📖 On page 143 of 425 of A Riddle in Ruby by Kent Davis

📖 On page 143of 425 of A Riddle in Ruby by Kent Davis

The story is starting to move along now. We’ve discovered where the father has been taken, but we’re still completely in the dark about why things are happening. The color and description of the world is coming more firmly into place.

🔖 "Opposite-of"-information improves similarity calculations in phenotype ontologies

Bookmarked "Opposite-of"-information improves similarity calculations in phenotype ontologies (bioRxiv)
One of the most important use cases of ontologies is the calculation of similarity scores between a query and items annotated with classes of an ontology. The hierarchical structure of an ontology does not necessarily reflect all relevant aspects of the domain it is modelling, and this can reduce the performance of ontology-based search algorithms. For instance, the classes of phenotype ontologies may be arranged according to anatomical criteria, but individual phenotypic features may affect anatomic entities in opposite ways. Thus, "opposite" classes may be located in close proximity in an ontology; for example enlarged liver and small liver are grouped under abnormal liver size. Using standard similarity measures, these would be scored as being similar, despite in fact being opposites. In this paper, we use information about opposite ontology classes to extend two large phenotype ontologies, the human and the mammalian phenotype ontology. We also show that this information can be used to improve rankings based on similarity measures that incorporate this information. In particular, cosine similarity based measures show large improvements. We hypothesize this is due to the natural embedding of opposite phenotypes in vector space. We support the idea that the expressivity of semantic web technologies should be explored more extensively in biomedical ontologies and that similarity measures should be extended to incorporate more than the pure graph structure defined by the subclass or part-of relationships of the underlying ontologies.

@lpachter Your cup of tea over at UCLA next week? Regulatory & Epigenetic Stochasticity in Development & Disease http://www.ipam.ucla.edu/programs/workshops/regulatory-and-epigenetic-stochasticity-in-development-and-disease

@lpachter Your cup of tea over at UCLA next week? Regulatory & Epigenetic Stochasticity in Development & Disease http://www.ipam.ucla.edu/programs/workshops/regulatory-and-epigenetic-stochasticity-in-development-and-disease


👓 A Conversation with @LPachter (BS ’94) | Caltech

Read A Conversation with Lior Pachter (BS '94) (The California Institute of Technology)
Pachter, a computational biologist, returns to CalTech to study the role and function of RNA.

Why the Obamacare repeal effort is suddenly a huge mess | Axios

Read Why the Obamacare repeal effort is suddenly a huge mess by Caitlin Owens (Axios)
The future of Medicaid expansion is a big disagreement — and the divide over replacement is getting bigger.

Chief digital officer steps down from White House job over background check | Politico

Read Chief digital officer steps down from White House job over background check by Tara Palmeri and Daniel Lippman (POLITICO)
The background check must be completed by White House staffers for positions that cover national security.

Read posts nearly perfected!

Hoorah, hooray!

In a project which I started just before IndieWebCamp LA in November, I’ve moved a big step closer to perfecting my “Read” posts!

Thanks in large part to WordPressPressForward, friends and help on the IndieWeb site too numerous to count, and a little bit of elbow grease, I can now receive and read RSS feeds in my own website UI (farewell Feedly), bookmark posts I want to read later (so long Pocket, Instagram, Delicious and Pinboard), mark them as read when done, archive them on my site (and hopefully on the Internet Archive as well) for future reference, highlight and annotate them (I still love you hypothes.is, but…), and even syndicate (POSSE) them automatically (with emoji) to silos like Facebook, Twitter (with Twitter Cards), Tumblr, Flipboard, LinkedIn, Pinterest, StumbleUpon, Reddit, and Delicious among others.

Syndicated copies in the silos when clicked will ping my site for a second and then automatically redirect to the canonical URL for the original content to give the credit to the originating author/site. And best of all, I can still receive comments, likes, and other responses from the siloed copies via webmention to stay in the loop on the conversations they generate without leaving my site.

Here’s an example of a syndicated post to Twitter:

I’m now more resistant to a larger number of social media silos disappearing with my data. Huzzah!

What’s next?

 

DreamHost is a proud sponsor of @indiewebcamp meetups!

Reposted a tweet by DreamHostVerified accountDreamHostVerified account (Twitter)
DreamHost is a proud sponsor of @indiewebcamp meetups! Right out of our #PDX office, no less! #webdesign #bloggingpic.twitter.com/bFsowoe4vK

Croissants by Vincent Talleu

Watched Croissants from YouTube
Uploaded on May 12, 2009
How I make croissants.

http://www.brockwell-bake.org.uk
http://www.sustainweb.org/realbread
http://www.vincent.talleu.com

I made this video when I worked in south of France a few years ago. I now work at "The Artisan Bakery" in London, where the croissant we make are even better, but I'm really a bread baker and our bread is the best.
Jeremy Cherfas is right, I think the majority of the secret is the tools. I am quite jealous of that massive dough roller, but I don’t think that a typical little home pasta machine would be quite as easy to use as Jeremy might hope.

My other favorite was the magic croissant cutter. I’ll have to look for one of those the next time I’m at a restaurant supply house. I imagine they’re pretty rare. It reminded me a little bit of the old school hand push lawn mowers.

The quick camera pan down at 5:34 with the CCR musical overlay was a lovely touch, but is a painful reminder of the fact that this type of mass manufacture is overkill for the home chef who may want as many as a dozen at a time (remember, pastries start their inevitable death the minute they’re done cooking). Though I do have to say watching this makes me want to open up a bakery, but which days is that not a thought I have?

The nice part about having this much dough was seeing some of the myriad of creative things one could do other than just croissants. Now, off to find a nice oranais.

Donald Trump | Charlie Rose

Watched Donald Trump Interview Friday 11/06/1992 from Charlie Rose
Rebroadcast — Monday 02/20/2017
Donald Trump talks about his recent "comeback" after flirting with bankruptcy, his support of Mike Tyson after his imprisonment for rape, his divorce from Ivana Trump, and the rumors that he would run for president.

It’s amazing watching this interview from over 23 years ago. Charlie Rose takes it possibly too easy on Trump because of his entertainer status. There’s a lot of hemming and hawing on Trump’s side and he still shows these same verbal tics as he dodges questions in a somewhat charming manner. There’s no adherence to facts, yet everything is “just great”, “the best”, “this”, “that”, and so on.

It’s amazing to see some of the things Rose brings up then are still issues now. Questions about his manner and vanity still linger all these years later. The difference is that he at least acknowledged them to some extent back then.