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Supercomputer analysis of Covid-19 leads to new theory

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Re: Supercomputer analysis of Covid-19 leads to new theory

#21

Post by mnw21cam »

dekhn wrote: post #13
secondcoming wrote: post #7

Earlier quoted context omitted.

Maybe to test the algorithms and results, so that next time something like this happens there can be a list of suggested treatments ready far sooner.

The issue is that, from what I can tell, the authors just used R to analyze some data, with no explicit parallelism. You would do a better job just renting time on AWS, saving money for everybody.

Depends how much of the "supercomputer" the calculation used. If it reserved a single CPU core on a single node, then that'd be cheap, allowing the rest of the system to get on with something else. There's no reason AWS would be cheaper.

Re: Supercomputer analysis of Covid-19 leads to new theory

#22

Post by hosh »

gchokov wrote: post #9

Vitamin D for the win!

We don’t know the dosage or protocol for stopping the bradykinin storm, or even if this hypothesis is confirmed through more tests ... but it seems sensible to me to make sure one has a healthy level of Vitamin D, and that is actionable for a lot of people.

Re: Supercomputer analysis of Covid-19 leads to new theory

#23

Post by zby »

They found out that some genes related to ACE in comparison to genes related to ACE2 are more 'expressed' in Covid patients than normally and they conclude that that must have resulted in too much bradykinine. Hmm - that strikes me as kind of roundabout - why they couldn't just measure bradykinine levels directly? Is that too hard?

"Here, we perform a new analysis on gene expression data from cells in bronchoalveolar lavage fluid (BALF) from COVID-19 patients that were used to sequence the virus. Comparison with BALF from controls identifies a critical imbalance in RAS represented by decreased expression of ACE in combination with increases in ACE2, renin, angiotensin, key RAS receptors, kinogen and many kallikrein enzymes that activate it, and both bradykinin receptors. This very atypical pattern of the RAS is predicted to elevate bradykinin levels in multiple tissues and systems that will likely cause increases in vascular dilation, vascular permeability and hypotension."

Re: Supercomputer analysis of Covid-19 leads to new theory

#24

Post by natechols »

mnw21cam wrote: post #21
dekhn wrote: post #13

Earlier quoted context omitted.

The issue is that, from what I can tell, the authors just used R to analyze some data, with no explicit parallelism. You would do a better job just renting time on AWS, saving money for everybody.

Depends how much of the "supercomputer" the calculation used. If it reserved a single CPU core on a single node, then that'd be cheap, allowing the rest of the system to get on with something else. There's no reason AWS would be cheaper.

The supercomputer in this article is extremely specialized hardware design to maximize peak performance across all nodes. Using just a single CPU core to run a bioinformatics study would be like taking an army tank to drop the kids off at soccer practice.

Re: Supercomputer analysis of Covid-19 leads to new theory

#25

Post by SideburnsOfDoom »

nr2x wrote: post #10
klysm wrote: post #3

The anthropomorphization of computers (especially powerful ones) is pretty annoying. A _person used a supercomputer_ to analyze Covid-19, and I’m guessing the theory didn’t just ‘emerge’ from the computer.

Likewise while a computer can produce data quite well, theories are still a purely human domain.

A set of correlations identified automatically in the input data - is that a theory, or merely output data?

Re: Supercomputer analysis of Covid-19 leads to new theory

#26

Post by nradov »

hellofunk wrote: post #18

> Interestingly, Jacobson’s team also suggests vitamin D as a potentially useful Covid-19 drug. The vitamin is involved in the RAS system and could prove helpful by reducing levels of another compound, known as REN. Again, this could stop potentially deadly bradykinin storms from forming. The researchers note that vitamin D has already been shown to help those with Covid-19. The vitamin is readily available over the…

See Dr. Gerry Schwalfenberg's letter on the "Vitamin D hammer" for treating respiratory viruses. While not a controlled study it does point toward an avenue for further research.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4463890/

Re: Supercomputer analysis of Covid-19 leads to new theory

#27

Post by shubhamjain »

hellofunk wrote: post #18

> Interestingly, Jacobson’s team also suggests vitamin D as a potentially useful Covid-19 drug. The vitamin is involved in the RAS system and could prove helpful by reducing levels of another compound, known as REN. Again, this could stop potentially deadly bradykinin storms from forming. The researchers note that vitamin D has already been shown to help those with Covid-19. The vitamin is readily available over the…

This Medium article was written on March 10 [1].

"Put simply, medics found that severely ill flu patients nursed outdoors recovered better than those treated indoors. A combination of fresh air and sunlight seems to have prevented deaths among patients; and infections among medical staff.[1] There is scientific support for this. Research shows that outdoor air is a natural disinfectant. Fresh air can kill the flu virus and other harmful germs. Equally, sunlight is germicidal and there is now evidence it can kill the flu virus."

[1]: https://medium.com/@ra.hobday/coronavirus-and-the-sun-a-less...

Re: Supercomputer analysis of Covid-19 leads to new theory

#28

Post by dekhn »

vardump wrote: post #17
searine wrote: post #11

Earlier quoted context omitted.

>I can't really see why you would need a supercomputer to do the analysis they did The article is fluff. 98% of all bioinformatics is done on "supercomputers" or 'high performance computing environments" saying the researchers used supercomputers to analyze the expression data is like saying someone used a shovel to dig a hole.

Don't we all have supercomputers in our pockets?

No. Although our phones are extraordinary, they are not supercomputers. Supercomputers, more or less by legacy historical defintions, are collections of computing resources connected by a fast network with the goal of scaling to solve problems that could not be solved with conventional systems. Phones aren't really designed to solve that kind of problem.

That said, many problems that previously would have required a supercomputer, can now be solved on phones.

Re: Supercomputer analysis of Covid-19 leads to new theory

#29

Post by woeirua »

Seems like it should be really straightforward to determine if this hypothesis is right by measuring bradykinin levels in Covid patients versus non-Covid patients.

One thing that I think strongly suggests that this hypothesis is wrong is that there is no strong relation between ACE-inhibitors and Covid mortality. Indeed, most of the studies that I've seen suggest that ACE-inhibitors have a somewhat protective effect whereas ARBs actually seem to have a minor detrimental effect [1]. So for the article to claim that covid behaves pharmacologically like ACE-inhibitors seems wrong at face value.

[1] https://www.nejm.org/doi/full/10.1056/NEJMoa2007621

Re: Supercomputer analysis of Covid-19 leads to new theory

#30

Post by natechols »

dekhn wrote: post #2

I can't really see why you would need a supercomputer to do the analysis they did (it shows SC centers are getting desperate for users; I wouldn't even have been allowed to run this code on a supercomputer when I was an academic, because it didn't need interconnect for strong scaling.

I was wondering about this too - when I saw the title I assumed it was a molecular dynamics study.
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