Folding Forum

1. Who (I'm assuming health organizations and scientists, but I'm looking for a more specific answer) submits models/scripts/data/work units for processing? Are the submitted scripts by the health organization/scientists or are they paying for at least the python modules to be written by folding home. It seems like there are some scripts and input/output data publicly available from what I could understand from and find in the coronavirus repo. If these scripts and data are usually sent by health organizations/scientists and/or collaboration with fah, are these scripts usually private?

2. Where do health organizations/scientists go if they wish to calculate how a protein folds with fah? Do they simply contact them through social media or is there some private/public with restrictions repository at Stanford or somewhere that allows people to add what they want to be calculated?

3. Is this open source or is this just open source components with a closed source core? The FAQ says that some of the main components are closed source for "security", but then there's the reply to this tweet (https : //twi tter. com /xoryouy ou/ status/1 238932329583828999 (I broke it because it won't allow posting urls for users without posts yet)) saying it's all open source and that openmm is the client. Is this true or is openmm just a open source library used with closed source plugins being fah or something else?

FAH was created specifically for academia. Grad Students studying advanced biochemistry need effective tools to do research for their thesis... and all peer-reviewed papers are placed in the Public Domain. Private companies don't use FAH for their proprietary research but they can freely use the published results.

Health organizations certainly do conduct private research. They might install OpenMM or GROMACS on their computes, just like they'd have their own microscopes and testing labas and whatever they considered important. They do not get to submit projects to be folded by FAH Donors. I suppose they could suggest research ideas to a student or a professor but for it to remain proprietary, I doubt that would be a preferred course of action.

FAH is mostly open source and there are plans to open the remainder but that wouldn't give a private firm access to FAH's WU distribution activities.

By the way, other *@home projects do establish contracts with private organizations. Ask them the same questions. You may be donating to the creation of an expensive patented drug without your knowledge.

bruce wrote:By the way, other *@home projects do establish contracts with private organizations. Ask them the same questions. You may be donating to the creation of an expensive patented drug without your knowledge.

Are you talking about Rosetta?

yetoo wrote:1. Who (I'm assuming health organizations and scientists, but I'm looking for a more specific answer) submits models/scripts/data/work units for processing? Are the submitted scripts by the health organization/scientists or are they paying for at least the python modules to be written by folding home. It seems like there are some scripts and input/output data publicly available from what I could understand from and find in the coronavirus repo. If these scripts and data are usually sent by health organizations/scientists and/or collaboration with fah, are these scripts usually private?

If a University is interested in F@H they usually set up their own servers and send out work units via Stanford's servers
Here is a list of projects, if you peek at the Project Number, each mentions where it is hosted. https://apps.foldingathome.org/psummary

yetoo wrote:3. Is this open source or is this just open source components with a closed source core? The FAQ says that some of the main components are closed source for "security", but then there's the reply to this tweet (https : //twi tter. com /xoryouy ou/ status/1 238932329583828999 (I broke it because it won't allow posting urls for users without posts yet)) saying it's all open source and that openmm is the client. Is this true or is openmm just a open source library used with closed source plugins being fah or something else?

My mental image is almost exactly the opposite of what you describe. The results are all open source, anyone can review the data. The science is all open source, anyone can read or improve the algorithms.

http://www.gromacs.org/
https://simtk.org/projects/openmm

What is proprietary is the communications code between your PC and the servers. By controlling this, they hope to limit cheating. Security through obscurity. This can be a very low bar as there is not money to be won by folding. But egos are such that some would cheat to get to the top of the leader board.

(Years ago, you could cheat SetI@Home by copying your data when you were at 99.9% done and then sending them to everyone you know. Everyone in the gangtribe would get all the points for 0.1% of the work. This scheme would never have worked in Folding@Home as it only sends out data once, where Seti sent out multiple copies. They were forced to track who each copy was sent to. Work that does not benifit science.)

So in my mind the core is Open Source and just some minor code is proprietary. to keep us all honest.

JimboPalmer
Where would one register to put there project on that list? Regarding the proprietary code, why can't they just have a api that only trusted installations can access via hashes and protocol validity checks? Surely, it must be possible for servers and other distributed computers to be able to check the validity of the installation accepting work from? I mean, they seem to be doing it already with signed data produced with fah and the blueprint on the server somehow, but it seems they could go a step further.