RSVPed Attending IndieWebCamp London 2020
IndieWebCamp London 2020 is a gathering for independent web creators of all kinds, from graphic artists, to designers, UX engineers, coders, hackers, to share ideas, actively work on creating for their own personal websites, and build upon each others creations.
The camp has already announced that all participation will be remote and it looks like there will be some good support for remote attendance

I’ll be attending remotely from Los Angeles as best as I can given the time difference and hope to get some fun new things working on my website this weekend. The etherpad for session proposals is already up for those who want to start posting their discussion ideas. 

Read - Reading: Memory Craft: Improve your memory using the most powerful methods from around the world by Lynne KellyLynne Kelly (Allen & Unwin)
📖 On page 130 of 320 of Memory Craft

I’m loving all these examples of memory devices she’s discovered and describing in this section. Not much of this is covered in much (any?) of the other common literature on memory.

Read Please do a bad job of putting your courses online by Rebecca Barrett-Fox (anygoodthing.com)
I’m absolutely serious.
For my colleagues who are now being instructed to put some or all of the remainder of their semester online, now is a time to do a poor job of it. You are NOT building an online class. You are NOT teaching students who can be expected to be ready to learn online. And, most importantly, your class is NOT the highest priority of their OR your life right now. Release yourself from high expectations right now, because that’s the best way to help your students learn.
Bookmarked Tg-list -- transgenic-list (lists.transtechsociety.org)

The transgenic-list (tg-l) was created by Peter Sobieszczuk in 1996, to serve the global research community specializing in genetic modifications of laboratory animals. Since then, three academic institutions have hosted the tg-l: the IGBMC in Strasbourg, France; the University of Manchester, UK; and the Imperial College in London, UK. In 2011, the transgenic-list was moved to the ISTT web server. The ISTT would like to acknowledge the excellent work of Peter and his assistants in establishing the list for the benefit of everyone who has been a part of this list. The tg-l has proven to be a valuable source of knowledge and advice, helping many newcomers to the field of animal transgenesis, and facilitating the exchange of protocols and experiences.

The ISTT is most proud to host the tg-l for the benefit of the entire community of scientists, technicians, students and all others, interested in animal transgenesis.

Tg-l members are active researchers at all levels, from graduate students to full professors, and the technicians, managers, and directors who operate transgenic core facilities.

The tg-l is public (subject to email address verification), unmoderated (messages will not be altered by the list administrator) and closed (only subscribers may post messages). The tg-l currently has about 1800 subscribers from all over the world.

To see the collection of prior postings to the list, visit the Tg-list Archives. (The current archive is only available to the list members.)

Bookmarked Genomic epidemiology of novel coronavirus (nextstrain.org)

Maintained by the Nextstrain team. Enabled by data from GISAID
Showing 838 of 838 genomes sampled between Dec 2019 and Mar 2020.

Latest Nextstrain COVID-19 situation report in English and in other languages. Follow @nextstrain for continual updates to data and analysis.

This phylogeny shows evolutionary relationships of hCoV-19 (or SARS-CoV-2) viruses from the ongoing novel coronavirus COVID-19 pandemic. This phylogeny shows an initial emergence in Wuhan, China, in Nov-Dec 2019 followed by sustained human-to-human transmission leading to sampled infections. Although the genetic relationships among sampled viruses are quite clear, there is considerable uncertainty surrounding estimates of transmission dates and in reconstruction of geographic spread. Please be aware that specific inferred transmission patterns are only a hypothesis.

Site numbering and genome structure uses Wuhan-Hu-1/2019 as reference. The phylogeny is rooted relative to early samples from Wuhan. Temporal resolution assumes a nucleotide substitution rate of 8 × 10^-4 subs per site per year. Full details on bioinformatic processing can be found here.

Phylogenetic context of nCoV in SARS-related betacoronaviruses can be seen here.

We gratefully acknowledge the authors, originating and submitting laboratories of the genetic sequence and metadata made available through GISAID on which this research is based. A full listing of all originating and submitting laboratories is available below. An attribution table is available by clicking on "Download Data" at the bottom of the page and then clicking on "Strain Metadata" in the resulting dialog box.

Read a tweet (Twitter)
Bookmarked Nonadditive Entropies Yield Probability Distributions with Biases not Warranted by the Data by Ken Dill (academia.edu)
Different quantities that go by the name of entropy are used in variational principles to infer probability distributions from limited data. Shore and Johnson showed that maximizing the Boltzmann-Gibbs form of the entropy ensures that probability distributions inferred satisfy the multiplication rule of probability for independent events in the absence of data coupling such events. Other types of entropies that violate the Shore and Johnson axioms, including nonadditive entropies such as the Tsallis entropy, violate this basic consistency requirement. Here we use the axiomatic framework of Shore and Johnson to show how such nonadditive entropy functions generate biases in probability distributions that are not warranted by the underlying data.
Bookmarked Application of information theory in systems biology by Shinsuke Uda (SpringerLink)
Over recent years, new light has been shed on aspects of information processing in cells. The quantification of information, as described by Shannon’s information theory, is a basic and powerful tool that can be applied to various fields, such as communication, statistics, and computer science, as well as to information processing within cells. It has also been used to infer the network structure of molecular species. However, the difficulty of obtaining sufficient sample sizes and the computational burden associated with the high-dimensional data often encountered in biology can result in bottlenecks in the application of information theory to systems biology. This article provides an overview of the application of information theory to systems biology, discussing the associated bottlenecks and reviewing recent work.

Own Your Followers: Redirecting Feeds on the Web

Every four months or so I go through and tidy up many of my feeds. Invariably a dozen or so feeds die out, but I’m noticing a recurring quirk. Most of them are within my IndieWeb folder!

A lot of the changes seem to be related to people who are shifting from one shiny toy or project to another. They all seem to say something like:

Hey Mom! Look at my fancy new static site that builds in 0.001 seconds!
Can you believe what Drupal supports in the IndieWeb now? See ya! 
I’ve moved back to good ol’ WordPress. Ahhh…
Micro.blog is awesome and requires such little maintenance. I migrated… while on vacation… in the wilderness… from my cell phone!!!
Wheee!

They’re often redirecting all their old URLs to the new site, but the one URL they commonly neglect is to create a redirect for their primary RSS, Atom, JSON or other feeds to their new feed structure. This means that the feed goes dead, and I (and others) have to notice it, then revive it. For some who simply have h-feed structures on their home page things may continue apace, particularly for the Microsub readers out there, though I haven’t been using those for as long to see as many issues.

Why are you doing all that work and making your followers do the extra manual work to go back and resubscribe?! Over the past four or five years there have been fifty or more people I’ve seen do this dance (some multiple times and even a few every 4 months or so). I totally get why they do it (because why not?!) But there should be a better way of keeping track of our major URLs and redirecting them properly.

From a continuity or even business perspective, this could be an even bigger thing as sites will likely spend a lot of time building an audience and could potentially throw it all away with the flip of a switch. I’ll be the first to admit that most of these people may not have a lot of people following them via RSS or similar means, but still?! It seems like at least once a week there’s some big newspaper, magazine, or corporate site I want to follow and I have to complain about finding their feeds. Why would you want to start all over again? 

If a social media framing is easier for some, it’s the equivalent of changing your Twitter handle for your account with a hundred thousand followers to something new with no followers instead of creating a dummy account and swapping the usernames so you can have the new name, but keep all your followers.

There are also a few serial bloggers/writers who will start up a project for 3-6 months and build a following only to shut things down though they’ll keep the domain name. Why not redirect that primary domain to one of their other or newer projects and redirect those feeds as well? You’ve spent the time building an audience, why wouldn’t you want to keep it? Am I missing something fundamental here?

We often say, own your online identity, own your domain, and own your data. Perhaps we need to remember to also “own” our friends, family, followers, our community, or more broadly our audience?

Until then, I’m still flailing away out here. Manually changing your feeds in my reader…

A Micropub client idea: Liveblogging!

I’ve been thinking about Twitter threads, tweetstorms and liveblogging for the better part of the week, and last night I had an idea that has stuck with me.

With the idea of Micropub allowing the ability to create updates, why couldn’t one build (or even modify) a Micropub client to create an interface to write relatively short updates with (date and timestamps to appear in the text) that, when published, concatenated that new piece of content into a longer piece of running text to send an updated Micropub request to an article or note on a site to allow that article to become an updating liveblog post?

I’m a bit shocked that no one has done it before now, and I suspect that one of the pre-existing micropub clients out there could probably add the functionality as a one day project at an upcoming IndieWebCamp.

I don’t suspect it was the sort of Micropub functionality that Kevin Marks was thinking about doing this weekend, but Noter Live comes pretty close to having a lot of this sort of UI already. Instead of just doing a single Micropub post at the end of a Twitter thread, why couldn’t it do an initial post at the beginning and then update the site with subsequent updates as it goes along while also acting as a means of syndicating the posts to Twitter and then returning those Twitter permalinks as syndication links on the user’s own site?

Bookmarked Explainable Artificial Intelligence and Machine Learning: A reality rooted perspective by Frank Emmert-Streib, Olli Yli-Harja, Matthias Dehmer (arXiv.org)
We are used to the availability of big data generated in nearly all fields of science as a consequence of technological progress. However, the analysis of such data possess vast challenges. One of these relates to the explainability of artificial intelligence (AI) or machine learning methods. Currently, many of such methods are non-transparent with respect to their working mechanism and for this reason are called black box models, most notably deep learning methods. However, it has been realized that this constitutes severe problems for a number of fields including the health sciences and criminal justice and arguments have been brought forward in favor of an explainable AI. In this paper, we do not assume the usual perspective presenting explainable AI as it should be, but rather we provide a discussion what explainable AI can be. The difference is that we do not present wishful thinking but reality grounded properties in relation to a scientific theory beyond physics.
Checked into VONS
Definitely a lot of stockpiling going on here. All the shelf-stable foods, basic medicines, and paper goods have been looted. All the checkouts were open save one and all of the lines went the entire length of the store. I don’t think I’ve ever seen a grocery store so busy or have such lines.
Read Glendale Unified district to close all schools for students through April 3 by Vera CastanedaVera Castaneda (Glendale News-Press)
The Glendale Unified School District Board of Education will close schools to students from March 16 to April 3. School sites will remain partially open for staff.
I’ll have to admit I’m kind of looking forward to homeschooling a bit.