A Volunteer Supercomputer Team is Hunting for Covid Clues (defenseone.com) 91
The world's fastest computer is now part of "a vast supercomputer-powered search for new findings pertaining to the novel coronavirus' spread" and "how to effectively treat and mitigate it," according to an emerging tech journalist at Nextgov.
It's part of a consortium currently facilitating over 65 active research projects, for which "Dozens of national and international members are volunteering free compute time...providing at least 485 petaflops of capacity and steadily growing, to more rapidly generate new solutions against COVID-19."
"What started as a simple concept has grown to span three continents with over 40 supercomputer providers," Dario Gil, director of IBM Research and consortium co-chair, told Nextgov last week. "In the face of a global pandemic like COVID-19, hopefully a once-in-a-lifetime event, the speed at which researchers can drive discovery is a critical factor in the search for a cure and it is essential that we combine forces...."
[I]ts resources have been used to sort through billions of molecules to identify promising compounds that can be manufactured quickly and tested for potency to target the novel coronavirus, produce large data sets to study variations in patient responses, perform airflow simulations on a new device that will allow doctors to use one ventilator to support multiple patients — and more. The complex systems are powering calculations, simulations and results in a matter of days that several scientists have noted would take a matter of months on traditional computers.
The Undersecretary for Science at America's Energy Department said "What's really interesting about this from an organizational point of view is that it's basically a volunteer organization."
The article identifies some of the notable participants:
It's part of a consortium currently facilitating over 65 active research projects, for which "Dozens of national and international members are volunteering free compute time...providing at least 485 petaflops of capacity and steadily growing, to more rapidly generate new solutions against COVID-19."
"What started as a simple concept has grown to span three continents with over 40 supercomputer providers," Dario Gil, director of IBM Research and consortium co-chair, told Nextgov last week. "In the face of a global pandemic like COVID-19, hopefully a once-in-a-lifetime event, the speed at which researchers can drive discovery is a critical factor in the search for a cure and it is essential that we combine forces...."
[I]ts resources have been used to sort through billions of molecules to identify promising compounds that can be manufactured quickly and tested for potency to target the novel coronavirus, produce large data sets to study variations in patient responses, perform airflow simulations on a new device that will allow doctors to use one ventilator to support multiple patients — and more. The complex systems are powering calculations, simulations and results in a matter of days that several scientists have noted would take a matter of months on traditional computers.
The Undersecretary for Science at America's Energy Department said "What's really interesting about this from an organizational point of view is that it's basically a volunteer organization."
The article identifies some of the notable participants:
- IBM was part of the joint launch with America's Office of Science and Technology Policy and its Energy Department.
- The chief of NASA's Advanced Supercomputing says they're "making the full reserve portion of NASA supercomputing resources available to researchers working on the COVID-19 response, along with providing our expertise and support to port and run their applications on NASA systems."
- Amazon Web Services "saw a clear opportunity to bring the benefits of cloud... to bear in the race for treatments and a vaccine," according to a company executive.
- Japan's Fugaku — "which surpassed leading U.S. machines on the Top 500 list of global supercomputers in late June" — also joined the consortium in June.
Other consortium members:
- Google Cloud
- Microsoft
- Massachusetts Institute of Technology
- Rensselaer Polytechnic Institute
- The National Science Foundation
- Argonne, Lawrence Livermore, Los Alamos, Oak Ridge and Sandia National laboratories.
- National Center for Atmospheric Research's Wyoming Supercomputing Center
- AMD
- NVIDIA
- Dell Technologies. ("The company is now donating cycles from the Zenith supercomputer and other resources.")
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Doubtful and anyway that door closed when Trump decided to try the "blame China" tactic. Obviously the last thing they are going to do now is cooperate with any investigation that could find them at fault, at least until after he is out of office and diplomatic normalcy is restored.
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Even if it's a bio weapon, i don't think china have any sort of cure, so it wouldn't yield much results.
Also things point more to being a "china study a terrible virus from bats to prove they can outdo america in treatment research, but stuff ends leaking out", rather than "purposeful attack"
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It would have been the worst bio-weapon ever, China lost an estimated 36% (last I read) of their GNP in the first quarter.
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It was something under china's control, it would be affecting the US a lot harder than it did china.
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Re:yawn (Score:5, Insightful)
California is a Red State?
It hit New York and bordering New England states early and hard. During this time while it was spreading, we were trying to determine how well would masking work, what businesses are considered essential, how much distance should we have, how to enforce it... New York has been able to get a handle of it, mostly. While it seems that other States, decided to wait for a federal response vs taking matters in their own hand and trying to lead their own states into safety.
Things like masking, keeping distance, limiting the number of people in a shop, cleaning measures.... All really do add up and help, reduce the number of cases.
If you really want to be political, I would suggest that the voters take a look on how your leaders respond to this problem. Are they leaving it up the Federal Government (in that case they are not leaders just partisan talking heads). Are they heeding their advice from Cable News channels and not from the experts (Then they are just out for the populous vote, and doesn't really care about you or your community). Or are they trying to get the most factual information even if it is politically inconvenient, encouraging their communities to work together to fight it, working hard to put in balanced temporary laws, with appropriate repercussions for not following them. You know actually lead for the health and safety of your community.
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In terms of number of cases per day California is doing really bad. In terms of population % California may be a bit better but the population of Texas and Florida are no slackers either.
The problem is a Lack of leadership independent of their political affiliation. Having Trump leading the federal government isn't helping, however when you have an Idiot as a Boss, if you really care about your community, you just don't listen to to him, and do it the way you know that works.
Your political alignment isn't
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Right and the "we reopened to soon" crowd also needs to answer the question "what will be different later?"
I get a few answers:
First that is still a maybe. "Yeah yeah but China:, sure everything that come out of China writ COVID-19 is has be 100% true and timely. Second a vaccine might be far less than 100% effective, it might not remain effective if the virus mutates. If its only say 40% effective that might not be enough to deliver herd immunity even if everyone got dosed! I think r
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All told there isnt a clear moment when "reopening makes sense" unless you expect something to change. Metrics like once cases are under X don't really make sense, because we should expect cases to just spike again unless something has changed.
It depends mainly on three things: what you re-open, how you get assholes to wear their masks, and the last thing which goes directly to your point:
Do you have enough staff doing contact tracing and telling exposed people to quarantine to track down X new cases per day?
We do here in MA, barely. We're holding level-ish right now. Most of new england is.
Data from the contact tracing team will inform us on what's safe to open further and what safety precautions need to be in those places. We're taking it st
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Data from the contact tracing team will inform us on what's safe to open further and what safety precautions need to be in those places. We're taking it step by step, like we should. So no there is no "clear moment" there is a sequence of carefully planned steps.
And that is what I would term unacceptable. I would be your political opponent on that if I lived in MA. Sorry but step by step isn't workable, unless you will put dates on those steps.
The "one life is to many brigade" might not care but little by little this nation is being changed and each day this goes on that change becomes a little more fixed. There are not like 6 read that again SIX mega corps that are propping up the entire market. The economy is being destroyed! We will no longer be a nation of s
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As Groucho would say, we've already established that you're prostitute, so now we can just negotiate on price.
You'd not do well in MA as a political candidate. We're not perfect, but we mostly take care of each other up here.
We do put dates on our steps, by the way. And we also warn that they may adapt depending on the results. Because we aren't stupid, and we don't have the hubris to believe we can declare what reality will be ahead of time. We know plans need to have contingencies.
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So, just for everyone's edification, here's how you competently read COVID-19 stats, since so many people don't seem to know how:
Find a state-by-state chart which is normalized by state population, and shows the daily (not cumulative) case rate and can do a logarithmic scale.
One can be found at https://91-divoc.com/pages/cov... [91-divoc.com] (4th chart down).
Once you have that chart and have set logarithmic view, you look at a state's line. A straight slanted upward line means an exponential outbreak. The steeper that
Re:yawn (Score:4, Insightful)
Don't be obtuse. In New York there have been between 500 and 800 new cases per day for the past week. Florida just spiked from 6300 to 15300. California has been between 6000 and 11000 evening out towards 8000. Cause of death examinations in NYC suggest that there were cases there weeks before there were officially cases there.
From the Wall Street Journal:
"Researchers at the Icahn School of Medicine at Mount Sinai have found there was “untracked global transmission between late January to mid-February,” according to research published in April. Those researchers found that the virus had been circulating in New York City as early as mid-February, with versions of the virus that originated in Europe or North America.
Total number of cases over time doesn't say anything about the current state of virus management, and spread of the disease before we really anything about this disease— in NYC, Boston, etc.— isn't an accurate reflection of virus response quality at the state/local level. However, Trump was warned about COVID in more than a dozen intelligence reports in January and February. If the federal government had not dissolved the pandemic response team, or Trump actually read his Intelligence briefings, we could have been actively looking for signs of this illness in populations earlier, and perhaps gotten a leg up on PPE production.
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Not Fauci's first rodeo screwing things either.
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I see "don't be obtuse" is a bridge too far.
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Look for it to get dramatically worse in the stupid states, Disneyland just opened for business over the weekend.
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power and profit oriented medicine/pharma groups continue to avoid or attack prophylaxis and early generic treatment options.
What on earth are you talking about? Did you make this stuff up, or do other morons feed it to you?
Re:yawn (Score:5, Informative)
Wild conspiracy theories, complaining about Democrats when in fact it's Republican controlled areas that are in the deepest shit right now... Yeah, I think we can safely ignore that guy.
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Hillarious -
We all know that all of this Covid BS will magically disappear around November 4th this year
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did you miss the "HYDROXYCHLOROQUINE CAN KILL YOU" all over the place on CNN and MSDNC?
Re:yawn (Score:4, Insightful)
I normally like to group all of them into Cable News.
They all have 24 broadcast schedules in which they feel the need to fill up. Being that they are nation wide, they mostly have to cover federal politics, and some world news. Each story needs to be short under 15 minutes, and written so an 8th grader can understand it. To keep viewers they need to often make these dry topics interesting so they will often put in commentaries from people who are passionate (not necessarily knowledgeable) about this topics. To say things that make us clap or boo at them.
This has changed the nature of our political alignments, less from ideas, and methods. But towards how we feel about our favorite sports team. Go Yankees Boo Red Sox! But what really makes the Yankees so much better than the Red Sox? Even as we will still cheer one and boo the other if the time you like isn't winning, and if the other is winning you still think they suck! Just like in Sports and Politics, we have people who change sides, and the ideals governing the core beliefs of each political party can change on a whim. I remember a time where the Democrats where complaining that the republicans where letting too many immigrants in the US. And harden Republicans were like, we need these immigrants as they are doing important work, that we don't have the ability to fill ourselves.
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It might be short. (see Darwin Awards)
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Re: yawn (Score:5, Funny)
and chew one multivitamin tablet over 4 days,
Jesus, just how big are those tablets?
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Re: yawn (Score:2)
I believe they're recycled ningi, since nobody could ever own enough to buy one pu.
(HHGTTG)
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I blame the galactic banks for not handling small change.
Re: yawn (Score:2)
We can't say what will work. The effects vary by genetics, blood type and which of the CoV-2 viruses is involved.
Intel? (Score:2)
Do they *have* a super computer? (Score:3)
You don't see Intel on a list of organizations donating time of their supercomputer.
That leads to the obvious question - does Intel *have* a supercomputer they could be donating time on? I don't follow supercomputers, so I don't know. All I know about supercomputers is that of the top 100 fastest computers in the world, 100% run Linux. Just like this router here with 32MB of storage. That's quite remarkable.
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You don't see Intel on a list of organizations donating time of their supercomputer.
That leads to the obvious question - does Intel *have* a supercomputer they could be donating time on? I don't follow supercomputers, so I don't know. All I know about supercomputers is that of the top 100 fastest computers in the world, 100% run Linux. Just like this router here with 32MB of storage. That's quite remarkable.
Intel has a supercomputer. Unfortunately, it runs Windows 10 and keeps rebooting forced updates and the applications keep dying without any usable error messages other than "Your application has stopped working." Then they tried to change some settings and got caught up in registry hell.
When things get really bad (Score:4, Interesting)
When the immunological fit has hit the shan pull out the dexamethasone. I've seen articles about a doctor in the Los Angeles area at Cedars Sinai who noticed COVID cases gone critical very strongly resemble good old fashioned cytokine storms. He dragged dexamethasone out of his kit bag and has not lost a patient so treated. They recover out of ICU within about 24 hours. More recently I've seen reports of a British "discovery" of pretty much the same thing. And the news does not find something like that exciting, it would kill the news cycle they are milking.
And a look at the studies for hydroxyquinoline suggest early treatment with it can lead to lighter symptoms. Remdesivir is also a significant help early in the disease cycle.
I'm not sure bazillions of CPU cycles are needed to figure out this sort of thing. But, I suppose it is fun to put this together.
{^_^}
Re:When things get really bad (Score:5, Insightful)
> And a look at the studies for hydroxyquinoline suggest early treatment with it can lead to lighter symptoms.
It doesn't help CoVID at all. The British study made this mistake and killed several patients enrolled in it.
Hydroxyquinolone is good for amoebic dysentery but not effective for nCoV-19.
Hydroxychloriquine, when given as a prophylaxis with Zinc appears to help the body fight off the virus by acting as an ionophore and getting Zn into the endosomes where it can help clean up the viral mess. It may dampen the CK2 mechanism specifically.
The Big Pharma coalition is busy constructing HCQ studies without Zinc because they know that most people aren't paying attention and will see HCQ acting by itself having little effect. Even doctors and epidemiologists (90% of everybody isn't at the top of their game). The Indian studies are using dietary foods high in Zinc, others are giving bioavailable supplements, but The Lancet got caught with its pants down by publishing the Surgisphere study that appears to have 100% faked data, because its "results" fit the gated institutional narrative. The Lancet's peer "reviewers" never questioned the literal impossibility of Surgisphere's listed Methods because it fit their confirmation biases.
Remdesivir is expensive as hell and may only have a mild effect but that may be outweighed by long-term morbidity costs.
Nebulized steroids, early, seems to help patients kick the disease. The physician who was the Texas chief physician for a number of years has been using it over more than a thousand patients with confirmed disease hasn't lost a single one and, importantly, probably prevented most long-term damage. Japan and Taiwan have been doing this for months to similar effect.
Systemic steroids, like dexamethasone absolutely do help, but it's not all that hard to prevent almost all patients from getting to that point. The information black-hole in the top-most-afflicted nations is somewhere between indicating a systemic problem and highly suspicious. "Third World" and "Developing Nations" countries are doing better than the US, UK, Canada, etc. The difference needs a sober explanation.
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Why don't you go to a COVID-19 party and prove it. Or maybe ask that 30-year-old who did that in Texas. Oh wait. You can't. He died.
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As we accumulate risk factors, thorough repletion becomes even more important, even if insufficient.
Right now, people are losing their lives over misinformation and disinformation put out by media and politicians. Some of these are actively committing terrorism, in several forms.
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Balance between generating data and analyzing (Score:4, Insightful)
There is a problem in different sectors: it is easier to expand efforts which analyze data than it is to expand on generation of data. The result is that the analyzers start to put out reports which seem convincing but which are actually weak. The result is false confidence in the science.
The antivirals studies(HCQ/Remdesivir) are a good example. What you need to get a reliable and expensive test . Instead you get mediocre tests and a lot of analysis on existing data. The result is there remains a lot of room for disagreement and opposing convictions.
Climate studies have suffered a lot from that. Journalism suffers a lot.
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I'm talking of shit studies of the type 'Garbage in Garbage out'. Not studies which are compromised because of conflicting interests, though that happens too.
corrupt science (Score:1, Insightful)
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Scientific corruption is a problem. Reduced trust in science is corruption. My comment however is not about corruption but about where to invest. And then investing in good data is expensive and the work is difficult. It is much more attractive to invest in the processing of the data and in trying to make the most of the data which is available.
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sorry , editing error. I ment 'Reduced trust in science is a problem.'
Re: Balance between generating data and analyzing (Score:2)
The best tests are by microarray, which exist. PCR is the worst.
Typically only the throat is tested, you need to test both throat and blood for the virus and the blood for the antibodies. And, no, swab isn't good enough, according to doctors I've talked to.
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well, what is the right word again? A study? I am thinking of selecting a bunch of people and have them use the medicine in a double blind manner with parameters which are defined upfront, not afterwards. And get that right. Now because there is wild variablity in how people are affected by the virus is is not easy to get a good sample of people and because for those affected most heavily it is hard to do double blind so it is difficult to get a good study.
I don't worry too much about PCR not being good en
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False positives are near-zero. False negatives are 40%.
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I've read problems with sampling: the swab often doesn't capture enough virus if the infection has already moved down the airways,
and I've read about problems with how exactly you run the tests. It's a kind of selective amplification which can fail to amplify enough. The way you work around that leads to some variability in sensitivity. Running it multiple times for instance. I thought you could reduce false negative to below 40%
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The Japanese were using their supercomputers to model things like the spread of micro droplets in various environments in order to develop more effective techniques for protecting people. They had some interesting results, for example a simply plastic barrier between people on opposite sites of a desk isn't all that effective. They did modelling of train and aircraft cabins too.
And you can help too (Score:5, Informative)
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Re: And you can help too (Score:4, Insightful)
Bitcoin drowns any signal from other distributed computing, as far as climate goes.
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Someone should invent a FoldingCoin that pays you to donate CPU cycles to worthy causes.
Unfortunately it won't pay out enough, the cost of mining equipment (i.e. GPUs and later FPGAs) will outweigh any return.
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Correction: It is 1.5 exaflop. 1500 petaflops. Can be seen here https://stats.foldingathome.or... [foldingathome.org] 1.4 exaflops now. Most computations coming from Linux machines, closely followed by windows ones.
It was 2.4 exaflops for a while with a peak at 2.6. More than all the TOP500 computers reunited at the time. There have already been publications from that volunteer work and more are coming. :)
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Get drunk instead (Score:2)
A nice idea (Score:2)
But a little bit late in the day wouldnt you say? They should have started this in march.
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But a little bit late in the day wouldnt you say? They should have started this in march.
This approach is broadly applicable to other diseases, though. It could be the Silicon Valley disruption of medicine that we have all been waiting for.
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The Silicon Valley disruption of medicine started in Armonk, NY with IBM, and really, it wasn't just about medicine but about computer systems that enabled the ridiculously detailed and find grained accounting and financial scorekeeping of the business of medicine.
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But a little bit late in the day wouldnt you say? They should have started this in march.
Why? It wasn't a problem in March.
March 2: "You take a solid flu vaccine, you don't think that could have an impact, or much of an impact, on corona?"
March 2: "A lot of things are happening, a lot of very exciting things are happening and they're happening very rapidly."
March 4: "If we have thousands or hundreds of thousands of people that get better just by, you know, sitting around and even going to work â" some of them go to work, but they get better."
March 5: "I NEVER said people that are feeli
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"Why? It wasn't a problem in March. "
I don't know what country you're in but here in the UK the lockdown started in March when it very much WAS a problem.
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The consortium was launched March 22. https://venturebeat.com/2020/0... [venturebeat.com]
Life, Covid-19, and everything... (Score:5, Funny)
Computer: The answer to Life, Covid-19, and everything is...
Crowd: Yes?
Computer: ...you are not going to like this...
Crowd: Get on with it!
Computer: The answer to Life, Covid-19, and everything is...
Crowd: Yes?
Computer: ..is wear a face mask when you go out.
Crowd: What?
Computer: That's the answer. I checked it very carefully.
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So it is a big pseudo-machine (Score:2)
So they are putting together a massed computer network designed to provide the perfect answer for COVID-19. What are they putting together to assure they are asking the correct question? If you do not ask the right question you might well miss the best corrective measures for a bad situation. Optimization efforts seem to work that way.
{o.o}