Kendall Square Tech/Biotech/Biopharma Needs to Get Vocal About Transit!
Earlier this week, the current big Boston-area mass construction transit project, known as GLX, went through a near-death experience. The project, having been mismanaged to be over budget and behind schedule in the early going, was approved to survive in a stripped down form. Numerous political types were quoted supporting the project, albeit complaining about contributions their towns were making to keep the project alive. What wasn't heard was any sort of support from the tech, biotech and biopharma companies which crowd Kendall Square.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - May 19, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Exploring Critiques of Siddhartha Mukerjee's The Gene, An Intimate History
My finely tuned skills in the art of procrastination KOed my plans to see Siddhartha Mukerjee's talk tonight at a local bookstore (apparently with Henry Louis Gates) to promote Mukerjee's new book The Gene: An Intimate History -- the event sold out. Perhaps I could have found a scalper, but I decided I'd just head home. Mukerjee's first book, the cancer history The Emperor of All Maladies, was very well received (even spawning a PBS series), and I was impressed that Mukerjee took the time to contact me after I wrote a review in this space. The new book has been taking quite a bit of criticism, and eve...
Source: Omics! Omics! - May 17, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Exploring Critiques of Siddhartha Mukerjee's The Gene, An Intimate History
< span style= " font-family: inherit; " > My finely tuned skills in the art of procrastination KOed my plans to see Siddhartha Mukerjee & #39;s talk tonight at a local bookstore (apparently with Henry Louis Gates) to promote Mukerjee & #39;s new book The Gene: An Intimate History -- the event sold out. Perhaps I could have found a scalper, but I decided I & #39;d just head home. Mukerjee & #39;s first book, the cancer history The Emperor of All Maladies, was very well received (even spawning a PBS series), and I was impressed that Mukerjee took the time to contact me after I wrote < a href= " http://omicsomics.blogspot...
Source: Omics! Omics! - May 17, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
finding new intron-exon junctions using the public Encode RNASeq data
I've been asked to look for some new / suspected / previously uncharacterized intron-exon junctions in public RNASeq data.
I've used the BAMs under http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCaltechRnaSeq/.
The following command is used to build the list of BAMs:
curl -s "http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeCaltechRnaSeq/" |\
tr ' "' "\n" | (Source: YOKOFAKUN)
Source: YOKOFAKUN - May 16, 2016 Category: Bioinformatics Authors: Pierre Lindenbaum Source Type: blogs
Hiatus, indefinite
May. No blog posts yet in 2016. “What’s going on Neil?” asked no-one at all. For anyone who may be wondering…
Last November, I resigned from my position with my previous employer after almost 7 years. Just before Christmas, I was offered a position as a data scientist with Life Letters, a Sydney-based healthcare technology start-up. I started working there in early January and so far, it has been a terrific experience. Had I known how enjoyable it could be, I would have made a move like this 10 years ago. Career advice: there are many more jobs that can engage scientists and utilise their skills than academic resea...
Source: What You're Doing Is Rather Desperate - May 4, 2016 Category: Bioinformatics Authors: nsaunders Tags: career personal this blog Source Type: blogs
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.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - April 27, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
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.Read more ...
Source: Omics! Omics! - April 4, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
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 genomeHey @DrKatHolt @rrwick, there's a Bandage plot on the front page of the @nytimes today! #NoFooling @MarkKunitomi pic.twitter.com/a1n6QyQWr3— Adam Phillippy (@aphillippy) April 1, 2016 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!)This whol...
Source: Omics! Omics! - April 2, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
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 bookRead more » (Source: Omics! Omics!)
Source: Omics! Omics! - March 30, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
PacBio's big splash
[18 March 2016 -- my original inclusion of the Pac Bio marketing image 6 years ago was claimed to be a DCMA violation -- I've simply removed it, though I do think this would fall under fair use ]The Pacific Biosciences instrument is officially unveiled now, with those lucky/smart (or SMRT?) enough to go to Marco Island filling in all of us not in that position. Sounds like a great lot of hoopla, though they didn't drag the Hornet for the splashdown. First of all, it's a beast. "In this corner, weighing in a nearly an imperial ton...". Too bad their marketing picture has nothing good for judging the scale -- it's apparent...
Source: Omics! Omics! - March 17, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
PacBio's big splash
[18 March 2016 -- my original inclusion of the Pac Bio marketing image 6 years ago was claimed to be a DCMA violation -- I ' ve simply removed it, though I do think this would fall under fair use ] < br / > < div class= " separator " style= " clear: both; text-align: center; " > < a href= " http://www.unh.edu/research/sites/www.unh.edu.research/files/DMCA.jpg " imageanchor= " 1 " style= " margin-left: 1em; margin-right: 1em; " > < img border= " 0 " src= " http://www.unh.edu/research/sites/www.unh.edu.research/files/DMCA.jpg " / > < /a > < /div > < br / > The Pacific Biosciences instrument is officially unveiled now, w...
Source: Omics! Omics! - March 17, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
A Mosquito ExAC?
Okay, there's a scheme for a crazy big genomics project has bitten me, infecting my brain. It's definitely not something I'm in a position at all to execute on, but I throw it out as an idea in case anyone finds it useful. And admittedly, it is pretty much stealing straight from the ExAC human exome aggregation project, which contains huge numbers of human exomes. Behind all those is a lot of phenotype data. Now, inspired by recently re-reading Laurie Garrett's The Coming Plague and also faced with daily news items on the Zika virus epidemic, I've had this question: what if the same approach wer...
Source: Omics! Omics! - March 13, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Oxford's Riposte To Illumina Trade Action
Along with the "No thanks, I've already got one" online session, the other big Oxford Nanopore news is the public release of Oxford's response to the trade complaint filed by Illumina which was attempting to exclude all Oxford Nanopore devices from the U.S. markets. Nature News' Erika Check Hayden has posted the document on Dropbox, which was a big help. While no documents from Oxford's side concerning the simultaneous patent lawsuit have yet surfaced, it is reasonable to expect that it will use many of the same arguments.Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - March 8, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Oxford's Riposte To Illumina Trade Action
Along with the & quot; < a href= " http://omicsomics.blogspot.com/2016/03/oxfords-no-thanks-ive-already-got-one.html " > No thanks, I & #39;ve already got one < /a > & quot; online session, the other big Oxford Nanopore news is the public release of Oxford & #39;s response t < a href= " http://omicsomics.blogspot.com/2016/02/digging-into-illumina-lawsuit-vs-oxford.html " > o the trade complaint filed by Illumina < /a > which was attempting to exclude all Oxford Nanopore devices from the U.S. markets. Nature News & #39; Erika Check Hayden has < a href= " https://t.co/Ai3lKponEt " > posted the document on Dropbox < /a > ,...
Source: Omics! Omics! - March 8, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
Oxford's "No thanks, I've already got one"
Oxford Nanopore today hosted a Google hangout titled "No thanks, I've already got one". Only this morning did it occur to me I could have re-watched Monty Python and Holy Grail and scored it as blogging-related time! Oxford CTO Clive Brown went through a number of interesting (and in many cases, long-awaited) announcements on the release of multiple key upgrades to the platform (note: unless otherwise specified, images swiped from ONT).Read more » (Source: Omics! Omics!)
Source: Omics! Omics! - March 7, 2016 Category: Bioinformatics Authors: Keith Robison Source Type: blogs
