Anyone else doing Folding@Home?

[classicdrogn]

I might as well join the same team if yu're doing one. Not that it really matters compered to the science getting done, but counting up the points is fun, even if the RX 470/480/570/580 graphics card family apparently hates the F2H client so I'm just on cpu.

[Bob Schroeck]

I've been running Folding@Home for several weeks now, and I'm part of the City of Heroes Homecoming team.

[classicdrogn]

Cool. All set then! I'm just using "velocirapture" for a handle since I don't have a CoH account of any stripe, but like I said before, any of that is just a sideline to the science getting done. Not that I'm getting nearly the results of some high-end systems just running on CPU, even a Ryzen 3600, but it's more than I'd be contricuting otherwise, so yeah.

I will say that the current work unit running is the most interesting one I've seen in the visualizer so far, with lots of little loose ends flailing around and the main blob wiggling and pulsating in and out like a "living alien organ" prop from an 80s Dr. Who episode. Looking up the project number tells me it is part of the COVID-19 research, but no further details, and I don't have the bio/O-chem background to understand much of them anyway. If there's some way to set the visualizer to look at a specific data set rather than what's running when you hit the button to open it from FAHControl, it's 14534. I mean, there must be since the whole point is to crunch through these for researchers to look at, but I haven't explored too deeply into that end of it.


edit: And that one finished while I was writing, while opening up the new one (13851) shows it springing apart into two separate blobs from snapshot 2 to 3! Very cool.

[Bob Schroeck]

I've not been using the visualizer much -- I think I used it for the first time in weeks last night right after I updated the F@H software with the new release. My then-current work unit basically manifested as a shapeless blob with wibbly bits on the ends.

[classicdrogn]

I had one a little while ago that had a benzine ring and a carbon chain with an azide on the end clasping and opening up like the hitch on a railroad car on each end. I'm sure I'll get tired of looking at them eventually, but for now the nerdy blobs are shiny and new.

[classicdrogn]

Projects 16437

Cause: covid-19

This project simulates the "dimerization" domain dimeric-form of the Nucleoprotein of SARS1 from the 2003 outbreak. The nucleoprotein is involved in genome packaging of the virus, which means that it binds the genetic material of the virus, RNA, and packages it up, helping it remain stable as the virus assembles. This packaging also allows the RNA to avoid our immune response that would normally chew up this viral RNA.

Nucleoprotein contains 2 folded domains, the RNA binding domain and the "dimerization" domain, with a "floppy" disordered linker connecting them. In projects p16436 we are simulating the RNA binding domain, and in this project we are simulating the other folded domain, involved in dimerization of the nucleoprotein as it assembles together to package the viral genome. This project specifically simulates the dimeric form when it assembles form. In p16438 we are simulating the monomeric form in isolation form, which has been less well characterized.

Our hope is that by simulating both domains, we can build a more complete picture of the viral behavior by modeling the floppy linker between them, and have a better understanding of how this virus works to evade the host-immune response, and potential therapeutic strategies.

this one isn't so active to look at, though it does have a dual-lobed structure like a brain or a pair of lungs, but dang son. Figuring out exactly how this bug evades the normally pretty beastly human immune system? That's the kind of thing that is the reason I decided to join in on F@H.

[Star Ranger4]

Also on the HC Team, HC_Star_Ranger4

I've never really gotten the visualizer to work I thought?
   

It looks like the parts arn't talking to each other...

[classicdrogn]

Sometimes the visualizer does look a little weird, with a few floating parts or in stick-and-ball mode a rather spotty collection of sticks. I've seen this more when it hits 100% and loads a new WU while still running.

[Star Ranger4]

maybe. but if you look down at the lower left, it says this is the demo protien and its not connected to whatever my WU is?

[classicdrogn]

Ah, I see. Well, I don't really know how that works or integrates together. Best guess is that might be some kind of permissions problem?

[Bob Schroeck]

You need to launch it from inside the advanced control program (right-click on the F@H icon in the tray, and pick Advanced Control) by hitting the viewer button in the top right corner of the status tab. Or run Protein Viewer from the tray icon the same way. If you launch it any other way it goes into demo mode.