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HGP Counterfactuals, Part 4: Sequencing Tech Landscape Circa 1992
In thisseries leading to a pair of Human Genome Project alternative histories, I've been warming up with a trio of analyses of the technology landscape. At first I couldn't decide on the order to post these in, but then it was clear to me: a progression of scale fromphysical maps of the genome tohow to organize the sequencing of the BACs, and now to the actual sequencing technologies which were in play. In particular, how there was a very rapid evolution from 1992 (when I first was deeply exposed to this angle by attending Hilton Head) to 1997 (when I defended, but also the outcome was clear). In this time pe...
Source: Omics! Omics! - November 13, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs

HGP Counterfactuals, Part 2: The Forgotten Maps
Yesterday's post explored the concept of alternative histories, or counterfactuals and laid out why they might be a useful way to think about the value of the Human Genome Project. In this installment, I'll explore what I will call the forgotten maps, the critical elements of the HGP which are all too easily forgotten. These were both critical and expensive components of the project, so forgetting them is a mistake. Their prominence has faded as new technologies have come in and subsumed them, or they were mostly means to the end of a first human sequence, but understanding the project requires understanding ...
Source: Omics! Omics! - November 11, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs

10 Years of Omicing!
Today marks a special day - it was10 years ago that I launched this endeavor. I'm going to take time today, and perhaps a few times in the near future, to look back on the journey. Ten years of blogging also happens to be around my anniversary of starting work at Millennium, which means I've been a professional in biotechnology for two decades. So I must be old; indeed, this summer I celebrated birthday 30 (numeric pedants might make thebase charge that I am misleading by not writing that 0x30) and about a quarter century since I launched into bioinformatics full time. So a bit of nostalgia seems not out of...
Source: Omics! Omics! - October 27, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs

Segmental Duplications and Deletions in Books of History and Life
I have long had a historical interest in the U.S. Civil War. In fifth grade we had an all-day field trip to theGettysburg Battlefield, which is very well preserved, and it enthralled me. A few years later I would hike all over the battlefield with my Boy Scout troop, which is probably even closer to experiencing a taste of what it was like to be soldier. Of course, we had good hiking boots - a proximate cause of the battle occurring there was an attempt by the Confederates to raid a shipment of shoes which had just arrived in the town. My great-grandfather served in the Union Army, though entirely on garrison duty. �...
Source: Omics! Omics! - October 26, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs

Hello WDL ( Workflow Description Language )
This is a quick note about my first WDL workflow (Workflow Description Language) https://software.broadinstitute.org/wdl/. As a Makefile, my workflow would be the following one: NAME?=world $(NAME)_sed.txt : $(NAME).txt sed 's/Hello/Goodbye/' $ $@ $(NAME).txt: echo "Hello $(NAME)"> $@ Executed as:$ make NAME=WORLD echo "Hello WORLD"> WORLD.txt sed 's/Hello/Goodbye/' WORLD.txt> (Source: YOKOFAKUN)
Source: YOKOFAKUN - October 26, 2016 Category: Bioinformatics Authors: Pierre Lindenbaum Source Type: blogs

How Genomes Revolutionized Proteomics
Myrecent piece on the folly of moonshot projects caught the eye of a Silicon Valley blogger named Kumar Thangudu (@datarade), who gave me some nice praise. But along with that were some notes of his on other big science projects, and one he targeted was the Human Genome Project, with a sarcastic comment about the paucity of drugs coming from the HGP. Them's fighting words! So I launched a tweet stream his way outlining a number of impacts of HGP on biomedical science, and he was very nice and suggested I write more on that. I'm thinking of a number of angles on the topic, but here goes a bit of nostalgia that I...
Source: Omics! Omics! - October 25, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs

How Genomes Enabled Proteomics
Myrecent piece on the folly of moonshot projects caught the eye of a Silicon Valley blogger named Kumar Thangudu (@datarade), who gave me some nice praise. But along with that were some notes of his on other big science projects, and one he targeted was the Human Genome Project, with a sarcastic comment about the paucity of drugs coming from the HGP. Them's fighting words! So I launched a tweet stream his way outlining a number of impacts of HGP on biomedical science, and he was very nice and suggested I write more on that. I'm thinking of a number of angles on the topic, but here goes a bit of nostalgia that I...
Source: Omics! Omics! - October 25, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs

Messaging Counts
Myrecent piece on SeqLL's reboot of the Helicos sequencing technology attracted a number of helpful comments either on blogger or via email. Several of which pointed out the high suitability of this box for counting applications such as expression profiling, ChIP-seq and copy number analysis. Julia Karow of GenomeWeb graciously provided me with a copy of her piece, which underscored the value of GW in having real reporters dig into a s ubject. Much of what she dug up concerns SeqLL's future plans and for the near term mostly confirms suspicions that the technology will mostly look like the previous Helicos box,...
Source: Omics! Omics! - October 24, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs

SeqLL: Helicos van Winkle
Helicos was the first company to launch a single molecule DNA sequencing system. They never sold many systems (my estimate is fewer than 20), but some of those sites really loved their machines. One beauty of the system was a very simple sample prep: fragment your DNA, add terminal transferase and dATP and the sample was ready-to-hybridize. Helicos demonstrated a number of interesting applications, such as direct loading of RNA onto the system and performing capture on the flowcell. But with anemic demand and mounting losses, the company faded, finallyfiling for bankruptcy in November 2012. One true believer bought u...
Source: Omics! Omics! - October 22, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs

IGenomX Launches New Linked Read Chemistry
A hot concept in the genome world is how to capture long-range information, enabling assembly through repeats, resolving haplotypes, resolving copy number variation and many other applications in which short reads from short fragments are just not sufficient. A number of approaches have been proposed and published over the years, with some hitting commercial markets and significant use.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - October 20, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs

Genia Publishes Polymerase-to-pore docking scheme
Back in April, Iwrote up a PNAS publication from Genia and collaborators that described the modified nucleotides they have developed for their sequencing-by-synthesis with nanopore detection sequencing scheme. I had the opportunity to chat with George Church (who is an adviser both to my company and Genia, and a co-author on the paper) just after that and he remarked that there was a companion paper in the works describing the polymerase engineering for the system. That paper is now out in PNAS (and Open Access) and I'll take a little walk through it.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - October 18, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs

Sequencing, not random probes, are future of microbiological diagnostics
Okay, I'll admit I take requests. Throw a topic at me by Twitter or email, and if it piques my interest and I feel like I can say something intelligent, then I'll take it on -- but not necessarily instantly. That's the genesis of today's item, a tweet from Kyle Serikawa directed at me, asking if anew paper from groups at Rice and Baylor College of Medicine in Science Advances on a proposed microbial diagnostics (a paper highlighted by Eric Topol) had any legs.Huh. Well, intellectually clever, but isn't#Nanopore already leading the way in direct ID?@OmicsOmicsBlog, have any thoughts?#pathogenshttp...
Source: Omics! Omics! - October 16, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs

DNA: How Clean is Clean Enough?
Nick Loman has a new blog post nicely covering the current state of affairs for DNA preparation in the field. Earlier this year I hadsome thoughts about DNA preparation and the degree to which our current methods reflect history rather than some ideal. Even before Nick's post I had some new thoughts on the topic, but seeing his exposition helped me consolidate my own musings.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - October 12, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs

Let ’ s (briefly) revisit the Nobel API
It’s always nice when 12-month old code runs without a hitch. Not sure why this did not become a Github repo first time around, but now it is: my RMarkdown code to generate a report using data from the Nobel Prize API. Now you too can generate a “gee, it’s all old white men” chart as seen in The Economist – Greying of the Nobel laureates, BBC News – Why are Nobel Prize winners getting older? and no doubt, many other outlets every year including me at RPubs, updated from 2015. As for myself, perhaps I should be offering my services to news outlets instead of publishing on blogs and obscur...
Source: What You're Doing Is Rather Desperate - October 9, 2016 Category: Bioinformatics Authors: nsaunders Tags: programming statistics api nobel Source Type: blogs

Four Things You Might Be Surprised Can't Be Done On An iPhone or iPad
In well under a year, I've been sucked into Apple's mobile ecosystem. Partly this was due to lobbying from TNG (he fervently denies receiving any commissions, but I'm still suspicious). Partly it was due to the Android world not really locking me in; there were just too many things that weren't quite right. First, the family caught me ogling an iPad Pro and talked me into getting one. Once I had that, there was confusion over which text channel messages had been sent and getting an iPhone to consolidate them (since iMessage would go to both devices) started making sense. Plus my Samsung phone was ...
Source: Omics! Omics! - September 6, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs