Hunting the CoV

Projects 16800-16803,16805-16808

Cause: 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.

List of Contributors

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

URL: https://www.biophysics.se/index.php/projects/delemottelab/

2020-07-03
(Project: https://stats.foldingathome.org/project?p=16805. 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 protein model folding computer collect points during folding. (It’s just for fun. Competition is in our genes, F@H plays with that.) 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. (So far it consist of only one member, but as of already is among the top 10% of all teams.)
        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) of FAHcontrol, 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 an internal 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. So I added an external fan (14W). My other computer is a laptop computer. I chose the “Light” setting (which means that the GPU will not be used for folding).
        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: 2020-07-03

Lorenzo and Isabella

Bycatch from my Snark hunt:

The, well, ambiguity of that “shadow”is known. Also there were some Freudian assumptions regarding what the salt could stand for. But so far I didn’t find any remarks on the impossibility of having a shadow being covered by white salt which isn’t covered by that shadow. To someone who learned physics that is a quite obvious question.

more

2017-12-17, update: 2020-04-11

Hideously Ugly

Jun 13, 1862: Saw Millais’ “Carpenter’s Shop” at Ryman’s. It is certainly full of power, but hideously ugly: the faces of the Virgin and Christ being about the ugliest.

I found this quote in Lewis Carroll’s Diaries on Twitter.

And I found the following quote from Charles Dickens in Pre-Raphernalia, Raine Szramski‘s blog with “Pre-Raph Sketchbook Cartoons”.

You behold the interior of a carpenter’s shop. In the foreground of that carpenter’s shop is a hideous, wry-necked, blubbering, red-headed boy, in a bed-gown, who appears to have received a poke in the hand, from the stick of another boy with whom he has been playing in an adjacent gutter, and to be holding it up for the contemplation of a kneeling woman, so horrible in her ugliness, that (supposing it were possible for any human creature to exist for a moment with that dislocated throat) she would stand out from the rest of the company as a Monster, in the vilest cabaret in France, or the lowest ginshop in England.

Two almost naked carpenters, master and journeyman, worthy companions of this agreeable female, are working at their trade; a boy, with some small flavor of humanity in him, is entering with a vessel of water; and nobody is paying any attention to a snuffy old woman who seems to have mistaken that shop for the tobacconist’s next door, and to be hopelessly waiting at the counter to be served with half an ounce of her favourite mixture. Wherever it is possible to express ugliness of feature, limb, or attitude, you have it expressed. Such men as the carpenters might be undressed in any hospital where dirty drunkards, in a high state of varicose veins, are received. Their very toes have walked out of Saint Giles’s.

 

Perhaps Dickens initially saw the reproduction of Millais’ painting in the Illustrated London News (1850-05-11) and couldn’t forget that first impression. It seems that the engraver of the reproduction was a bit biased against Millais’ Carpenter’s Shop. (Twitter)


 

Whether ugly or not, Henry Holiday probably liked the painting of his teacher. He might have alluded to Millais’s Christ in the House of His Parents when he illustrated Lewis Carroll’s The Hunting of the Snark.

 

Category: Christ in the House of his Parents

 
2019-06-14, updated 2020-01-29

What – me worry?


Source for “Alfred E. Neuman”: en.wikipedia.org/wiki/File:Mad30.jpg

After a Butcher/Jowett comparison I run into a page published by Arthur Neuendorffer. (Art perhaps is in Oxford what Alois Kabelschacht is in room 354 of the Max Planck Institute for Physics in Munich.) Art discovered a resemblance between Henry Holiday’s depiction of The Butcher in Lewis Carroll’s The Hunting of the Snark and Alfred E. Neuman. He wrote: “When Mad Magazine was sued for copyright infringement, one defense it used was that it had copied the picture from materials dating back to 1911.” Incidentially, my first copy of the The Hunting of the Snark was an American edition published in 1911.

 
It seems, though, that Alfred E. Neuman and the Butcher are quite distant relatives:

I met the Snark in 2005

Before my Snark hunt started in 2008, I mainly focused on Henry Holiday’s illustration to the 5th fit in Lewis Carroll’s The Hunting of the Snark. Since 2005 (as a member of a works council specialized on OHS issues) I used that illustration as a depiction of improvable workplace design. I also inserted the illustration into a Wikipedia article in 2008. Probably from there it was copied into another Wikipedia article in 2012. That one again inspired a Forbes article about well-being in the workplace in 2013.

In 2008 I read Carroll’s and Holiday’s complete tragicomedy. Then I made an incidental discovery.

A Snark Excerpt as Graph


The image visualizes hypergraph properties of a part (lines 547 to 556) of Lewis Carroll’s The Hunting of the Snark. (I fixed the transposition error “Page 18” in the original image. In the 1st 1876 Snark edition it’s page 81.)

Image source:
Ronald Haentjens Dekker and David J. Birnbaum.
“It’s more than just overlap: Text As Graph.”
Presented at Balisage: The Markup Conference 2017,
Washington, DC, August 1 – 4, 2017.
In Proceedings of Balisage: The Markup Conference 2017.
Balisage Series on Markup Technologies, vol. 19 (2017).
https://doi.org/10.4242/BalisageVol19.Dekker01.

A remark which I received from David J. Birnbaum: Gijs Brouwer implemented the visualization, and Astrid Kulsdom transcribed the information based on the data model inside the application. Gijs’s animated version of the image is available at https://github.com/HuygensING/TAG/blob/master/snark-fly.mp4.

Page 81 visualization | Print/Mobile | EPUB | Twitter | Facebook

Happy Chinese New Year



 

Update 2019-06-11