Self-Assessing My Python
I've been programming 90+% in Python now for over a year and a half -- when I joined the Strain Factory I vowed to finally make the break from Perl. Partly this was disgust with so often finding libraries I wanted to be missing or broken, and partly it was recognizing that the Factory is primarily a Python shop and I would have the most impact if I worked in thelingua franca.I was first exposed to Python back at Codon Devices, but there was a strong C# faction there and I fell in love with that language, so my primary dabbling in Python was learning enough to glue the key Python code into my C# with IronPython. I...
Source: Omics! Omics! - August 30, 2020 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Two Pandemic-Related Programming Problems
I will offer here two bioinformatics programming problems which I think are interesting, useful and should be approachable by an advanced undergraduate. For a variety of reasons I've been thinking a lot of about skill levels and how to assess them. One key reason is we have two open slots in our group, so I'm plowing through CVs and engaging in the usual hiring funnel struggle -- how do you winnow CVs to phone screens and then down to interviews? We also thought we might, but now won't, bring on a one year intern. But I'm also trying to take a look at my own skill set with a critical eye. Plus I...
Source: Omics! Omics! - July 23, 2020 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Virtual London Calling, Veritably Late, Part II: Platform Development
Last time, I covered Oxford NanoporeLamPORE COVID-19 detection scheme. London Calling was over a week ago, so the chance to scribble before its all old news is rapidly shrinking. As noted yesterday, Clive Brown didn't speak here but instead will broadcast at some future date; it was left to his top technical lieutenants to cover the developments in the platform which have happened since the Community Meeting in New York back in early December. I've tried to hit the highlights here, but don't claim to be comprehensive.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - June 28, 2020 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Virtual London Calling, Veritably Late Copy: Part I, LamPORE
London Calling was last week, held online due to the pandemic. My plans to attend in person were one of a myriad of travel arrangements upended by the calamity, though that is utterly trivial in comparison to the tragedy of so many lost lives, damaged survivors and economic ruin. Attending remotely also made it harder to ignore my work duties, which are at a crescendo (well, not really: it's been this intense for months). But all the talks are available online, so I have stolen some time to review the Oxford Nanopore technology announcements. There wasn't a Clive Brown talk; apparently he will deliver a b...
Source: Omics! Omics! - June 23, 2020 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Roche Expands Sequencing Nanopore Presence by Acquiring Stratos Genomics
Ugh. I let the month of April slip away without writing and now have almost let May do the same. But some leftover euphoria from a huge experimental breakthrough on our current diagnostics project at the Gene Factory plus the feeling I shouldn't let news tied into an earlier post slip off, and here I am. When I wrote aboutsequencer startups back in Februarybased on their websites, I put Stratos Genomics near the front of the pack. Roche Molecular apparently agrees,announcing a week ago that they are acquiring Stratos.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - May 28, 2020 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
One Gemini Celebrates Another
One of most truly useless pieces of information lodged in my brain is my zodiac sign; not once in my life have I had any interest in it. But, given the available draws, it isn't too bad, as it's also the name of perhaps the most underappreciated engineering project of the second half of the 20th Century: Project GeminiRead more » (Source: Omics! Omics!)
Source: Omics! Omics! - March 29, 2020 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
1918 Flu Pandemic & Popular Culture: Take Two
My piece on the near amnesia in U.S. culture of the 1918-19 Influenza pandemic provoked a number of helpful comments, emails and conversations. While I would stand behind the statement that it left a light footprint, there are a number of interesting cases, some of which I would never have found by conventional means. Sometimes the collective wisdom of the internet is best for uncovering things, even when you're married to someone who catalogs books for a living.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - March 20, 2020 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
This Time ThermoFisher Catches QIAGEN
This past fall there was a rumor that QIAGEN was being pursued by an acquirer, with the initial tip being scientific conglomerate ThermoFisher but then other possibilities floated by. QIAGEN was seen as ripe for such an action as their long-time CEO had stepped down. QIAGEN made a very public announcement that they would continue independently under their new CEO, but that is no longer the case: ThermoFisher will acquire them, pending regulatory approvals, for something arou nd 11.5BRead more » (Source: Omics! Omics!)
Source: Omics! Omics! - March 9, 2020 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Post-AGBT: Miroculus
AGBT ended over a week ago and I've been procrastinating ever since in going through notes and writing up companies. First few days I had the excuse of family time on beautiful Sanibel Island to the north, but since Monday other than obsessing about COVID-19 (and cancelling travel plans) I have no excuses. First up, the microfluidic library prep companyMiroculus, based on my notes from talking to their Chief Commercial Officer, Adam LoweRead more » (Source: Omics! Omics!)
Source: Omics! Omics! - March 7, 2020 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Why Didn't the 1919 Flu Leave A Bigger Cultural Imprint?
The still growing COVID-19 pandemic has reminded me of a question I've batted in my head a few times. In 1918 and 1919 a global influenza pandemic killedon the order of 50 million people worldwide. The scale of the jump in flu deaths in the U.S. can be seen inthe below plot. That's more than the number of civilians and military personnel estimated to havebeen killed during World War I. Yet despite this, it would seem that there has been very little impact on culture (at least the culture I am aware of).Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - March 6, 2020 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
MGI Deconstructs the Sequencer
At some fancy restaurants one can get a"deconstructed dish". As I understand it, as I don't frequent such restaurants, a deconstructed BLT would have the bread, bacon, lettuce and tomato each as their own individual item, but prepared in a novel way which highlights the strengths of each ingredient. When I got a preview last night of Rade Drmanac's closing AGBT talk on achieving a $100 human genome (reagents price only), that was the vision I had: Drmanac and his team have created their Tx system by deconstructing the optical high throughput sequencing-by-synthesis instrument.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - February 25, 2020 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
MGI Dual Drop of CoolMPS News Ahead of AGBT
Friday morning I got excited because a preprint showed up at BioRxiv detailing the CoolMPS sequencing technology from MGI (aka BGI aka Complete Genomics). First announced in Fall 2018, this approach sounded, well, cool. Using fluorescently labeled antibodies specific to each reversible terminator seemed like a crazy pipe dream. So getting a good look at it in a manuscript is an event! But then Friday afternoon MGI hada second big pre-AGBT reveal: launch of their sequencing systems in the U.S. later this year. Below is a quick run-down of the sequencer announcement; the pre-print has many details I'm still pars...
Source: Omics! Omics! - February 21, 2020 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
CoolMPS Revealed
Having summarized MGI's announcement they are launching into the U.S. market this spring and started digging into the performance characteristics of MGI's instrument lineup, let us now turn to theirBioRxiv pre-print on the CoolMPS chemistry, as it has many useful technical details.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - February 21, 2020 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
A Lazy Look at The Field of Sequencing Startups
AGBT looms ahead of me next week which serves as impetus to let fly an idea I've had simmering for a while: to look at sequencing startups by a particular type of information they choose to reveal. I'm not expecting any big announcements at AGBT from this space, though would be thrilled to be surprised. But there is the risk of getting contaminated with some on-the-sly scuttlebutt, so better to get this done now. By the way, in the full disclosure category, I have consulted for a few companies here and have NDAs either on my own or via employers; everything here is based on public information.Read more » (...
Source: Omics! Omics! - February 19, 2020 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Skimming Seq
My last post discussed BioJulia in the face of a challenge from the new Seq programming language. Tonight I'm going to take a bit more of a look at Seq itselfand touch on both why I'm tempted to try it and why I remain reticent to do so. I hope if any of the Seq team sees this they will regard it as some parts constructive criticism and some parts market feedback.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - February 17, 2020 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
