DNA vs. the Machine
Last week's news contained a story sure to raise eyebrows.  A group of computer security researchers from the University of Washington claimed to have demonstrated that they could hijack a computer via sequencing a carefully-constructed DNA fragment.  Visions of NextSeqs rampaging through the streets immediately sprung to mind.  The paper is interesting and has some useful warnings for the bioinformatics community, but certainly the news coverage has been strong on hype and alarmism.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - August 15, 2017 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Computational Biology & Math: Am I Just Faking It?
Over on Quora a common type of question is"Can I be a computational biologist if I am now an X".  Personally I take a very broad view and think just about anyone with intellectual curiosity can become any kind of scientist.  A related type of question is"how skilled do I need to be in Y to succeed in computational biology", where Y is most often programming, biology or math.  I got thinking about this and started wondering whether I am actually at all skilled in math.  Here is the results of that analysis.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - August 5, 2017 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
A Third GridION X5 Pricing Plan
When Oxford Nanopore announced theirGridION X5 instrument in March, I and others attempted to parse the difference between the two pricing plans  -- and I made a bit of a hash of it.  The X5 runs 5 MinION flowcells independently in parallel from a single desktop instrument, which also includes FPGA-based acceleration of basecalling plus a license to perform sequencing-for-hire.  Indeed, Matt Loose tweeted out an image of an"X6" and then mention of an"X7"; the X6 had a MinION plugged into the USB port and apparently the FPGA unit can keep up with seven flowcells all running simultaneously.  Now Oxfor...
Source: Omics! Omics! - July 21, 2017 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
STAT Proves Not Resistant To Antibiotic Tropes
Tuesday's Boston Globe carrieda piece originating from STAT news on an interesting natural product antibiotic, pleuromutilin.  A research grouprecently published a new total synthesis of this fungal terpene, an advance which promises to enable greater medicinal chemistry around the molecule.  That part is cool.  Unfortunately, when it gets to the biology of pleuromutilin the piece by Eric Boodman completely spits the bit, trotting out some horribly inaccurate tropes.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - June 28, 2017 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
New Life in the Sanger Market
In my bit on"I'm not dead yet" technologies recently, I included large scale Sanger sequencing. That reflects to a large degree my personal experiences and biases.  Targeted Sanger is great for spot checking the occasional junction or misbehaving clone or strain, but I forget that many clinicians still see it as a gold standard.  Apparently there are others who disagree with me, as Thermo Fisher recently launched a new Sanger instrument targeted at small lab s, andaccording to GenomeWeb Promega plans an instrument offering in the same space as well.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - June 14, 2017 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Ice Ghosts:A Shortage of Maps
I'm going to step outside the usual topic space here and cover an interesting but frustrating book I read partly on the flight to London Calling (which is about the only connection it has to genomics). Â Ice Ghosts, by Paul Watson, covers the searches for the lost Franklin Expedition, a mid-1800s British Navy attempt to find the Northwest Passage. Â It's a pretty good book, after all it did win a Pulitzer Prize, Â The topic is thrilling: explorers under difficult conditions and a mystery that lasted over a century. Â There are lessons for science in general, such as the value in carefully evaluating oral histories ...
Source: Omics! Omics! - June 6, 2017 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
What Is (and Is Not) Sequence Assembly?
In the closing talk of the pre-London Calling workshop, Hans Jansen had closed his presentation with a question whether at some future date sequence assembly would become obsolete.  This was meant to be an aspirational vision for a distance timepoint, but one correspondent on Twitter saw it as hype.  I got in a bit of a discussion, constrained by the dreaded 140 character limit, which ended up largely illustrating that I have a somewhat more restricted definition of assembly than some people.  I'm going to explore this and you can judge for yourselfRead more » (Source: Omics! Omics!)
Source: Omics! Omics! - May 22, 2017 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
London Calling 2017: Plant & Animal de novo Genomes
Okay, I'm desperately behind on writing up the external science from London Calling.  Not helpful that I claimed I would not only do so, but in multiple installments.  A number of the plenaries focused on large genome assembly, so that's what I'll tackle now -- plus a few other bits.  See also myStorify summaries, which include other reports on the conference.  Also check out my storifies on theSMRT Leiden conference, which ran at the beginning of the same week and discusses many similar topics.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - May 18, 2017 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
SFAF & I'm Not Dead Yet Technologies
Jonathan Jacobs posted his annual reminder that theSequencing, Finishing and Analysis in the FutureMeeting (SFAF) will be this week. Â Alas, that meeting hasn't had many more tweeters in the past than Jonathan, but perhaps this year there will be more. Â There's a glut of genomics conferences to track, compile tweets and opine on -- besidesLondon Calling, there's beenSMRT Leiden and Biology of Genomes, all in the span of two weeks! Â This post is going to be a bit short on actual writing and more to just flag some talks at SFAF that grabbed my attention. Â What I realized is that the talks at SFAF illustrate th...
Source: Omics! Omics! - May 14, 2017 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
London Calling 2017: A Theme of Consolidation
London Calling 2017 came to a close last Friday. Â Any excuses of jet lag or nights running up ONT's bar tab won't hold up much longer, so time to finish this post (I really did start the night after Clive's talk!) I'm going to largely divide coverage on the dividing line of who presented: today's piece on Oxford Nanopore presentations, particularly Clive Brown's, and in the near future at least one focusing on the science users presented. Â For other summaries of the action, I've created astorify of just blog posts and similar summaries of the meeting, as there were a great number (and I am on ...
Source: Omics! Omics! - May 9, 2017 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Nanopore Workshop Notes
I attended on Wednesday theLondon Callingpre-conference workshop, an add-on for those wishing for help getting started with MinION sequencing. Â Judging from who I spoke to, many participants were utterly new to nanopore sequencing and more than a few were like me in that they had tried the platform and wanted to do better. Â My colleague has gotten some very good results recently, which has re-fired my determination to get good at that my self. Â Below are some limited notes I took that may be of general interest. Large portions of the workshop will go largely uncovered, as I focused on what was surprising or new.Read mor...
Source: Omics! Omics! - May 4, 2017 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
London Calling 2017: A Preview
Oxford Nanopore's London Calling confab runs Thursday and Friday, with a training workshop on Wednesday.  I'll be there -- who can resist a conference nearly at the Tower of London? -- and will also be testing whether my personal"field of nanopore sequencing suppression" can defeat ONT's best trainers.  Here's some preview of what I'll be particularly looking for, though being surprised will be lots of fun too. Much more fun that reading (the wrong) patents!Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - May 2, 2017 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Oxford Nanopore's Enigmatic Patent Litigation
Oxford Nanoporehas launched lawsuits in the UK and Germany against Pacific Biosciences, alleging infringement of a European patent licensed from Daniel Branton's lab at Harvard,EP1192453, which is apparently exclusively licensed to Oxford. Â When I wrote about Pacific Biosciences first lawsuit against Oxford Nanopore late last year I titled it"PacBio's Quixotic Patent Litigation", as it appeared the Oxford could easily dodge the lawsuit by abandoning the 2D sequencing technology, which Oxford is in the process of doing. Â I've swapped in"enigmatic" for this title, as I'm not even sure wh...
Source: Omics! Omics! - May 1, 2017 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Exercise: A Sequence Signature for Transcription-Translation Coupling in Bacteria?
A pretty common question over on Quora is something along the lines of"how do I learn bioinformatics".  Great question!  Tonight I'm going to outline a project which I think would make a good first bioinformatics project.  It is rich in content and keys off an interesting new non-computational result.  And since I've left graffiti on multiple Quora threads that I would write something like this in the immediate future, here it is!Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - April 26, 2017 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Pinniped Karyotypes & N50 Statistics
In myrecent piece on long read assembly, I laid out part of the case against the N50 statistic. Â Historically, the issues with the statistic have been around the fact it can be gamed at the expense of assembly correctness or assembly coverage. These are concerns for the typical sort of short read assemblies we've grown used to: lots of contigs and the temptation (perhaps justified) to try to go for higher N50s by more aggressive merging or by filtering out the short contigs. Â Elin Videvall over at The Molecular Ecologist has a nice ongoing series of posts illustrating the statistic and these commonplace issues:What â...
Source: Omics! Omics! - April 22, 2017 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
