The hard part is asking the question in a way a computer can provide a meaningful answer.
In spite of its title, the article gives us no clue how the investigators used the supercomputer.
Supercomputer analysis of Covid-19 leads to new theory
131–140 of 154 posts
Re: Supercomputer analysis of Covid-19 leads to new theory
#132Re: Supercomputer analysis of Covid-19 leads to new theory
#133Earlier quoted context omitted.
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 vir…
That air is a natural disinfectant is super interesting. I read that vitamin D and observed benefits for those who have vitamin D is a correlation. Meaning that taking vitamin D supplements might not be as helpful as getting sunlight (a natural way to get vitamin D)
Maybe it's not even a "disinfectant". It's just that you aren't re-breathing stale air with droplets in it, when outside. Assuming, of course, you aren't wearing a mask. :-)
Re: Supercomputer analysis of Covid-19 leads to new theory
#134Earlier quoted context omitted.
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.
> that is actionable for a lot of people Really hoping this is better by the next few months or my Seattle winter will be even more pill popping to maintain basic human functionality....
If you cook or grow your own food (microgreens, mushroom in a kitchen cabinet), there are alternatives.
For example: https://www.milkwood.net/2014/03/31/want-extra-vitamin-d-pla...
This works for both shiitake and button (portobello) mushrooms.
This trick came from Paul Stamets, one of the world’s foremost mycologist. He is based out in Casscadia. You may have to track down exactly what “2 days” means... I wouldn’t be surprised if he went looking for a way to maintain his Vitamin D health.
You only need 10g of this four times a week, according to this article. While it is summer time in Seattle, you can prepare a bunch and then dry them, so they last until next spring.
Re: Supercomputer analysis of Covid-19 leads to new theory
#135Boy oh boy that computer sure is super! (har har!)
Re: Supercomputer analysis of Covid-19 leads to new theory
#136Whether or not this hypothesis is truly correct, it still seems valid and I would much rather take Vitamin D then Chloroquine...
Vitamin D is lipid-soluble - your body will not flush any excess, and build-up can have negative health consequences. Probably don't start taking vitamin D supplements without getting your current vitamin D levels tested first.
Re: Supercomputer analysis of Covid-19 leads to new theory
#137The hard part is asking the question in a way a computer can provide a meaningful answer.
In spite of its title, the article gives us no clue how the investigators used the supercomputer.
The intro made it sound like they just ran an exhaustive search of all nCoV genes against a database of known genes and their effects.
Re: Supercomputer analysis of Covid-19 leads to new theory
#138Earlier quoted context omitted.
I can't find details either, but I think they just used R for the post-processing, and there's a lot of computation behind this sentence: > RNA-Seq analysis was performed using the latest version of the human transcriptome I found this article discussing read mapping for RNA sequence analysis: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4833417/ > In particular, RNA sequencing (RNA-seq) technology,1 which provides a…
What good is a paper if their methods are a single sentence? Ugh. Reads mapping is a massively embarassingly parallel computation, again not something you would need or want a supercomputer for. You mainly need disk IO to/from the source reads and the mapping table you produce.
The description of RNA-seq analysis spans nearly the entire paragraph, by my interpretation and limited understanding of the methods.
> RNA-Seq analysis was performed using the latest version of the human transcriptome (GRCh38_latest_rna.fna, 160,062 transcripts to which we appended the SARS-CoV-2 reference genome, MN908947). Mapping parameters were set with a mismatch cost of two, insertion and deletion cost of three, and both length and similarity fraction were set to 0.985. TPMs were generated for all 160,063 transcripts for the nine COVID-19 samples and the 40 controls (Supplementary file 2). The resulting transcript mappings for genes of interest were manually inspected to account for any expression artifacts, such as reads mapping solely to repetitive elements such as the Alu transposable element or all reads mapping to a UTR or pseudogene therein. Transcripts whose counts came solely from (or were dominated by) reads at repetitive elements were removed from the analysis. For the controls cases we ran an outlier analysis using the prcomp function in the R package factoextra. Input data were TPM for transcripts that averaged greater than one across all samples (30,102, Supplementary file 2).
Re: Supercomputer analysis of Covid-19 leads to new theory
#139Earlier quoted context omitted.
I can't find details either, but I think they just used R for the post-processing, and there's a lot of computation behind this sentence: > RNA-Seq analysis was performed using the latest version of the human transcriptome I found this article discussing read mapping for RNA sequence analysis: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4833417/ > In particular, RNA sequencing (RNA-seq) technology,1 which provides a…
What good is a paper if their methods are a single sentence? Ugh. Reads mapping is a massively embarassingly parallel computation, again not something you would need or want a supercomputer for. You mainly need disk IO to/from the source reads and the mapping table you produce.
If it's simple alignment like blast, they don't need the interconnect. But supercomputers provide all the other necessary needs: fast processors, connected nodes, accelerators, massive I/O bandwidth. Why build a cluster without a fast interconnect to complement those features? That's just turning down research customers. And 15% on top of the other hardware is nothing. The main costs is all the power, custom software, and support staff. And not all bioinformatics is ops on strings with minimal message passing.
For these guys, it's likely their best and only option. They probably weren't given the money to build a cluster optimized for their needs or to maintain a cloud instance. Why? Its oakridge, their main priority is HPC physics. It's hard to argue when you have access to such a HPC center. And HPC sites need all the customers they can get, lest their clusters get shoved into the cloud. It's a real fear. They'd end up with hidden costs, data lockin, and poor interconnects. To help pay for those peak massive simulations, traditional HPC need to fill up that last 10-15% and bioinformatics needs most of what they offer. Perhaps all that hard won knowledge will rub off on the burgeoning field too. :)
A vision of bio-oriented HPC is IU's clusters. Though they have a shiny new cray shasta with ampere and slingshot, several of their other clusters are 10 gigs with high mem nodes. All connected to the same storage too. The hospital is the main customer and dictates their designs.
Ditto on the paper though. It's what I disliked about Bioinformatics. All the glory to the researchers designing the experiments and they can't even bother to mention what software they used.
Re: Supercomputer analysis of Covid-19 leads to new theory
#140They 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…
> why they couldn't just measure bradykinine levels directly? Is that too hard? It is. To measure gene expression, you isolate total mRNA and sequence it. This tells you the expression of all genes simultaneously. The protocol is fairly standard, cheap, and quick. That doesn't tell you anything about bradykinine, though, because there is no mRNA that codes for it. In contrast, no such protocol exists for proteins. Se…
This comment on quantitative protein assays is only partly correct. It is definitely harder than quantitative assays of messenger RNA (aka “gene expression” and not as comprehensive. But there are now hundreds of quantitative proteomic studies that survey 5000 or more proteins in single samples (and their peptide fragments). Search PubMed for the author “Aebersold R”.