AidanSonoda:

Well, the errors seem to have spread to all but one of my machines...

I posted to the version 5.36 error thread in the Rosetta forum summarizing the error situation once more. It turned out that a quarter of the teams' hosts are having errors more lor less on a regular basis - not just Aidan's. Let's see whether this will get some response...

EDIT: Could it be that all of these errors are screen saver related, btw ? I am seeing a lot of complaints about screen saver freeze-ups in the Rosetta forum (this would explain why I am not seeing any errors on my computer - there is no Rosetta graphics for Linux). 

Hi, I've been a long time lurker at this site, and I've decided to join your rosetta team as well.

Mardonius:

Hi, I've been a long time lurker at this site, and I've decided to join your rosetta team as well.

Hey, great! Welcome to the team - let's hope there are many more 'long time lurkers' out there. ;-)

It's not impossible that the screen saver is part of the trouble.  Two of my machines are service installations (hence, no graphics) including the one error free machine and another that has had no errors in the last 20+ results.  However, these are also my two fastest machines, and the ones most likely to run continuously...so I'm not willing to draw any significant conclusions.  I wouldn't be totally surprised if removing the screensaver solved my problems, unfortunately that would not be that easy to do given the locations of my machines.  I'll hold out for a reply to either of our posts.  If no new information is forthcoming then I'll attempt to disable the screensavers.  Perhaps others could try the no graphics approach and see if it solves the problems and let us know?

 

--Welcome Mardonius, to the thread and especially the team. 

Let's see if we can get more linux boxes on this team! I've looked at the list of team machines and all I see are XP and Win2K. Hoelder1in's and mine are getting lonely! My processor may be over 6 years old but it's pulling its weight and representin' for the Tux posse!

My posts on this topic, in which I am not easily excelled, have not been substantially addressed at all.

Disconcerting...

Mr. Farlops:

Let's see if we can get more linux boxes on this team! I've looked at the list of team machines and all I see are XP and Win2K. Hoelder1in's and mine are getting lonely! My processor may be over 6 years old but it's pulling its weight and representin' for the Tux posse!

...and  with the recent Novell-Microsoft deal I am not even sure my SuSE Linux still counts as 100% Linux.;-)

Sadly, there are currently only 8% Linux hosts crunching for Rosetta - so with two Linux boxes in the team, we are even a little bit above average. I am glad you keep yours crunching, Pace, or it would indeed feel lonely around here. Also, with the relatively small fraction of Linux boxes, there is probably no hope that the Rosetta team will ever develop a Linux screensaver and we will likely also miss out on the upcoming interactive graphics where the participants will be able to actively guide the search for the lowest energy structures (see David Baker's Journal for details).

Other stuff to report: The CASP7 results are out ! It seems the Baker Lab (with the help of Rosetta@home and the bettterhumans.com team members) did reasonably well, but there is still room for improvement.  This is how to read the plots:  each of the yellow lines is a prediction by one of the teams participating in CASP7; black is for Baker Lab (lower is better).

Bin Qian, Rhiju Das, and David Kim from the Baker Lab are presenting their results at the CASP7 conference this week. See the titles and abstracts of their contributions on page 17-20 (PDF page 6-9) of the abstract booklet.   

Oh, and I haven't yet said hello to hmooers, our 17th team member: Welcome to Rosetta@home and the team!

Chironian:

My posts on this topic, in which I am not easily excelled, have not been substantially addressed at all.

Disconcerting...

Actually they were, here, here and here. I guess hypnosis doesn't do that much for memory after all.

Hoelder1in,

Wow! Less than 8% are Linux? We're above average then! Copacetic! Now that I'm in the rat race again, I'll see if I can tack another, faster Linux box on the team.

And bah! Who needs screen savers in the Linux version? The client cranks throught the data just the same doesn't it? It still gives me the toasty feeling that I'm contributing to science in a small way!

My personal comp and laptop are both Linux (Gentoo running FVWM).  Though they don't crunch, and one is nearly ten years old; they are without a doubt my best machines from a productivity point of view.  I recognize the superiority of Linux (for power users at least)--perhaps it is telling that all the idle machines I could find are windows.  Anyhow, if I come into some money and build that Intel Core 2 Duo machine I've been planning we'll have another Linux SMP kernel at work plus the homePC it would replace.  Indeed, boredom might induce me to convert my P4 to something like Vector Linux. Evidently, that would make us a Linux heavy team, statistically...which might be a reason in itself. 

 

Long Live Tux.

So what you plan to do with this science project is complacently alter a multi-billion year old genetic decision tree, replacing it with the equivalent of some piece of plastic twig, like something from a five and dime store. Is that it?

Do you actually think your opinion about "health" is relevant to Natural Selection, or can "improve" human events by imposing your opinions about life from your own provincial pseudo-philosophy?

Because verily, most people who are diseased are so because they loathe life and do not wish to live, because they are clumsy and crude with how they utilize their creative, critical, and innate healing potentials.

What are the consequences of editing the John Nash's out of the human genetic pool? Or do you even think about abominations of this magnitude, when your "experts", who have no inkling of the computational fire-power that life itself wields, make all the calls about what a "Better Human" is, while not even being able to penetrate or question their own prejudiced assumptions?

I am not interested in descending into a debate with you about these issues. You shouldn't take that as an indication of the fear inspiring powers or your intellect (as you evidently do), but rather a commentary upon how laughable your venom and puffed up choice of language actually is. If you had framed your concerns in a manner that in any way indicated a desire for reasonable discussion I expect you would have found other members of this forum very willing to carry on a dialog. Since you have chosen words that immediately mark you as arrogant, self-appointed intelligentsia looking for a soap box; you shouldn't be surprised at receiving a luke-warm response.

Matters of tone aside, you have repeatedly failed to make any of your points particularly lucid.  The fact is that I am a reasonably intelligent man.  Fortunately for my social life, I don't consider myself "not easily excelled," but I am usually able to understand things that are elucidated in competent English.  Even my friends Mr. Farlops and Hoeder1in, both demonstrably more intelligent than I and certainly better versed in the subject matter, seem to have found your posts wanting for clarification.  Now, if you would be willing to restate your arguments, in language that shows off less and communicates more. I would be happy to provide you with an in-depth and level response.

...some more updates and progress reports that David Baker posted in the Rosetta@home forum over the weekend - thought I copy them over here in case you missed any of this:

HIV vaccine design:

so far 12 vaccine designs have passed the first tests: we can make them in large quantities, and they interact tightly with antibodies known to neutralize the HIV virus. These designs are now being tested by our collaborators to determine whether they elicit a neutralizing response to the virus. We expect that this will not be achieved immediately and we are currently generating another round of designs. We will describe this work at a meeting of the Gates foundation in Seattle this coming Monday-Wednesday which brings together the different HIV vaccine design efforts they are supporting. I am looking forward to discussing ways in which the computations you are helping us with can contribute to all of these vaccine design efforts.

protein-protein docking:

The most recent illustration was just yesterday when Chu presented the results of your protein-protein docking calculations at our weekly lab seminar. They are really amazing--he showed that for the first time it is possible to allow full flexibility of both protein backbones and dramatically improve the accuracy with which the structures of protein-protein complexes can be predicted. This simply would not have been achieved without the large scale computing boinc and all of you are making possible as the space of possibilities is FAR too big to be searched with conventional computing resources. The very striking improvements in protein structure prediction evident in the CASP7 tests (see my journal) are another very recent example.

CASP7:

The viewgraphs from the CASP7 conference of last week have now been placed on the web. This includes presentations by Bin Qian and Rhiju Das from the Baker Lab, explaining their algorithms and showing lots of examples (their last viewgraph acknowledges the contributions of 100,000 Rosetta@home participants and shows a screenshot of the homepage) and by the CASP7 'assessors' doing a detailed comparison of the quality of the predictions by the different groups. The Baker Lab is one of the top two groups that stand out, the other being Yang Zhang from the University of Kansas. David Baker mentioned that he had already invited Zhang to Seattle and that datasets and code are being exchanged to learn from each others approach:

There are two sources of information which protein structure prediction can draw on: evolution and physics. Zhang's approach is excellent at using all evolutionary information available from related protein structures, wheras our search for the global energy minimum uses physical chemistry information. As you suggest, the two approaches are quite complementary and we can each learn from each other. I invited Zhang to the University of Washington last month for a seminar, and we spent an excellent day discussing routes for collaborating, and we are currently exchanging datasets and programs. Using evolutionary information will help us narrow down the part of the space that needs to be searched so that we can better focus your searches on areas where the global energy minimum (correct structure) is likely to be, and thus improve prediction of larger more complex protein structures.

Chironian:

So what you plan to do with this science project is complacently alter a multi-billion year old genetic decision tree, replacing it with the equivalent of some piece of plastic twig, like something from a five and dime store. Is that it?

It's clear to me that you meant that as put-down but, actually, yes--that really is one of the purposes of this project.

But in this case the twig will be so convincing that the body won't really notice the hack. One could argue that the goal of drug therapy since the beginning of medicine was a search for more and more convincing artificial twigs to hack the tree of life with. Rosetta springs from a long tradition.

Chironian:

What are the consequences of editing the John Nash's out of the human genetic pool?

What if we could grant someone the mathematical insight and creative power of John Nash without the schizophrenia? The Rosetta project might directly or through serendipty lead to an option like that. Maybe you think this is impossible but how we know until we do the research? Do you have some constructive criticism or this just useless defeatism? 

Chironian:

...when your "experts", who have no inkling of the computational fire-power that life itself wields...

Sorry but I'm not impressed. If dumb chemistry and environmental selection can build all this diversity in 5 billion years, engineering can do the same in a much shorter interval because engineering is faster and more flexible than natural selection. We've been at this, what, five or six hundred years? Already we've have machines that equal the complexity of simple organisms. What is that, a million-fold increase in the rate of change? Hand-waving about "computational intractibility" is crypto-vitalism.

I suggest you read some good books on complexity and emergence (Cohen and Stewart's Collapse of Chaos is a good one.) because, you keep misquoting and misunderstanding these concepts.

Mr. Farlops:

...some good books on complexity and emergence (Cohen and Stewart's Collapse of Chaos is a good one.)...

I wonder what Rosetta can teach us about emergence vs. reductionism: it indeed seems to be possible to compute biology from atomic physics - Rosetta has already demonstrated that, though it is incredibly -almost prohibitively- hard. The Blue Brain project  comes to mind which similarly attempts to compute mind from neurons (here is an interesting talk by Blue Brain director Henry Markram, btw). Interestingly, an accompanying project, called Blue Neuron, attempts to model neurons at the molecular level, sort of establishing the connection to the kind of research that Rosetta is doing. So perhaps the available computing resources are about to reach the threshold where it becomes possible to compute emergence ?

I didn't read the Cohen/Stewart book but looking through my bookshelf was reminded of when I read "Does God play dice ?", one of the earlier books by Ian Stewart on chaos theory, published, I think, around the same time as Richard Dawkins' "The blind watchmaker", both of which prompted me to buy my first computer (later than most) to fool around with fractals and genetic algorithms and I guess my participation in Rosetta is still part of the same mindset.

Thanks and congratulations to Aidan who reached the 100,000 credits milestone today. Lets hope there will be many more team members to make it to 100,000. And, welcome to David, our latest addition to the team. Interesting Rosetta profile, btw.

I was having computer problems so I reformatted. Turned out to be a memory problem, but I dont have windows any longer. I wont have windows up and running again until another week or so.

Anyways, I would be running Rosetta right now if it wasn't for the fact that Rosetta doesn't recognize 64 bit BOINC clients. I might have been one of those 8percent this whole time if that wasn't the case.

I suppose I could run the 32 bit client, but that is too much hassle... if they aren't going to make the effort to work with my system, i'm not going to make the effort to use their software... that is the same reason i am not using flash (just gnash). I tried Folding@home though and it was much less refined, so I would really like to see 64 bit support for Rosetta.