Thursday, April 28, 2016

Genia Publishes Platform Progress

Nanopore sequencing developer Genia published in PNAS last week a study demonstrating the basics of their current approach to sequencing.  I say current, because Genia has gone through a number of iterations and on at least two occasions promised to be going into beta in a 6-9 month timeframe.   The paper demonstrates the basic concepts of a sequencing system and generates some short reads, but also suggests that Genia won't be hitting beta sites in the near future either.

Tuesday, April 05, 2016

Protein Homeostasis: Has it Hit The Classrooms Yet?

I wrote a piece earlier this year suggesting that introductory Biology textbooks should emphasize protein complexes more.  My basis for assuming that they generally don't isn't very good: a single textbook in use in TNG's high school class, which sports a copyright date from a decade ago. I also remember what I was taught in high school and college courses, which I would rate as not bad and truly excellent (respectively), plus I was a teaching fellow for one semester of intro bio at Harvard.  I now have another suggestion to cram into every biology course: an overview of ubiquitin-proteasome system.

Sunday, April 03, 2016

Mosquito Genomes: Chance for Long-Range Companies to Shine

Friday's New York Times carried a front-page illustration of the current status of the Aedes aegyptii genome, accompanying an Amy Harmon story on efforts to improve the currently highly fragmented state of this genome

The pice has seen a lot of opinion on Twitter with regard to its value and other issues (such as calling an assembly a map -- which to me is correct as the perfect genome sequence is the ultimate physical map!)

Thursday, March 31, 2016

Reflections on And The Band Played On

Fellow blogger, colleague and science history buff Ash pointed out to me recently that Randy Shilt's And The Band Played On for Kindle was on sale.  I hadn't read the book, nor seen the miniseries, so I snapped up a copy.  It's a good read -- though at times a hard one - I don't believe I've ever read another work of non-fiction where such a high fraction of the named individuals are dead by the end of the book

Wednesday, March 30, 2016

Who Wants To Write A Review Article?

Yes, this is a solicitation.  I'm on the Editorial Board of the journal Briefings in Bioinformatics,.  I'm looking for authors who would like to write high-quality, compact reviews.  If you are interested, or you want a little back-story, then keep reading.

Tuesday, March 29, 2016

At the Edge of The Cloud

I've used cloud computing at Amazon Web Services (AWS) off-and-on now for over five years.  The cloud has all sorts of handy advantages -- flexible access to large amounts of compute, inexpensive access to any flavor of Linux you wish, the ability to guiltlessly kill a huge server you just fatally cratered with the wrong command.  And until now, I''ve always been able to find machines that fit my needs -- perhaps sometimes just fitting or with a bit of compromise   But, now I've hit the wall: nobody at this time offers a really serious cloud machine with 500Gb of RAM.

Friday, March 25, 2016

Selective sequencing: A Programming Opportunity!

I ask a bit of indulgence from my regular readership for this piece, as I am going to explain a number of things in depth that probably will be very familiar to them.  My hope, perhaps fantastic, is that this piece will get out to some who are not so familiar with such topics, as I think the problem at hand might be very fascinating.