lets give some back ground first. im a ICT techie at a high school and the computer are left on basicly 24/7 as we have to update every thing at night .. (we have solar power so not harming the environment). ive been asked to find out what we can do with the computers at home. after running Rosetta for a while i thought i would do this but i have to write a proposal on how it would help the world ect ... any help would be appercaited . just to let you know we have 1000 + hosts and 250 + are C2D's

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You are the one that is to write the proposal. I'll be glad to help you, but I'd like you to post a draft of what you already know and are thinking should be included your proposal. You should also take in to account who the readers of your proposal will be. So, is it the school board? Your computer teacher? Your science class? If we understand your audience, that will help us to help you write a bang up proposal.

Your profile says you are in the UK, so, if nothing else, during Winter months, they could view the crunching CPUs as being a way to use some of the solar power before ultimately helping to heat the building. CPUs produce more heat (and use more power) when they are actively crunching then when idle.

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Add this signature to your EMail:
Running Microsoft's "System Idle Process" will never help cure cancer, AIDS nor Alzheimer's. But running Rosetta@home just might!
https://boinc.bakerlab.org/rosetta/

Hi Matthew, great to hear you're interested in helping the project with what sounds like a large group of *green* computers!

I'd suggest reading back through Dr. Baker's journal (he's the lead scientist running Rosetta@Home), the last few months have been exciting and you should get a ton of content for any proposal:

https://boinc.bakerlab.org/rosetta/forum_thread.php?id=1177

If you have any specific questions, post them here and they should be answered fairly quickly (and be visible for others who have the same questions).

Cheers,
Ethan

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I'm sure one of the Dev's or D.Baker may take a phone call to explain it to them.

Have a read of D.Bakers journal especially recent one's as well.

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Team mauisun.org

let us know if you need more info than what is on the web page (you could look at the disease related research section on the home page for starters)

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let us know if you need more info than what is on the web page (you could look at the disease related research section on the home page for starters)

ive looked there .. and thats all getting included i will post a copy for you all to read as soon as i finish the draft. yes were in the Uk ..its for the governors and people that basically control the dept. as like all other things in this world now every thing has to be justified even anti virus sorfware we have to formaly ask permission to install due to some protection regulations :S

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i could do with one of these too. I think a generic but very professional looking one would be really useful. I was thinking about this a while ago and I think a html one would be perfect - you could have hyperlinked words incase anyone wants to read further on a topic, without over-complicating the main document.

I'll post where i got to when i get home tonight.

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Don't forgtet to mention that it could be used to either teach / gain interest in sciences.. It could even be used to 'advertise' the college/school (where is it by the way ?) by promoting the activity in the local paper or website.

Also mention that the BBC uses the platform for it Climate Change experiment and that IBM uses it for the World Community Grid project. That usualy gives much more 'umph' than an as such unknown institute and university in the US.

If all else fails grab some of the video's / media that is available... and if all else really does fail shock them with a picture of David Baker himself ;-) lol

I'm UK as well by the way so know how it works.

The only problems you should condsider is
1) Increased electricity usage compared to just leaving them at idle.
2) Increased noise (same as above, depends on the type of computers, RM by any chance ?)
3) Increased bandwidth usage, (strongly suggest setting them up as 24hr Run Time to reduce this) it may not be a porblem but I know for some schools it could well be a problem.

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Team mauisun.org

3) Increased bandwidth usage, (strongly suggest setting them up as 24hr Run Time to reduce this) it may not be a porblem but I know for some schools it could well be a problem.

And through a proxy if possible!

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Well, as for the "how Rosetta will help the world" part, I think the homepage gives you all the reference material you should need. And we can help you better understand any of the concepts that aren't clear.

Fluffy and others have gotten on to another angle which is "what resistence you are likely to encounter with the idea". From that angle, we've got a great thread going with lots of those thoughts, some solutions, some good links, but overall it will help you get in to the heads of how the admins may see your proposal. Here's a link.

Your proposal should probably have portions written with each perspective in mind. Probably start and end with the "help the world" part, and put some of the methods of overcoming resistence in the middle... and try not to make that part too long. Try to concisely assert that you understand the legitimate concerns people have to doing such a thing, and explain how these concerns are addressed or mitigated.

And yes, I definately agree that you should point out how the students can get involved both with signing up computers to the project but also with learning about the biology, the proteins, the medical science, the computer science of distributed computing, the networking, and all the rest. Rosetta is a great "real world" problem for students to do reports and projects around. And the project has many various components to it, so you can dig deeper in to whatever specific aspects are most interesting to you.

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Add this signature to your EMail:
Running Microsoft's "System Idle Process" will never help cure cancer, AIDS nor Alzheimer's. But running Rosetta@home just might!
https://boinc.bakerlab.org/rosetta/

As far as the most exciting aspects, I would lead and end with those.

* They are working closely with the Gates Foundation and have a grant to work with 15 HIV vaccine candidates.
* Potential to help fight malaria & Alzheimer's. Malaria is a forgotten disease and afflicts nearly the whole continent of Africa.
* If the precise 3D structure of proteins can be predicted and known, then drugs can be used to combat problematic proteins (diseases). Their latest results at CASP are very encouraging! If these computers can predict the structure down to the same precision as an xray crystallography (sp?), then the information can be used to create drugs to fight these diseases.

computer-wise: the project is secure. the crunching runs at the lowest priority and gets out of the way if a user wants to use the CPU for something else. Many users do not notice any slowness in their computers while crunching and doing something else.

One sticky point if they question you AFTER the proposal is "who owns the results?" The results are available to the public and then drug companies or even charitable foundations (such as the Gates Foundation) could create drugs from the results. There may be a patent period for the drugs, and after that ends then generics will be available. We're still better off as a result! If HIV, Alzheimer's, and/or malaria could be solved, then we are much better off.

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@Paydirt

If these computers can predict the structure down to the same precision as an xray crystallography (sp?)

You appear to say in this sentence crystallography is a prediction method. I'm quite sure you do not actually mean that. Correct me if I'm wrong. The reason I'm commenting on this at all,is because it might be used in a proposal

I guess 'structural determination method' would be more appropriate as it applies to both virtual and physical methods.

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Right, my verbiage is not precise and should not be used. Maybe I should not have replied. A crystallography is an observation method, not a predictive method, but I'm guessing it is costly and takes a significant amount of time?

I was more brainstorming of the more exciting, general things that I knew about.

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X-Ray crystallography can be pretty quick when applied to small molecules or simple crystals with few atoms per unit cell. Still, calculating the structure of large proteins from X-Ray data is a challenge.

The major problem before being able to take an X-Ray is refining the proteins. It means finding a source in which the desired protein is relatively abundant (e.g. a special tissue in a certain animal/plant) and finding a way of separating it from the whole rest of the cells without damaging the protein and altering its structure.

After that you have to crystallize it in a way that gives you usable single crystals, which can be a nightmare as your parameters are pretty limited, if you do not want to spoil it by still altering the structure after taking the protein all that way. As you deal with very light atoms, you pretty surely need to take an X-Ray at low temperatures. Crystals containing water, which is almost inevitably the case with proteins, often break and there goes you single crystal. The obstacles can be really discouraging.

[EDIT] I forgot: for larger proteins you will of course need their sequence, else you are just groping in the dark when trying to calculate an X-Ray structure from scratch. After the Human Genome Project that should not be the biggest problem, but otherwise, e.g. when dealing with animals or plant whose genome is unknown, you of course will have to do that too. Just regard it as painful as the rest, as you'll need a lot of pure protein for it.[/EDIT]

Then you have your X-Ray data and start a nice puzzle with some hundred atoms for the protein and of course for water and possibly salts too. Takes time, patience and, so you still have one at this stage, a really loving partner.

All in all it is a kind of work where often a group of several people may share their doctorate (or subsequent doctorates) just to get a single structure in a time frame of two, three or even more years. This of course means spending a lot of money. And just think of all those "John Doe" Proteins that are just somewhere in a cell, seeming to do nothing special, which you will be really hard put to separate as they are just there, but not in especially high number. (And as these are not kind of prominent you will hardly get a special grant to turn to research on them while there seem to be more valuable targets.)

So, Rosetta may take the fun out of the game for some hardcore researchers, but according to my experience these people may also turn to apnoe diving or heliskiing on the Mount Everest, it is about as satisfying for those who take fun in a maximum of pain. Most others will just fall to their knees and thank the Lord for it.

Just compare it: years with open end research and the nagging doubt whether it really is the native structure until it has been affirmed by the same or some other method or taking a big computational effort and being pretty sure that what you get is good enough to tell you anything there is to know about a protein. Not to speak of future advances, after all we just have begun to turn to the computational way and there is no doubt the methods and computers will improve drastically over time. And the more people contribute the sooner will Rosetta be able to try out new ways in depth. CASP7 clearly showed that the Rosetta community has contributed something of great value.

Almost a proposal in itself ;-)

If your proposal could be done on a DVD, perhaps you could incorporate the new video into it.

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Add this signature to your EMail:
Running Microsoft's "System Idle Process" will never help cure cancer, AIDS nor Alzheimer's. But running Rosetta@home just might!
https://boinc.bakerlab.org/rosetta/

If your proposal could be done on a DVD, perhaps you could incorporate the new video into it.

Right i will take all the points to heart im going to sit down this week to write it .. been so hectic .

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Matthew? Were you able to find the material you were looking for you write a bang up proposal?

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Add this signature to your EMail:
Running Microsoft's "System Idle Process" will never help cure cancer, AIDS nor Alzheimer's. But running Rosetta@home just might!
https://boinc.bakerlab.org/rosetta/