# Contribute to finding cure for coronavirus



## The red spirit (Sep 29, 2015)

We all know that coronavirus is pretty harmful for us and recently some countries getting locked down. This isn't fun and it's the major health concern over all world. Many people don't feel so good about current situation and stock up on supplies. However, usefulness of such things isn't very well known and it's unclear if they are buying too much stuff that may end up unused. 

Most of these things happen because we have no direct ways to fight this new virus. Seemingly research about it is becoming the most important thing at the moment and you can contribute to it.

I would like to ask perC'ers for contribution and install program called BOINC. It runs on many platforms, including phones. It's free and it works by distributing very computationally heavy workloads for many other computers. Also this happens during idling, so it doesn't interfere with other tasks (it can be configured to work at full blast too). BOINC is just such workload client and you can join many projects. As far as I know [email protected] is participating in finding coronavirus cure and you could check out project's website here:
https://boinc.bakerlab.org

So, it would be really nice if we contributed. It doesn't cost anything, it's free and pretty easy to use. 

If you prefer [email protected] software, then you can use it too. They also have coronavirus specific workloads. Here is their page about it:
https://foldingathome.org/2020/02/27/foldinghome-takes-up-the-fight-against-covid-19-2019-ncov/

To set up [email protected] you only need to download their software. It works really similarly to BOINC client, however it was made just for one project in mind, so there's no adding or removing projects. Just like BOINC, it's free, easy to use. However, it doesn't work on phones. 

If you want to learn more about the concept you should read more:

Simple explanation https://www.techopedia.com/definition/7/distributed-computing-system

Advanced explanation https://en.wikipedia.org/wiki/Distributed_computing


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## Fennel (Jan 11, 2017)

Interesting... I'd have to read up on it first though. Not sure if it's safe.


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## The red spirit (Sep 29, 2015)

Fennel said:


> Interesting... I'd have to read up on it first though. Not sure if it's safe.


Both projects are decently safe. They aren't anything new and have been there for many years. They already have shown some positive results. I think that they somewhat contributed in ebola research.


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## The red spirit (Sep 29, 2015)

https://twitter.com/CoreWeave/status/1238451810152693760

Companies are letting [email protected] to run on their hardware. Seemingly distributed computing in general is on rise now. It's really unsurprising why.


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## Grandmaster Yoda (Jan 18, 2014)

https://foldingathome.org/2020/03/1...e-doing-and-how-you-can-help-in-simple-terms/


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## The red spirit (Sep 29, 2015)

In depth information what projects like [email protected] and [email protected] do

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Source: https://www.reddit.com/r/BOINC/comments/2ur01x/eli5_what_is_the_difference_between_rosettahome/

"*Complete answer*: Proteins are the building blocks of our human body and they are themselves built out of smaller pieces called amino acids. Proteins are an extraordinary complex piece of biological machinery, capable of self assembly and continuous transformations and adaptations which are caused by what's happening around them.

They can change shape according to temperature, chemical elements present around them and other dynamics which I won't delve into, but perhaps the most remarkable fact is that proteins are basically capable of self-assembly from scratch assuming everything around them is 'right'. This drawing shows the folding process, aka: how a protein self assembles itself into its final shape.

Being the complex machinery they are, you can imagine that sometimes things can go wrong during their self assembly (an accident often known as 'mis-folding') and [email protected] focuses on reproducing all the exact steps of such a process a huge amount of times and in different conditions so that they can sometimes witness a mis-folding and then try to understand what caused such accident to happen in that particular simulation. The causes can often be more than one and to really understand what's happening you need to have a lot of mis-foldings to observe and ideally you want to have as many information as possible about such events, which is why [email protected] simulates the folding process atom by atom, an expensive computational endeavour which is known as Molecular Dynamics).

Mis-folding is a pretty big deal since its believed to be the cause of several important diseases which we can't cure yet and which are also known as Proteopathies.

Now, like just about everything in life, there are different approaches that can be used to solve a single problem and each of these has its own drawbacks and strong points. My point is: simulating a protein atom by atom and seeing what happens instant by instant is in itself a computationally long and painful process which gets longer and more painful the more atoms you need to simulate (bigger proteins) and the longer the time span you want to simulate, which basically means that lots of compromises have to be done if you want to use this approach with our current technological level: some of these compromises may involve running simulations with simplified models, simulating very small proteins or very small time frames.

Enter Rosetta. We already know that simulating huge proteins atom by atom for any extensive length of time is computationally very intensive (read: time wasted not doing something else, money spent to run computers to full throttle) and lots of processes can still be reproduced with sufficient approximation even without simulating atom by atom. Remember that drawing? Rosetta is not focused on what happens in the drawing but on predicting what kind of final status (Quaternary structure) you would get if you started with the initial status (Primary structure) given several variables about the surroundings. Lots of assumptions are made and lots of approximable details are left out: A typical Rosetta task still runs 'steps', but this time they are not trying to compute where each atom will be according to physical laws (by physical laws I mean, among the other things, attraction and repulsion forces between atoms. This is what [email protected] focuses on). Instead, Rosetta does a somewhat random 'move' of a whole chunk and it only goes to the next step when one of the random moves has made the whole protein more stable than before (aka: it has a 'lower energy level'). This was typical Rosetta workunit BOINC graphics when it used to have it.

This works because in nature everything around you is constantly trying to move to more stable configurations (lower energy levels). By everything I mean the universe as a whole, from radioactive decay to thermodynamics, weather forecasting, stellar dynamics and any physical process you can name.

As you are beginning to notice, by skipping the bulk of computationally intensive stuff which was the atom by atom simulation, we can now afford to run many more simulations of much bigger proteins and of much longer time frames, for a much greater number of proteins.

Both projects have made scientific publications, both projects have their merits and are both doing something useful to humanity which is identifying a problem and taking some kind of approach to understand it better."

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Note: for accessing links please go to original post link.


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## The red spirit (Sep 29, 2015)

There is some progress already:
https://www.ipd.uw.edu/2020/02/rosettas-role-in-fighting-coronavirus/

Also coronavirus folding group is growing exponentially:
https://www.reddit.com/r/COVID19/comments/ffwtg4/in_just_six_days_youve_made_the_rcovid19/

Still, the more contribution there is the faster scientists can work. So, anyone willing to help is welcome.


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## The red spirit (Sep 29, 2015)

*Fake FAQ (my own generated questions)
*

*1.Why downloading BOINC or [email protected] client takes so long?*

Currently speeds of both of those sties can be really low (20 kbps average). That is due to massive increase of traffic in them. When many computers try to connect and receive data from not so beefy server, then traffic slows down. Just two weeks ago there wasn't any corona virus project really going on and now it's top 9 most contributed project ([email protected]) on Earth. If you want to know more why exactly internet slows down, I recommend this video:





It doesn't directly explain why internet gets slow, but it tells a very important principle of how internet works. Overloading is a real thing and now due to massive increase of internet usage (70% increase as far as I know) many weaker points of network really struggle. Weaker servers might struggle and more importantly your ISP (internet service provider) might struggle too. That's why during coronavirus outbreak some of us might enjoy less than half speed of old school dial-up internet. 

*2.Why can't I get any workloads for so long?*

Just like internet connection, their workload distribution is rather slow too. There is finite amount of workloads available, some projects post their data. Due to slowed down internet and high demand of folding works, your requests can be ignored for a while and can take a lot of time to download (like 1 hour). 

In case of Rosetta, I saw that they don't have any workloads made for mobile platforms (Android, iOS) yet, so just use a PC. 

*3.Are laptops good enough for folding? *

Yes, officially they recommend you to keep it plugged in. However some tend to use more power than charger could provide. Also hardware can heat up and those tiny heatsinks might not be able to cope well with all that heat. Thus you should monitor temperatures and see if CPU or GPU throttles. 

*4.Is folding harmful for computers?*

Not really. However they are pretty heavy workloads and some computers aren't exactly designed for those, so they may experience accelerated wear and tear. 

Desktop users might want to underclock and undervolt CPU or GPU to reduce heat output, power usage and to reduce strain. 

*5.Who is in control of folding projects?*

[email protected] belongs to Pande Lab, which is directed by professor Vijay Pande. Usually computed data is used for their lab, however in cases like this they might share their findings with others. More about them:
https://foldingathome.org/about/

[email protected] belongs to University of Washington. This folding project isn't used for profit, only for academic/research purposes. Their specific place is in Institute of Protein Design in The Baker Lab. Links for further reading:
https://boinc.bakerlab.org/rosetta/rah/rah_about.php
https://www.ipd.uw.edu
https://www.bakerlab.org

*6.When folding projects have started?*

[email protected] started in 2000
[email protected] started in 2005

(BOINC client was released in 2002)

*7.Is there any reward for doing this?*

Besides positive feelings of donating and sharing, there are none. Directly nobody is going to pay for your work, nor there are any gifts. It's a pure volunteering.

However, a rather young project called Gridcoin can reward your contributions with their own created cryptocurrency Gridcoin (GRC) (could be traded for usual money like dollars or euros). If you are interested, check out their official website:
https://gridcoin.us

Explanation of how it works:
https://github.com/gridcoin-community/Gridcoin-Wiki/wiki 

*8.Further reading links?*

Wikis:
https://en.wikipedia.org/wiki/Berkeley_Open_Infrastructure_for_Network_Computing
https://en.wikipedia.org/wiki/[email protected]
https://en.wikipedia.org/wiki/[email protected]

Official informational pages:
https://boinc.berkeley.edu/wiki/User_manual
https://foldingathome.org/about/
https://boinc.bakerlab.org/rosetta/rah/rah_about.php
https://boinc.bakerlab.org/rosetta/rah/rah_graphics.php

Official FAQs:
https://boinc.berkeley.edu/wiki/Advanced_FAQ
https://foldingathome.org/support/faq/
https://rosettaathome.weebly.com/faq.html


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## The red spirit (Sep 29, 2015)

So far I kept running BOINC with [email protected] during hours I was awake (I don't feel comfortable leaving electronics on while sleeping) and during these days I earned 7001 points.

Specs:
AMD FX [email protected] watercooled
12GB RAM
AMD RX 560

Used to run CPU 100% of time, but decided to run it 80% of time. Power consumption at 100% was 120 watts. Temperature of CPU is below 40C, chassis and case doesn't get hot or even warm. Despite wattage, this setup is sustainable for long workloads.


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## VoodooDolls (Jul 30, 2013)

la maleta y lo bulto llenalo de cualto


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## Lesoris (Oct 4, 2019)

This situation is scaring :frustrating:


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## The red spirit (Sep 29, 2015)

I read that IBM working on making Covid-19 specific tasks for their World Community Grid project. It's not there yet, but if they manage that in time than they have chances of attracting a huge audience. Many times bigger than Rosetta's and I hope that they will make ARM workloads, because Rosetta only has x86 workloads available despite their claims to run on Android.

Their contribution is welcome.


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## The red spirit (Sep 29, 2015)

I joined a team on Rosetta. Now they have a shit ton of work units available for COVID 19. I know that my computer isn't much, but so far my average score is highest in my country. My total score right now is 21358. That's not really much, but every contribution counts. 

Seemingly their user count increased 2 times since mass spread of coronavirus, so it looks like many people worldwide want to contribute. I'm pretty sure that ever stricter lockdowns and self-quarantines push many more to find ways to stop such lethargic lifestyle. 

I may consider creating Personality Cafe team to fight coronavirus.


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## The red spirit (Sep 29, 2015)

That's it, Personality Cafe team is a thing. Anyone interested about it can look at it here:
https://boinc.bakerlab.org/rosetta/team_display.php?teamid=19432

Anyone from perC and even not from perC are welcome to join it. There are no restrictions about joining a team and anyone can do it by themselves. Joining team in [email protected] is as easy as clicking join and you are in the team. There are no advantages of being in team rather than doing the same work alone, however it's nice to have a little community and members can have team chat if they want. Also points gained while being in team are counted as team's, somethign that isn't possible without team. You can also look at how much team has achieved on many statistics platforms and compare our results to other teams'. Feel free to join it and fight coronavirus together.

Edit:
Currently [email protected] only works on computers. Windows Linux and Mac users can participate. Android support technically exist, however no workloads are currently created for it and people don't really talk about workloads comming. So, right now only computers can contribute.


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## The red spirit (Sep 29, 2015)

*Personality Cafe's [email protected] team*

Yeah. A shameless plug that perC has its own [email protected] team. The sole existence of this thread is due to that in another thread not many want to read pages of info only to find this pretty important announcement, so I think it deserves its own thread. Here's the team page:
https://boinc.bakerlab.org/rosetta/team_display.php?teamid=19432

For those who don't know, [email protected] is a long running project (nearing two decades at this point), which is aimed at protein research. This project helps scientists at labs to investigate them and later create drugs for HIV, malaria, cancer, Alzheimer's, but lately they added Covid-19 aimed researches too and that's why I want this to be heard.

[email protected] works closely with scientists. The project itself helps them in tasks that otherwise would require renting a supercomputer, which is expensive and not always available. [email protected] makes access to such power much cheaper by breaking down massive tasks into small pieces and then distributing those pieces for volunteers, so that they could complete work in reasonable amount of time. By making this project open for all with computer, they managed to gather lots of processing power and thus it works. Their software is made to use unused CPU power, so that running those tasks doesn't interfere with your work (that can be reconfigured to work at full blast if wanted).

It seems that whole world is currently highly affected by Covid-19 virus and perC'ers seem to be writing about it too, so I thought it was relevant enough and created our own team. Now anyone can join this team and show that Personality Cafe is participating too.


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## The red spirit (Sep 29, 2015)

https://www.tomshardware.com/news/folding-at-home-worlds-top-supercomputers-coronavirus-covid-19

Humanity can do some great things once in while. [email protected] is also at mind blowing heights, right now it's roughly at 459 petaFLOPS. [email protected] right now is beyond 1 exaFLOP, making it the most powerful "computer" to the date.

https://techcrunch.com/2020/03/26/c...dsourced-molecular-science-to-exaflop-levels/

What an awesome time to be alive.


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## The red spirit (Sep 29, 2015)

Finally reached first 10 000 points


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## The red spirit (Sep 29, 2015)

And soon after my previous announcement Rosetta went pizdec. They say that they have 8000 tasks ready to be sent, but only 3 unsent. This is probably due to different status update times. Still, that means that Rosetta is out of tasks currently and hopefully temporarily (well it would be fun if their project was completed). So, at this point both [email protected] and [email protected] are out of steam. 

For now please enjoy this cute emoticon instead:
=^.^=


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## The red spirit (Sep 29, 2015)

Oh and since [email protected] is overwhelmed my machine now crunches WCG's Cancer Marker WUs. Previously I left it to run 30% of time, but due to unusual conditions today it's automatically at 100%.


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## The red spirit (Sep 29, 2015)

Yesterday Rosetta had some new WUs for Android. Tried to get them, but couldn't download them. Today they are all taken. Their tasks in progress are dropping sharply, there's 200 000 tasks less there. Some new users are coming here, however I noticed a slight reduction. Most likely some people got frustrated by not getting any kind of work from Rosetta. 

Anyway, WCG is planning to do something about Covid-19 too. They are already advertising their plans on their own website:
https://www.ibm.org/OpenPandemics

I'm starting to think that this fragmentation isn't doing anyone favours and is starting to become a race of who will be first to make the drug. Not sure how much work done is being shared between those projects, but seemingly nothing is being shared yet. Only papers with some conclusions are open for everyone. This isn't good enough and I think that they should be working together or at least sharing their data freely. Because now it looks like a rat race.

Similar to how all those Folding-esque projects do similar things, but don't achieve much. And yes there more folding projects than just Rosetta and Folding.


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