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Macroman
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Re: WCG and Pandemic-Related Projects


Create the mechanism by which patients can opt to forgo the protections of vaccine approval based on informed consent.

I respectfully disagree. A deliberative, controlled scientific process is necessary to prevent unforeseen unwanted consequences, such as Hoskins effects.
http://en.wikipedia.org/wiki/Hoskins%20effect


"First, do no harm..."
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Former Member
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Re: WCG and Pandemic-Related Projects

Guys, it's important to spread the word once the project is up. However, it's quite hard to get noticed in a place like Reddit or Facebook etc. I suggest that if you play any online game, post the the news to the forum of that game or send group email to your team members and tell them to spread the word as well. There are millions of gamers in the world and they usually have pretty powerful computers. That's the resource we need to tap into.

Color me skeptical on this new project. Very reminiscent of the flu project, FAH1, Ebola. All Autodock4/Vina projects from Scripps. All have produced next to nothing after years of work. If it goes like the other projects, it will start to great fanfare (remember Ebola) then after 8 to 9 months will start to die off and then after 2 to 3 years of running there will be a post stating that the researchers have all the data they need and will start analyzing the HUGH amounts of data and the project ends. Very little communication from the project. This just seems like a rehash of the same old stuff. The PI (Stefano Forli) for this new project was a researcher during the FAH Phase 1 stuff and took over for Alex Perryman when he left if I remember correctly. If this is intended to work during a Pandemic then there needs to be data analysis done from the start and expect to have a least some candidate compounds in wet lab testing in months, not years. I'm not convinced but hey, good for badges!!
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Jim1348
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Re: WCG and Pandemic-Related Projects

Color me skeptical on this new project. Very reminiscent of the flu project, FAH1, Ebola. All Autodock4/Vina projects from Scripps. All have produced next to nothing after years of work.

Took the words right out of my mouth/post. I will give it my usual level of support, but am not expecting miracles.

Of course, each virus is different, and there may be something about this virus that makes it more suitable for Autodock. However, I saw a mention of Autodock recently on either Folding or Rosetta (don't remember which) to the effect that although they require much more computation, they are more accurate. Time will tell, and each may make a contribution. Hats off to all the hardworking scientists, but I would not abandon all my other projects for it.
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Falconet
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Re: WCG and Pandemic-Related Projects

- IIRC, the FLU project didn't really do much other than releasing the data. I remember some post saying the virus was no longer an emergency so they were putting that research aside for now and focusing on the Dengue project, a project which did give us some good communication, IMO https://www.worldcommunitygrid.org/about_us/d...amp;sortBy=&pageNum=1.


There was a FAAH update in 2010 about a potentially "novel class of HIV fighting drugs" (something like that). And 10 years later, what happened regarding that research? Anything? It's hard for people to join if they see projects running for years and years and there isn't something detailing the current science status and updates on previous research.
Project communication has to be improved. We've been saying that for years lol.
I think there should be some sort of science section for each project with updates about what is being worked on and update it periodically (is a few lines of text every 3 or 4 months too much to ask?).

"As of XX-XX-XXXX, we are working on this and that. Also, we've continued following up on the research previously described in project update X and are seeing encouraging results which we hope to describe in more detail in a future update OR regarding the leads described in project update X, none of them panned out"

Just my opinion.
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[Edit 2 times, last edit by Falconet at Apr 6, 2020 2:40:36 PM]
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Jim1348
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Re: WCG and Pandemic-Related Projects

Just my opinion.

Works for me. Academic projects tend to be, shall we say, academic. There is nothing wrong with that. It adds to the body of knowledge. But we should be informed (quarterly is OK) of where we are, or aren't.

Most projects here are good. I am not complaining, just suggesting.
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Falconet
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Re: WCG and Pandemic-Related Projects

Just my opinion.

Works for me. Academic projects tend to be, shall we say, academic. There is nothing wrong with that. It adds to the body of knowledge. But we should be informed (quarterly is OK) of where we are, or aren't.

Most projects here are good. I am not complaining, just suggesting.



Of course. I'm fine with "simply" adding more knowledge. I just wish we had more updates on what is happening, that's all.
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[Edit 2 times, last edit by Falconet at Apr 6, 2020 2:57:26 PM]
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supdood
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Re: WCG and Pandemic-Related Projects

Just my opinion.

Works for me. Academic projects tend to be, shall we say, academic. There is nothing wrong with that. It adds to the body of knowledge. But we should be informed (quarterly is OK) of where we are, or aren't.

Most projects here are good. I am not complaining, just suggesting.



Of course. I'm fine with "simply" adding more knowledge. I just wish we had more updates on what is happening, that's all.

But is it really OK to only add the knowledge that 30 million chemical compounds aren't good candidates for therapeutic drugs for X disease? I realize that WCG is a great resource for the scientists with the amount of compute power and dedication of volunteers that we have here, but maybe we need to select the chemical compound libraries with more care instead of the "let's hit it with everything" approach that is typical for these projects.

When the scientists analyze our results and screen out compounds that were positive hits but are too expensive, rare, illegal, or poisonous to humans (I can't recall which project (Ebola? Zika?), but there was one that had all of these screened out from the promising candidates that we had computed), you have to wonder why they weren't screened out prior to going to WCG.

My hope is that the open source tools portion of the OpenPandemics project will allow scientists to properly screen the chemical libraries that we are docking against the target pathogens so that we aren't wasting CPU cycles on non-viable candidates.
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Re: WCG and Pandemic-Related Projects

I'm not saying it's not a useful project but based on history at WCG it probably isn't going to produce anything of any tangible value. I'm not one that requires constant communication but going back over the previous projects, nothing was actually produced of any clinical value. To me, the Ebola project was a complete dud. Towards the end, it even looked like the PI lost interest. It just looks too much like a "Johnny come lately" project just to say WCG has a COVID-19 project. Sorry, I'm skeptical...
Probably need to clarify the word useful... Even failures contribute to the body of knowledge but anything other than that is highly unlikely. What's the old saying about doing the same thing over and over and expecting different results. Ebola? Nothing. FAH1? Nothing, Flu? Nothing. Dengue? Nothing, Marlaria? Nothing, "COVID_19'"? .........
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[Edit 1 times, last edit by Doneske at Apr 6, 2020 5:46:10 PM]
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Re: WCG and Pandemic-Related Projects

Just my opinion.

Works for me. Academic projects tend to be, shall we say, academic. There is nothing wrong with that. It adds to the body of knowledge. But we should be informed (quarterly is OK) of where we are, or aren't.

Most projects here are good. I am not complaining, just suggesting.



Of course. I'm fine with "simply" adding more knowledge. I just wish we had more updates on what is happening, that's all.

But is it really OK to only add the knowledge that 30 million chemical compounds aren't good candidates for therapeutic drugs for X disease? I realize that WCG is a great resource for the scientists with the amount of compute power and dedication of volunteers that we have here, but maybe we need to select the chemical compound libraries with more care instead of the "let's hit it with everything" approach that is typical for these projects.

When the scientists analyze our results and screen out compounds that were positive hits but are too expensive, rare, illegal, or poisonous to humans (I can't recall which project (Ebola? Zika?), but there was one that had all of these screened out from the promising candidates that we had computed), you have to wonder why they weren't screened out prior to going to WCG.

My hope is that the open source tools portion of the OpenPandemics project will allow scientists to properly screen the chemical libraries that we are docking against the target pathogens so that we aren't wasting CPU cycles on non-viable candidates.

I'm hoping those libraries through the years have had additional property/finding markers added from research over time allowing a much narrower filtering before brute force computing effort is let loose on this problem... something that can be predicted to have nicely chemically fits to those spikes.
Anyway, IBM's Summit but now too Watson AI is working on the problem. What is going to be run here is Johnny come late... there are 90 labs around the planet working on synthesizing a vaccine right now. One had 1 billion dumped on it in NL by Johnson & Johnson + US government... money no object.
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[Edit 1 times, last edit by Former Member at Apr 6, 2020 5:10:45 PM]
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Jim1348
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Re: WCG and Pandemic-Related Projects

All true enough. Autodock uses the method of minimizing the free energy for the docked compound (more or less). Whether that produces useful results probably depends a lot on the accuracy of the models fed into it. I am willing to believe that the scientists have made progress on this front over the years, and may achieve some useful results. I just would not bet all my computing resources on it.

And it is not just directed to Covid-19, but to the coronaviruses in general. It could be a useful supplement to the other projects, even if not for a quick cure. We don't have to pass judgement on it immediately, just keep our eye on it.
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