News from Old Neighborhoods
Five years ago, the initial band of scientists at my current employer had just moved from the offices of our venture capitalist sponsor, Third Rock Ventures, into lab space in Cambridge sublet from Blueprint Medicines. The Athenaeum Building is a large brick-faced building which once held the publishing house by that name. Eleven Biotherapeutics was trying to engineer new immune-modulating proteins, initially focusing on a treatment to dry eye. Some of their IP I understand was pulled from the wreckage of C odon Devices. Also on the floor was Verastem, a company spun out of work from Robert Weinberg and Eric Lande...
Source: Omics! Omics! - November 20, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
The y-axis: to zero or not to zero
This article tells us that “it’s OK not to start your y-axis at zero”, but then states that “column and bar charts should always have zeroed axes”. They use a chart from the Twitter IPO as an example.
If you were waiting for the obligatory bad-mouthing of Excel, look no further than a follow-up Tweet by the chart author.
@DocJohnG True. Also contact Microsoft Excel, let them know the default y-axis is simply unacceptable; lazy people like me need nudging.
— D Yanagizawa-Drott (@yanagiz) November 11, 2016
Onwards. What if we use a line chart instead?
ggplot(subset(elections.2, vote =...
Source: What You're Doing Is Rather Desperate - November 20, 2016 Category: Bioinformatics Authors: nsaunders Tags: R statistics charts graph politics visualisation Source Type: blogs
Will Liquid Handling Robots Ever Join the 21st Century?
In the course of this blog, there are many topics I've thought about writing that I haven't touched. Sometimes it is due to the problem of the topic being too revealing to what I am working on, sometimes it is because I'm not satisfied with the result, but far too often I procrastinate so long that it no longer seems fresh. Or I'll just do it another time when the moment is right, which it never is. But a recent Twitter exchange reminded me of a long-suppressed lament on some expensive, finicky and problematic -- but very useful -- denizens of a modern lab: liquid handling robots.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - November 19, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
HGP Counterfactuals, Part 7: Wrapping Up
It's been interesting revisiting a bunch of now ancient history of the Human Genome Project with the goal of exploring other possibilities. Istarted by considering the entire concept of alternative histories, then reviewed theconstruction of physical maps,strategies which were considered for sequencing the clones comprising the minimum spanning map of the genome and theactual sequencing technologies employed, then considered scenarios in whichno HGP is launched or the project is given a much smaller budget andforced to focus on technology development. Tonight, I'll close this out by trying to summarize some of ...
Source: Omics! Omics! - November 16, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
HGP Counterfactuals, Part 6: Ax Sharpening Only
Atthe beginning of this series, I promised two alternative histories on the Human Genome Project. Yesterday I explored a timeline in which opponents of the HGP successfully kept it from ever being funded. Today, I'll try to imagine what would have happened if the project had been funded only to develop new sequencing technology. One warning: as part of this I will show the most reviled plot in genomics, but to make something other than the usual point.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - November 15, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
When only truthiness matters
As many others out there I am still trying to process the result of the US elections. I don ’t usually write about politics but I think this does have relevance to science. The result brought me flashbacks of the outcome of the Brexit vote. In both occasions I woke up to a result that I found shocking and disheartening. Both times I went to work in a dazed state of denial trying to come to terms with the fact that so many people have viewpoints that are so different from mine. Personally, I find repugnant that both elections were so much about racism and fomenting protectionist and anti-immigration movements. There are m...
Source: Evolution of Cellular Networks - November 13, 2016 Category: Cytology Source Type: blogs
HGP Counterfactuals, Part 3: BAC Sequencing Strategies
I introduced this seven-part series with an exploration of thevalues and challenges of counterfactual histories. Yesterday, I looked at the"forgotten maps" which laid out the genome ready-to-sequence as a minimum tiling set of BACs, made sure that those BACs faithfully represented the genome and that this set was tied at regular intervals to the genetic markers and cytogenetic locations which were the linga franca of human geneticists. Today, I'll look at strategies that were considered for sequencing all those BACs.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - November 12, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
HGP Counterfactuals, Part 1: An Introduction
My new correspondent, Kumar Thangdu, has posed some challenging questions with regard to the Human Genome Project. He's been good enough tocapture my initial tweet stream over at his blog, which was my initial defense. I then followed up withmy note on my one paper in proteomics, which I received favorable feedback on from one of my co-authors.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - November 10, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Oncology: The 10Km View
My Twitter correspondent Kumar Thangdu keeps throwing interesting but difficult questions my way, far faster than I can keep up. Not sure I'm even particularly skilled at many of these. But, one must try.@OmicsOmicsBlog The best thing we can do to cure cancer, might be to try not to cure cancer, but just fund basic research? accurate?— Kumar Thangudu (@datarade) November 8, 2016Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - November 9, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Homopolymers and Other Recurring Topics in Pore Taste
Some interesting comments showed up onmy piece covering Pacific Biosciences trade action launch against Oxford Nanopore. Alas, some silly comments showed up as well. Life on the Internet. In particular, Mohan Chennupati asked a series of questions that can be seen as more friendly to PacBio and less so to Oxford Nanopore than my analysis. They're all good questions and worth digging into, and you'll find some other commenters addressing them. I'll quote from his comments but rearrange the order a bit. I believe I've not changed their meaning or damaged his argument, but please check me. The ma...
Source: Omics! Omics! - November 3, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
PacBio's Quixotic Patent Litigation
I'm feeling very glad Iclosed out the Illumina/U. Washington litigation vs. Oxford Nanopore the other night, albeit very belatedly, as now Oxford is facing a similar set of legal actions, but this time initiated by Pacific Biosciences. PacBio hasfiled a complaint with the U.S. International Trade Commission (ITC) alleging that Oxford is infringing on an issuedU.S. patent, 9,404,146 (aka 146 Patent). Surely PacBio's management thought this was a good idea, but from this perspectiveRead more » (Source: Omics! Omics!)
Source: Omics! Omics! - November 2, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Tidying Loose Nanopore Patent Threads
A commenter onmy recent piece on Genia made a number of assertions with regard to nanopore patents. A more general one was a complaint that I had covered theopening salvo of the battle from Illumina and University of Washington andOxford's formal response andfeinting to the CsgG/R9 pore, but failed to cover the campaign's termination. It's a fair charge and I'll rectify this here. My (rather lame) excuse is the news broke while I was on vacation in the Pacific Northwest and trying to avoid any remotely professional activities, other than readingLuke Timmerman's Lee Hood biography. But, that do...
Source: Omics! Omics! - October 30, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Bill Gates Succumbs to Moonshot Madness
Another day, another misguided call for a moonshot in human disease. This time, it's Bill Gateslaying out four goals that he believes can be attained in the next decade, given the correct amount of dedication and determination. Among these goals are a vaccine for HIV and a cure for neurodegenerative diseases. I'll focus my comments on the neurodegenerative diseases with a few comments about fellow Blue Hen Joe Biden's cancer moonshot, but many of the criticisms apply to the HIV or just about any serious disease.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - October 5, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
ONT's Wafer Thin Update
Oxford Nanopore's Clive Brown gave an hour-long update on their platform last week. A busy social schedule featuring (on different nights) GMO beer and challah - plus six hours travel each way to the challah-fest. Add atop that a fast-moving upper respiratory tract infection, and I'm even more behind in blogging than usual for such events (plus I gathered another post idea away -- and had another suggested to me). Time to get working on the backlog!Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - October 4, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Writing a Custom ReadFilter for the GATK, my notebook.
The GATK contains a set of predefined read filters that "filter or transfer incoming SAM/BAM data files":BadCigar
BadMate
CountingRead
DuplicateRead
FailsVendorQualityCheck
LibraryRead
MalformedRead
MappingQuality
MappingQualityUnavailable
(...)
With the help of the modular architecture of the GATK, it's possible to write a custom ReadFilter. In this post I'll write a ReadFilter that removes the (Source: YOKOFAKUN)
Source: YOKOFAKUN - September 21, 2016 Category: Bioinformatics Authors: Pierre Lindenbaum Source Type: blogs
