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
XML parsing made easy: is that podcast getting longer?
Sometime in 2009, I began listening to a science podcast titled This Week in Virology, or TWiV for short. I thought it was pretty good and listened regularly up until sometime in 2016, when it seemed that most episodes were approaching two hours in duration. I listen to several podcasts when commuting to/from work, which takes up about 10 hours of my week, so I found it hard to justify two hours for one podcast, no matter how good.
Were the episodes really getting longer over time? Let’s find out using R.
One thing I’ve learned as a data scientist: management want to see the key points first. So here it is:
T...
Source: What You're Doing Is Rather Desperate - October 12, 2017 Category: Bioinformatics Authors: nsaunders Tags: R statistics parsing podcast rss twiv xml Source Type: blogs
Feels like a dry winter – but what does the data say?
A reminder that when idle queries pop into your head, the answer can often be found using R + online data. And a brief excursion into accessing the Weather Underground.
One interesting aspect of Australian life, even in coastal urban areas like Sydney, is that sometimes it just stops raining. For weeks or months at a time. The realisation hits slowly: at some point you look around at the yellow-brown lawns, ovals and “nature strips” and say “gee, I don’t remember the last time it rained.”
Thankfully in our data-rich world, it’s relatively easy to find out whether the dry spell is really ...
Source: What You're Doing Is Rather Desperate - October 11, 2017 Category: Bioinformatics Authors: nsaunders Tags: australia statistics ggplot2 rainfall sydney underground weather 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
Infographic-style charts using the R waffle package
Conclusion
That’s it, more or less. Are the icons any more effective than the squares? In certain settings, perhaps. You be the judge.Filed under: R, statistics Tagged: packages, rstats, visualization, waffle (Source: What You're Doing Is Rather Desperate)
Source: What You're Doing Is Rather Desperate - September 8, 2017 Category: Bioinformatics Authors: nsaunders Tags: R statistics packages rstats visualization waffle 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
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
Years as coloured bars
I keep seeing years represented by coloured bars. First it was that demographic tsunami chart. Then there are examples like the one on the right, which came up in a web search today. I even saw one (whispers) at work today.
I get what they are trying to do – illustrate trends within categories over time – but I don’t think years as coloured bars is the way to go. To me, progression over time suggests that time should be an axis, so as the eye moves along the data from one end to the other, without interruption. What I want to see is categories over time, not time within categories.
So what is the way to g...
Source: What You're Doing Is Rather Desperate - August 5, 2017 Category: Bioinformatics Authors: nsaunders Tags: R statistics ggplot2 visualisation 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
To do analysis stuff
First there was “insert statistical method here“. Now we have R – making it easy “to do analysis stuff“.
Via Elisabeth; I’ll hand you over now for an entertaining summary.
To be fair, analysis stuff describes my working life quite well.
Filed under: humour, publications, uncategorized (Source: What You're Doing Is Rather Desperate)
Source: What You're Doing Is Rather Desperate - August 2, 2017 Category: Bioinformatics Authors: nsaunders Tags: humour publications Source Type: blogs
Twitter Coverage of the ISMB/ECCB Conference 2017
Search all the hashtags
ISMB (Intelligent Systems for Molecular Biology – which sounds rather old-fashioned now, doesn’t it?) is the largest conference for bioinformatics and computational biology. It is held annually and, when in Europe, jointly with the European Conference on Computational Biology (ECCB).
I’ve had the good fortune to attend twice: in Brisbane 2003 (very enjoyable early in my bioinformatics career, but unfortunately the seed for the “no more southern hemisphere meetings” decision), and in Toronto 2008. The latter was notable for its online coverage and for me, the pleasure of...
Source: What You're Doing Is Rather Desperate - August 2, 2017 Category: Bioinformatics Authors: nsaunders Tags: bioinformatics meetings statistics eccb ismb twitter Source Type: blogs
