NOT-OD-17-110: Request for Comments: Proposal to Update Data Management of Genomic Summary Results Under the NIH Genomic Data Sharing Policy

November 17, 2017

https://grants.nih.gov/grants/guide/notice-files/NOT-OD-17-110.html

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The future of DNA sequencing

November 14, 2017

The Future of DNA Seq.
http://www.Nature.com/news/the-future-of-dna-sequencing-1.22787 Apps v Tech. QT: “Platforms for…#sequencing have changed dramatically…Yet the trajectories of other technologies…Internet, digital
photography…suggest…real disrupters will be the resulting applications, not the new tech”

QT:{{”
Killer applications –
Over the years, the platforms for DNA sequencing have changed dramatically (see ”). Yet the trajectories of other technologies for which there is a seemingly insatiable demand — smartphones, the Internet, digital photography — suggest that the real disrupters will be the resulting applications, not the new technologies.

“}}


Quantifying the local resolution of cryo-EM density maps | Nature Methods

November 14, 2017

Quantifying the local resolution of #cryoEM density maps
https://www.Nature.com/articles/nmeth.2727 “Theory…based on the following idea: a L Angstrom feature exists at a pt…if a 3D local sinusoid of wavelength L is statistically detectable above noise at that point.”

QT:{{”
We propose a mathematical theory and an efficient algorithm for measuring local resolution that address all of the above limitations. The theory (Online Methods) is based on the following idea: a λ-Å feature exists at a point in the volume if a three-dimensional (3D) local sinusoid of wavelength λ is statistically detectable above noise at that point. A likelihood-ratio hypothesis test of the local sinusoid versus noise can detect this feature at a given P value (typically P = 0.05). We define the local resolution at a point as the smallest λ at which the local sinusoid is detectable, and we account for multiple testing with an FDR procedure.
“}}


If we only ate organic it would be an environmental disaster | New Scientist

November 14, 2017

https://www.newscientist.com/article/2153272-if-we-only-ate-organic-it-would-be-an-environmental-disaster/


Air Travelers Resisting the ‘Incredible Shrinking Airline Seat’ – The New York Times

November 13, 2017

https://www.nytimes.com/2017/11/06/business/airline-seat.html?mc=aud_dev&mcid=tw-nytimes&mccr=NovTwitter&mcdt=2017-11&subid=NovTwitter&ad-keywords=AudDevGate


Heptadecagon – Wikipedia

November 13, 2017

https://en.wikipedia.org/wiki/Heptadecagon


Can Ketones Rev Up Our Workouts? – The New York Times

November 12, 2017

https://www.nytimes.com/2017/11/08/well/move/can-ketones-rev-up-our-workouts.html?partner=rss&emc=rss&smid=tw-nythealth&smtyp=cur


New Theory Cracks Open the Black Box of Deep Learning | Quanta Magazine

November 12, 2017

New Theory Cracks Open the Black Box of #DeepLearning
https://www.QuantaMagazine.org/new-theory-cracks-open-the-black-box-of-deep-learning-20170921/ Highlights the importance of a compression phase for generalization

QT:{{”
“Then learning switches to the compression phase. The network starts to shed information about the input data, keeping track of only the strongest features — those correlations that are most relevant to the output label. This happens because, in each iteration of stochastic gradient descent, more or less accidental correlations in the training data tell the network to do different things, dialing the strengths of its neural connections up and down in a random walk. This
randomization is effectively the same as compressing the system’s representation of the input data. As an example”
“}}


Alignment-free sequence comparison: benefits, applications, and tools

November 12, 2017

Might be useful for noncoding comparisons

Alignment-free seq. comparison: benefits, apps & tools
https://GenomeBiology.biomedcentral.com/articles/10.1186/s13059-017-1319-7 Great tidbits, viz: Shannon asked von Neumann what to call his info measure – “Why don’t you call it entropy…no one understands entropy…so in any discussion, you’ll be in a position of advantage.”

QT:{{”
“Reportedly, Claude Shannon, who was a mathematician working at Bell Labs, asked John von Neumann what he should call his newly developed measure of information content; “Why don’t you call it entropy,” said von Neumann, “[…] no one understands entropy very well so in any discussion you will be in a position of advantage […]” []. The concept of Shannon entropy came from the observation that some English words, such as “the” or “a”, are very frequent and thus unsurprising” ….
“The calculation of a distance between sequences using complexity (compression) is relatively straightforward (Fig. ). This procedure takes the sequences being compared (x = ATGTGTG and y = CATGTG) and concatenates them to create one longer sequence (xy = ATGTGTGCATGTG). If x and y are exactly the same, then the complexity (compressed length) of xy will be very close to the complexity of the individual x or y. However, if x and y are dissimilar, then the complexity of xy (length of compressed xy) will tend to the cumulative complexities of x and y.”

“Intriguingly, BLOSUM matrices, which are the most commonly used substitution matrix series for protein sequence alignments, were found to have been miscalculated years ago and yet produced significantly better alignments than their corrected modern version (RBLOSUM) []; this paradox remains a mystery.”
“}}


NIH awards to test ways to store, access, share, and compute on biomedical data in the cloud

November 11, 2017

NIH awards to test ways to store, access, share, and compute on biomedical data in the cloud
https://www.nih.gov/news-events/news-releases/nih-awards-test-ways-store-access-share-compute-biomedical-data-cloud