversity of California vs. Genia. James Hadfield'stake on possible Illumina announcements at the J.P. Morgan Conference includes an Illumina nanopore device. That's speculation; today we had a pair of tweets fromTwo Pore Guys previewing their sensing device and that they will be talking more at J.P. Morgan (all videos from 2PG).See the first pu...
Source: Omics! Omics! - January 4, 2017 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
University of California Cries " Thief! " on Genia Patents
AsI noted in my last post, the University of California has filed suit against Genia claiming that Genia co-founder Roger Chen misappropriated intellectual property from UC Santa Cruz and the laboratory of Mark Akeson (filings include a bunch of other well-known nanopore scientists, including David Deamer and Dan Branton). While the filings are mostly dry, they are enlivened occasionally by such colorful language as"evasive tactics","aided and abetted" and"stonewalled". Goaded by Mick Watson, I've dug into the court filings and some of the patents (and obtaining those filings apparen...
Source: Omics! Omics! - January 2, 2017 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
