Illumina Outlook II: The Fleet
Inmy prior installmentI looked at Firefly, now clearly a working instrument. Now I'll take a peak at the rest of the Illumina fleet.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - January 7, 2018 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Illumina 2018 Preview I: Firefly
Time to start gazing into my cloudy liquid crystal ball and attempt to see what will happen in the sequencing world in 2018. J.P. Morgan is next week, which puts a time box on getting predictions out. One thing I see on both my personal and blogging horizon are flying creatures bearing light. On the local front, TNG has decided to head this fall to the City of Brotherly Love to learn to fly and breath flame. But in the sequencing world -- well, I'm going to need to pack a huge Ball jar for my trip to AGBT this year, as I plan to hunt out a Firefly.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - January 2, 2018 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Remembering 2017's Losses
A new year beckons and with it a burst of enthusiasm for writing. Which also means combing through post ideas from last year that never quite were completed -- some as stubs or at least headlines. But before tackling the new, I feel I need to tackle some personal losses in 2017.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - January 1, 2018 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
2017 Nanopore Community Meeting: An Incomplete Summary
The 2017 Nanopore Community Meeting was over a week ago back in New York City, so I ' m grossly overdue in cobbling together some observations and opinion based on the tweet stream (I had a critical day job meeting at the same time and wasn ' t in New York). I diddash off the bit about SmidgION being potentially like the early Macs (though I got wrong the nomenclature, the original was the Mac 128K -- Mac Classic was a later model that resembled it). Oxford also deviated this autumn from the pattern of public information they had seemingly established, with major news at London Calling and smaller updates at th...
Source: Omics! Omics! - December 10, 2017 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
On the Problem of Sequence Leakage
I've been spending some time lately in an unfamiliar world: the eukaryotic section of NCBI's NR protein database. I've been almost exclusively a bacterial guy for six years, but the other side of starbase had an interest in find homologs of a particular protein so I went diving for some. That experience has reminded me of two serious issues with public sequence databases. Tonight I'll dash off a bit about one; expect the other complaint to show up in the not-so-distant future. And tonight's lament is the increasing dispersion of sequence respositories.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - December 7, 2017 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
SmidgION: Mac Classic for the 21st Century?
Apple launched the Macintosh computer witha famous television adplaying on the launch year, 1984. What emerged was what we now know as the Mac Classic. What may be less known is why the Mac Classic had that distinctive shape: it was intended to be backpack-portable, as Apple had a deal with a consortium of top U.S. universities to sell Macintoshes to their students. Perhaps even more forgotten is that one of those schools,Drexel University in Philadelphia, made owning a Macintosh arequirementfor students.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - December 3, 2017 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
A Nucleotide Mixture-Based Error Correcting Short Read Chemistry
Sometimes polony-style short read sequencing seems like old news. The underlying technology has been commercially available for over a decade. I focus much of my attention to gains in long read technologies, though incremental improvements to read lengths or polony densities still appear. Now in Nature Biotechnology a group from Peking University has publis hed a new twist on sequencing-by-synthesis that is claimed to offer significant improvements on read accuracy.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - November 6, 2017 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
AlphaGo & Biology
A comment was left on an early piece suggesting I comment on the recent AlphaGo paper and the possible applicability of this approach to biomedical sciences. I'm not sure I have anything terribly original to say, but who can refuse a request?Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - November 1, 2017 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Mission Bio Launches Tapestri Single Cell Platform
The fact that tumors and their immediate environment is genetically heterogeneous has long been known, but tools for high-throughput assessment of this heterogeneity have only recently become available. The whole field of single cell RNA-Seq has seen spectacular growth, as new methods enable greater and greater numbers of cells to be profiled from a sample. Profiling the DNA content on an individual cell basis has not been quite as much in the spotlight, but now a start-up calledMission Bio is launching a microfluidic library prep workflow, Tapestri, to enable amplicon panels to be run in single cell mode.Read more »...
Source: Omics! Omics! - October 17, 2017 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
iGenomX Riptide Kits Promise a Sea of Data
A theme for me in my six years on Starbase has been addressing the challenge of cost-effectively sequencing many small genomes. While sequence generation bulk prices have plummeted, all-in library construction cost has tended to stubbornly resist dramatic change. Large genome projects don't face quite such a pinch, but if you want to sequence thousands of bacteria, viruses or molecular biology constructs, paying many-fold more for getting a sequence into the box than you're paying to move it through the box ends up being a roadblock. Illumina's Nextera approach dropped prices a bit, but not really a sea ch...
Source: Omics! Omics! - October 13, 2017 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
PacBio's Frankenpatent on Error Correction
Well, here we go again. Pacific Bioscienceslaunched yet another patent lawsuittowards Oxford Nanopore at the end of September, and already the hounds are baying for me to look at the patents -- which I've foolishly established a reputation of doing. I will remind readers that, to use a construction that exasperates my son, I have no memory of these topics being covered during the time I was in law school. (said construction also works for divinity school, seminary, yeshiva, dental school, military academy, etc). Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - October 4, 2017 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Dispatches from CDC AMD Day 2017
I had the singular honor and pleasure of speaking this past Monday at the Center for Disease Control and Prevention'sAdvanced Molecular Detection(AMD) program's annual confab in Atlanta. Just visiting the CDC campus was already a bit magical -- along with the Kennedy Space Center and Cold Spring Harbor it's one of mythical places of human exploration to me. But to actually stand at the podium? Wow!I've collected below a bunch of separate mental threads, many of which probably should be expanded out to a full post in the future.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - October 1, 2017 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Why Is LISP So Rare in Bioinformatics?
LISP is one of the oldest computer languages and perhaps one of the most influential of the early ones. Some of the other well-known Eisenhower era languages -- Fortran, COBOL and ALGOL, have certainly left their mark, but LISP and derivatives such as Scheme or Common LISP certainly carries more cachet among"serious" programmers. COBOL has always been a bit of an easy joke and Fortran tends to mark you as old-school; use of APL (once a language of mine) would mark you as dangerously reactionary. ALGOL begat Pascal and Modula II and clearly had impact on the C syntax family of languages (including bioinforma...
Source: Omics! Omics! - September 24, 2017 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Teaching Biology Evidence: Old or New?
I've been toying over a week with writing something based on an interesting Twitter discussion started byDr. Laura Williams (@MicroWavesSci) of Providence College pondering the best way to approach teaching molecular genetics (really, science in general) at the undergraduate level. In particular, Professor Williams wondered about the dangers of branding various key experiments with the names of the experimenters, such as Hershey-Chase or Meselson-Stahl. The risk she points out is that this can devolve into an exercise in memorizing names and dates without assimilating conc epts, or conversely that some students wil...
Source: Omics! Omics! - September 18, 2017 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
The Curse of Spammotation Lives!
High throughput sequencing of genomes is over twenty years old, which demanded the development of automated pipelines for annotating this data. I've worked on such pipelines since the early 1990s, implementing them as a student and at two different corporate stops. Indeed, we were reviewing results from my pipeline versus some of the other ones out there to see what can be done better. And unfortunately, I've found infuriating problems with RefSeq entries annotated with NCBI's bacterial genome annotation pipeline. Now I'm usually one to sing the praises of NCBI -- they are a key resource for biologi...
Source: Omics! Omics! - August 29, 2017 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
