Hunting the CoV

Project 16803

Disease Type: covid-19

This is the first COVID19 project from our lab. We are assembling the envelope protein, which is an ion channel important for viral function. Learning about how it forms can inform the design of molecules that will prevent proper assembly.

This project is managed by Dr Lucie Delemotte at KTH/SciLifeLab.

URL: https://www.biophysics.se/index.php/projects/delemottelab/
(Project: https://stats.foldingathome.org/project?p=16803. I pasted the text into the image.)

 

Proteins are not stagnant—they wiggle and fold and unfold to take on numerous shapes. We need to study not only one shape of the viral spike protein, but all the ways the protein wiggles and folds into alternative shapes in order to best understand how it interacts with the ACE2 receptor, so that an antibody can be designed. Low-resolution structures of the SARS-CoV spike protein exist and we know the mutations that differ between SARS-CoV and 2019-nCoV. Given this information, we are uniquely positioned to help model the structure of the 2019-nCoV spike protein and identify sites that can be targeted by a therapeutic antibody. We can build computational models that accomplish this goal, but it takes a lot of computing power.

(Source: https://foldingathome.org/2020/02/27/foldinghome-takes-up-the-fight-against-covid-19-2019-ncov/.)

 
=== Linux ===
I run folding@home (F@H) on two computers. One operates under MS Windows, the other one is a five years old computer with a Linux operating system. That old computer became very slow due to mitigations against Intel CPU vulnerabilities, so I didn’t use it anymore. But I reactivated it for F@H operated under a bare bone Linux OS. As that computer doesn’t do anything else than folding, I disabled the Intel CPU protection by starting the kernel with “mitigations=off”. That re-enables hyperthreading etc. (Don’t do that if you use your computer on the network for other tasks besides folding.) It works for kernels at and above version 5.2 and increases the speed (and the F@H point count) significantly. If your computer boots into Linux with GRUB, add mitigations=off to the settings in GRUB_CMDLINE_LINUX_DEFAULT.

=== Teams ===
As part of the “gamification” concept of F@H, your computer(s) collect points during folding. It’s just for fun. Competition is in our genes. You can join teams in order to get to the top in a ranking of teams together with other contributors. By default you are in a Zero team. That’s fine. You don’t have to change anything if you just want to help folding protein models.
        Some contributors join teams of organizations (e.g. companies) in order to let these organizations look good. That’s fine too. There are various kind of teams.
        You also easily can create your own team. Due to my obsession, I of course created a The Hunting of the Snark team.
        Curecoin: The top team is the Curecoin team. There you not only get points, you also get some kind of currency. It’s not my thing. One reason for me not to join Curecoin is that the blockchain technology applied would add additional workload to my computer. On the other side, Curecoin isn’t bad either. The Curecoin team has even more points than the Zero team, but much less work units. I think, that is because many contributors in that team run computers with powerful CPUs and GPUs. They get work units done faster than less powerful machines, and the points computation algorithm of F@H acknowledges that. (Thanks to the required number crunching power, blockchain technologies helped the market for graphics cards and GPUs a lot.) Personally I don’t like Curecoin, but as always: Use it if you like it and if you know what you are doing. (Links: Am Rechner nebenher die Welt retten | http://ftreporter.com/all-you-need-to-know-about-Curecoin/)

=== Caveats ===
Depending on the setting (Light/Medium/Full), your computer can get quite hot. The older one of my computers does 24 hours/day folding in a cool room in the basement. It consumes a power of 26 Watts. The F@H setting is “Full”. It’s a fan-less mini computer, so no tear&wear of a fan needs to be considered. The computer won’t get damaged by the heat, because it adapts the CPU clock frequency in a way which doesn’t let it get too hot. In winter it won’t reach maximum temperature anyway. But in summer its temperature limits will get tested, even though the ambient temperature will stay below the 50°C maximum. My other computer is a laptop computer. I chose the “Light” setting (which means that the GPU will not be used for folding).
        I checked how the folding stressed the mass storage of my computers. My laptop computer uses a SSD drive, so tear&wear might be an issue. But I saw that the folding doesn’t stress mass storage too much. So I don’t worry about that.
        Super contributors use gaming computers with powerful CPUs and GPUs. And some show off impressive cooling machinery. Those gamers know what they are doing and can run F@H with maximum performance.

=== Smartphones ===
F@H does not run on smartphones, but there is a project for such devices. The Vodaphone “DreamLab” is a proprietary app. Of course it only runs during charging. I recommend to read the privacy statement.

=== Scams ===
Due to Covid19, F@H became much more popular, so take care not to install malware like fake applications which e.g. steal passwords. Don’t panic, but wherever scams are possible, you’ll have to deal with them. F@H is no exception. Possible scams are no reason not to contribute to F@H, but be aware of scams, e.g. foldingathomeapp.exe is malware! If you want to be on the save side, only install F@H software from foldingathome.org and don’t touch anything else.

=== Join ===
You can share computer time too.

F@H Team 263865 | COVID19 | Wikipedia |Twitter | Facebook (en) | Facebook (de)

2020-03-31, update: 2020-05-23

Snark Radio Play

It’s online again!

 


https://www.bbc.co.uk/programmes/b06sbrxh/clips (2020-01-02):

Tony Robinson narrates this fresh adaptation of Lewis Carroll’s classic masterpiece following a strange assortment of characters on their quest for an elusive beast.

Led by a bell-ringing Captain, this motley crew must brave terrifying danger in their chaotic pursuit of a creature known as Snark. Accompanied by specially composed music and songs, this surreal tale questions whether anything is really what it seems. …

First broadcast on BBC Radio 4 in December 2015.

Streaming: 2020-01-02 – 2020-01-31

Credits:
– Narrator: Tony Robinson
– Bellman: Eric Potts
– Baker: Paul Barnhill
– Butcher: Everal A Walsh
– Barrister: Jonathan Keeble
– Snark (in the Barrister’s dream): Jonathan Keeble
– Beaver: Stephen Hoyle
– Music and songs (composer): Katie Chatburn
– Music (performers):
    – Katie Chatburn
    – Dorry Macaulay
    – Kathryn Williams
    – Stephen Cordiner
    – Jasper Wilkinson
– Director: Charlotte Riches
– Author: Lewis Carroll

 
2020-01-02, update 2020-05-15

Gags and Serious Stuff

snrk.de

About this site:
Snrk.de mostly is about Henry Holiday‘s illustrations (engraved by Joseph Swain) to Lewis Carroll‘s tragicomical ballad The Hunting of the Snark.
        If – and the thing is wildly possible – the charge of writing nonsense were ever brought against the author of this great blog, I will not (as I might) point to the fact that throughout my Snark hunt, my two greatest assets have been mental stability and being, like, really smart; and that the crooked Boojum also played its cards very hard and, as everyone knows, failed to stop me – which would qualify me as not smart, but genius….and a very stable genius at that!
        As promised, I will not point to that – even though it would be true if I would state it three times. Very true. Very, very true. Rather, I point to those (like John Tufail and Mahendra Singh) who really helped and encouraged me and, last not least, to those many people who turned the Internet into a humongous museum through which I could stroll while loafing on my sofa. That was the place where my Snark hunt started in December 2008, and snrk.de is place for presenting my trophies since 2012.
        On 2017-10-09, snrk.de underwent a major change. I added a blog to the site and rearranged it completely. If you previously used links to snrk.de and your browser now doesn’t find them anymore: Some of these links still may work if you replace snrk.de by old.snrk.de.

In snrk.de you’ll find a few assumptions:
The Beaver‘s lace making is “wrong” (in Carroll’s view) if lace making stands for vivisection.
Lewis Carroll liked to create “portmanteau words”. I suggest that the Boots is the maker of Bonnets and Hoods.
Last not least, since 2010 I think that the most important assumption is that Thomas Cranmer could be among the historical persons to whom the Baker (with four nicknames related to something which was heated or burned) might be related. As a protestant, Cranmer wrote the Forty-Two Articles. Under threat, he left those articles behind like the Forty-Two Boxes, which the Baker left behind on the beach. Then Carroll associated the Baker with pets of catholic saints: Macarius’ hyenas and Corbinian’s bear. (See also: Angus MacIntyre’s suggestion “The Baker’s 42 Boxes are the original Protestant Articles of 1553, with Thomas Cranmer’s name on each.” in The Reverend Snark, Jabberwocky 23(1994), p. 51~52.)


About me:
I am an electronics and mechatronics engineer living near Munich in Germany. I know how to work scientifically, but not in the field of arts and literature. In that field of research I am an amateur. Therefore I don’t have to protect any reputation in academic Snarkology ;-). Nevertheless, if you publish papers about, for example, references from The Hunting of the Snark to Thomas Cranmer, please give credit to those, who addressed that topic already. That’s me (2015, 2015, 2016), but also Karen Gardiner (2018), Mary Hibbs (2017, pen names: Mary Hammond and Sandra Mann) and Angus MacIntyre (1994).


Blog:
※ Posts and Pages: I use WordPress to run snrk.de. WordPress offers to publish “posts” and “pages”. In this blog you will often find pairs of articles where one of them is a post and the other one is a page. In such a pair of articles, both have the same title where the post is a brief blog article and the associated page then goes into more detail.
Comments: I disabled the commenting function for almost all articles. Sorry, there is too much bot spam. But you can write to me.

2nd Blog:
I use boojum.snrk.de for rants and other stuff.

3nd Blog:
meikekluge.snrk.de is a blog which I maintain for my mother.


Contact:

In order to avoid collecting personal user data and to minimize spam, I disabled blog registration.


Privacy policy and data protection:
This site complies with the European General Data Protection Regulation. The blog snrk.de itself does not collect your private data. But some pages have embedded content (Twitter, Facebook, YouTube etc.) which might not respect your privacy sufficiently. If you don’t like that, don’t use snrk.de!


Licenses:
CC BY-NC-SA 4.0 is the license for images in this blog if not indicated otherwise.


Götz Kluge, Munich 2018-07-07, update: 2020-01-06

Museé Unterlinden Retweets


 

Knight Letter № 100

In July 2018, the members of the LCSNA (Lewis Carroll Society of North America) received the 100th Knight Letter.

(A friend told me that the caterpillar (here without hookah) on the front page is a Hickory Horned Devil.)

Also in this issue, Goetz Kluge makes the case that a seventeenth-century engraving may have influenced Henry Holiday’s last illustration for The Hunting of the Snark. Goetz’s excellent blog about all things Snark is at http://snrk.de/

Preface to the Knight Letter № 100, LCSNA, 2018
 

On pages 55~56 you find a few lines which I wrote about the Baker and Thomas Cranmer in The Hunting of the Snark.

There also is an accompanying web page.

Incidentally, in parallel to my little note in the Knight Letter № 100 on the Baker’s “hot” names and on Henry Holiday’s pictorial reference to Thomas Cranmer’s burning, a paper »Life, Eternity and Everything, Hidden Eschatology in the Works of Lewis Carroll« suggesting textual references from The Hunting of the Snark to Thomas Cranmer’s Forty-Two Articles has been published in The Carrollian (July 2018, № 31, p.25~41), a journal of the Lewis Carroll Society in the UK. The author, Karen Gardiner, is an Anglican priest. She also addresses the objections of Revd. C.L. Dodgson (aka Lewis Carroll) against the dogma addressed by Article № 42 of Thomas Cranmer’s Forty-Two Articles.

Karen Gardiner (2018) and I (2015), as well as Angus MacIntyre (1994) and Mary Hibbs (2017), we all suggested that there are such references to Thomas Cranmer and his Forty-Two Articles (the Baker’s forty-two boxes) – coming from different starting points and different backgrounds. As for me, initially I just looked for Lewis Carroll’s (C.L. Dodgson’s) textual references as guidance for finding pictorial references in Henry Holiday’s illustrations.

 
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(MG064)

2018-07-28, updated 2019-06-09