Recruitment Ideas.

Send a letter and information packet to CEOs', CFOs', I.T officers of all the health insurance companies(Life, etc), and these companies cracking down on lifestyle choices of their employees. Any of them that can't find a way to get you some CPU power are just hypocrits. They are always tooting the horn of lowering health insurance costs through better habits, excercise, diet, excercise, etc. So giving up some CPU to find new, better, and cheaper therapies should make a nice fit for them and give them another reason to toot their own horn.

I work in a company of over 2500. Many of the machines are idle most the day and left on at night. Even 10% of total CPUs is something. And yes it is one of those target companies. I just haven't had any luck with getting them on the bandwagon.

...Many of the machines are idle most the day and left on at night...I just haven't had any luck with getting them on the bandwagon.

I find it such a shame to waste idle computer resources that are powered on anyway, but as I learned at my own company, people are very suspect of anything they are not 100% comfortable with running on their computers. And it is a tough sell unfortunately. :(

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Regards,
Bob P.

...Many of the machines are idle most the day and left on at night...I just haven't had any luck with getting them on the bandwagon.

I find it such a shame to waste idle computer resources that are powered on anyway, but as I learned at my own company, people are very suspect of anything they are not 100% comfortable with running on their computers. And it is a tough sell unfortunately. :(

While that is true and something I don't like you have to consider other things (other than security, worries..)

When a computer is idle it does use less energy than when it is running at 100%. I remember from FAD a P4 2.4ish computer would use about 60W increase at the wall. Which for a home user isn't that much (unless you live in the UK :( ) But times it by a computer suite at say a University, Company or Internet Cafe it get expensive, not just that but noisier (modern day variable fan speeds) and then you have to cool the room ...

And with even newer computer where they drop to even lower energy usages while idle the difference get greater. So while you and I think it's a good idea, it does cost a lot extra in the end to run this program just in electricity costs. Never mind bandwidth costs and problems.


Anyways,
David it's a pleasure to read your blog/journal :-)

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Team mauisun.org

Excellent news that Rom is coming over to help kick those last few bugs out of the code

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When a computer is idle it does use less energy than when it is running at 100%. I remember from FAD a P4 2.4ish computer would use about 60W increase at the wall...And with even newer computer where they drop to even lower energy usages while idle the difference get greater. So while you and I think it's a good idea, it does cost a lot extra in the end to run this program just in electricity costs.

Excellent points! Now I do not feel so badly about being banned from using other company computers (although I am able to use my own desktop unit, so all is not too bad! ;)

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Regards,
Bob P.

While work is underway on getting rid of the most annoying problems with the Rosetta client, (yaaaa!), can the loss of productivity recently be associated with some of the errors when coupled with the longer run times? i.e. 8 hour run times with a WU that ran for 8 hours and returned data with an error? (As opposed to the 25-30 second error runs on one of the recent batches of WUs.) Or is it more likely that the effect is secondary to the errors.. i.e. people switching to only run Rosetta on a single system, rather than than multiple projects? Or putting Rosetta on hold until after the errors are worked out?

And is there any benefit from running that last stage a few times in smaller steps since after the first step, I'd assume that the direction to the lowest energy location might have changed?

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Maybe this can help a little to solve client problems:
I run Rosetta in two machines ( Pentium IV and AMD 4000 )
I've never had computation errors but in the AMD 4000 with an ATI X700 Pro Graphics card, if I'm visualizing the progress, many times the computer hangs.
Fortunately, the card's driver automatically recovers and tell me that some graphics error has been detected. A few times the recover has been impossible.
This never has happened in the Pentium IV with an ATI 9200 grahics card.
Also, I'm running Folding at Home. With a little overclocking, more than 50% of jobs end with a Nan result, with no overclocking all the jobs end right.
It seems that intensive FPU applications should check FPU exceptions and/or Nan results

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David,
You continue to mention the need for more computers, etc. There are 92,671 hosts that boinc stats knows of. Only 42,597 are active. The user stats tell a similar story (nearly half are not active).

While your journal is a good start I think you are missing why people choose Rosetta. It's the Graphics that are appealing. Projects without them (folding ones, orthologs, etc) are not as interesting. They also don't keep you motivated enough to keep going.

You need to involve the community more by, say, posting the week's (or day's) closest results to the native structure for each different work unit prominently on the main page with the user identified and their profile highlighted. This would keep people motivated. They want to see pictures of closeness. And they want to see pictures of how each different type of WU is working in terms of its prediction.

Perhaps that is not possible. But in doing so you would build user loyalty. The updates months ago was great, but it was at the conclusion. Even if daily or weekly images mean nothing scientifically they do mean something to the people involved and they also so how each calculation can differ. It also gives you the opportunity to create a weekly blog where you discuss each type of WU and it's advantages/limitations/observations.

You are a scientist but I know you are good at grant work. Here you need to get people involved to keep them active. And when I mean active I mean running all out to get a higher probability of inclusion for the week.

The science updates are good. I appreciate them. I am, however, offering an idea that would probably help you increase your users/hosts and/or total WUs. This would be good for the project as the model could be refined more quickly for the next run.

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David,
You continue to mention the need for more computers, etc. There are 92,671 hosts that boinc stats knows of. Only 42,597 are active. The user stats tell a similar story (nearly half are not active).

While your journal is a good start I think you are missing why people choose Rosetta. It's the Graphics that are appealing. Projects without them (folding ones, orthologs, etc) are not as interesting. They also don't keep you motivated enough to keep going.

You need to involve the community more by, say, posting the week's (or day's) closest results to the native structure for each different work unit prominently on the main page with the user identified and their profile highlighted. This would keep people motivated. They want to see pictures of closeness. And they want to see pictures of how each different type of WU is working in terms of its prediction.

Perhaps that is not possible. But in doing so you would build user loyalty. The updates months ago was great, but it was at the conclusion. Even if daily or weekly images mean nothing scientifically they do mean something to the people involved and they also so how each calculation can differ. It also gives you the opportunity to create a weekly blog where you discuss each type of WU and it's advantages/limitations/observations.

You are a scientist but I know you are good at grant work. Here you need to get people involved to keep them active. And when I mean active I mean running all out to get a higher probability of inclusion for the week.

The science updates are good. I appreciate them. I am, however, offering an idea that would probably help you increase your users/hosts and/or total WUs. This would be good for the project as the model could be refined more quickly for the next run.

David,
You could also create a neat little imbed that rotated the protein around giving a 360 of the closest and the native as in the boinc graphics:) Make the project appealing to people who have no interest in the science as science but in seeing what is being done and doing something that will help research out. Make it pedestrian.

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I thought I should mention that Rosetta@home Website is slow (taking almost half a minute to respond or even timing out) quite often. Happens every day. During times of slow performance, I have checked via ping and traceroute from different sources (Europe and US) to verify it's not a general connectivity issue.

It even happens during the weekends, like a few minutes ago.

It was a constant problem about 1.5 month ago (I understand it was due to R's network getting congested with all the WU traffic?), it's a little bit better now, but still a problem.

---

Best UFO Resources
Wikipedia R@h
How-To: Join Distributed Computing projects that benefit humanity

Maybe this can help a little to solve client problems:
I run Rosetta in two machines ( Pentium IV and AMD 4000 )
I've never had computation errors but in the AMD 4000 with an ATI X700 Pro Graphics card, if I'm visualizing the progress, many times the computer hangs.
Fortunately, the card's driver automatically recovers and tell me that some graphics error has been detected. A few times the recover has been impossible.
This never has happened in the Pentium IV with an ATI 9200 grahics card.
Also, I'm running Folding at Home. With a little overclocking, more than 50% of jobs end with a Nan result, with no overclocking all the jobs end right.
It seems that intensive FPU applications should check FPU exceptions and/or Nan results

I think this could be on the right track. Rosetta is doing really intensive floating point crunching compared to other projects, and could be really sensitive to overclocking; maybe this would account for some of the machine specific problems.
Rom is going to try extending the exception handling that David recently put in.

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David,
You continue to mention the need for more computers, etc. There are 92,671 hosts that boinc stats knows of. Only 42,597 are active. The user stats tell a similar story (nearly half are not active).

While your journal is a good start I think you are missing why people choose Rosetta. It's the Graphics that are appealing. Projects without them (folding ones, orthologs, etc) are not as interesting. They also don't keep you motivated enough to keep going.

You need to involve the community more by, say, posting the week's (or day's) closest results to the native structure for each different work unit prominently on the main page with the user identified and their profile highlighted. This would keep people motivated. They want to see pictures of closeness. And they want to see pictures of how each different type of WU is working in terms of its prediction.

Perhaps that is not possible. But in doing so you would build user loyalty. The updates months ago was great, but it was at the conclusion. Even if daily or weekly images mean nothing scientifically they do mean something to the people involved and they also so how each calculation can differ. It also gives you the opportunity to create a weekly blog where you discuss each type of WU and it's advantages/limitations/observations.

You are a scientist but I know you are good at grant work. Here you need to get people involved to keep them active. And when I mean active I mean running all out to get a higher probability of inclusion for the week.

The science updates are good. I appreciate them. I am, however, offering an idea that would probably help you increase your users/hosts and/or total WUs. This would be good for the project as the model could be refined more quickly for the next run.

Hi James, we have been trying to do something along these lines-- every evening we are posting a new result in the "top predictions" section, with an acknowledgement of the finder, which I then explain in the journal. do you think we should instead post the prediction on the main page where it is more visible?

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Hi James, we have been trying to do something along these lines-- every evening we are posting a new result in the "top predictions" section, with an acknowledgement of the finder, which I then explain in the journal. do you think we should instead post the prediction on the main page where it is more visible?

A rotating daily Top Prediction of the Day (TPD), similar to user of the day, would probably be neat. (I would not be opposed to replacing user of the day with top prediction of the day, but I am not sure how others would feel about that)

From these, you could select the Top Prediction of the Month (TPM).

If I somehow got the top prediction of the day, I would appreciate it being available to me forever in my result or profile page.

e.g.
Awarded the Top Prediction of the Day on DD-MM-YY for [protein name and link to graphics]

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When a computer is idle it does use less energy than when it is running at 100%. I remember from FAD a P4 2.4ish computer would use about 60W increase at the wall. Which for a home user isn't that much (unless you live in the UK :( ) But times it by a computer suite at say a University, Company or Internet Cafe it get expensive, not just that but noisier (modern day variable fan speeds) and then you have to cool the room ...

And with even newer computer where they drop to even lower energy usages while idle the difference get greater. So while you and I think it's a good idea, it does cost a lot extra in the end to run this program just in electricity costs. Never mind bandwidth costs and problems.

The price of electic is cheap in my area. I pay less than 6 cents USD per kilowatt hour. For the company I work at, a 60W changed at the wall is only going to cost them, a multibillion dollar company(lots of cash), 60K a year + any change in cooling. We have a long period of cooler weather on the south shore of Lake Erie. If the machines warm the buildings it just means the building heat runs less. Hot summer weather is short. I'm not saying it's not a big pill to swallow for a company, but for a health insurance company that wants to lower premiums for it's policy holders(mutual company), a much smaller pill to swallow. Reduce the CPU run time to 12 hours and ~half the cost.

Hi James, we have been trying to do something along these lines-- every evening we are posting a new result in the "top predictions" section, with an acknowledgement of the finder, which I then explain in the journal. do you think we should instead post the prediction on the main page where it is more visible?

A rotating daily Top Prediction of the Day (TPD), similar to user of the day, would probably be neat. (I would not be opposed to replacing user of the day with top prediction of the day, but I am not sure how others would feel about that)

From these, you could select the Top Prediction of the Month (TPM).

If I somehow got the top prediction of the day, I would appreciate it being available to me forever in my result or profile page.

e.g.
Awarded the Top Prediction of the Day on DD-MM-YY for [protein name and link to graphics]

I like the idea of replacing the user of the day with the top predictions of the day. It would be a great improvement since many of the Users of the Day didn't actually have anything in their profile.

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A rotating daily Top Prediction of the Day (TPD), similar to user of the day, would probably be neat. (I would not be opposed to replacing user of the day with top prediction of the day, but I am not sure how others would feel about that)

We are now posting these in the "news" section of the homepage! As David mentioned in his journal, we are looking into pritable certificates. We are also looking into adding "top predictions" to people's profiles. I'd appreciate any feedback on the format of the daily top predictions posts!

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We are now posting these in the "news" section of the homepage! As David mentioned in his journal, we are looking into pritable certificates. We are also looking into adding "top predictions" to people's profiles. I'd appreciate any feedback on the format of the daily top predictions posts!

I like it already.

Not sure if this is feasible, but everytime I notice a new protein being issued, I look it up in RCSB. Would it be possible to include the name of the protein as a link to some protein database where more information about the protein can be studied, e.g. RCSB, your own Robetta-server or something similar?

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With regard to making more CPUs available, I think the single biggest issue is the disparity between credits awarded to different machines, whether thats between OS's or from the use of 'optimised' BOINC clients. If that could be fixed somehow (and I'm not suggesting that's a small job!) then I believe there'd be a lot more interest from some of the big competitive teams. I read somewhere that that was TSCRussia's main reason for not joining here.

It might also be worth getting in touch with the BBC to get a mention on their website regarding their BOINC-based climate change project. I expect there'll be litterally millions of people reading about their project, and many of those won't fit the criteria for that project but would be welcomed here (I think they want PCs that are on pretty much 24/7). I'd expect the BBC to be pretty good like that.

HTH
Danny

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I'd like to ask about the distribution of results on the RMSD / energy charts.



Somehow I had imagined there'd be a "clustering" of those 5000 (I think that's the ones you're charting nowadays, right?) best results in the bottom left conrner of the chart.

But, looking at the charts, it seems that most results stay far away (due to local minima keeping them away?) and only few "lucky outliers" actually approach the global energy minima. Using the "planet exploration analogy", it looks as if a handful lucky explorers somehow "fall into a hole" and discover the lowest energy point.

So this is why you need more explorers (CPUs).

Also, maybe you could also plot the Energy of the "native" (experimentally derived) structure on the charts, for reference, like you did in the past?

What is the error in experimentally (X-ray crystallography or NMR) derived structures?

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Best UFO Resources
Wikipedia R@h
How-To: Join Distributed Computing projects that benefit humanity

Btw, HPF (running on IBM's World Community Grid and UD's grid.org) is soon going into Phase-II. It's using the Rosetta software, which we're helping improve here. It looks like they're now using the "full atom relax" mode?

Richard Bonneau, 13-Mar-2006 (source):
"The proposed project (HPF phase-2) will refine, using Rosetta in a mode that accounts for greater atomic detail, the structures resulting from the first phase of the Human Proteome Folding Project (HPF phase1). The project will focus on human secreted proteins (proteins in the blood and the spaces between cells). These proteins can be important for signaling between cells and are often key markers for diagnosis. These proteins have even ended up being useful as drugs (when synthesized and given by doctors to people lacking the pro-teins). The project will also focus on key secreted pathogenic protein. This project dove-tails with efforts at the ISB in Seattle to support predictive, preventative and personalized medicine (under the assumption that these secreted proteins will be key elements of this medicine of the future).

This project continues where the Human Proteome Folding Project leaves off. With the Human proteome Folding project we aimed to get protein function. With the second phase we would aim to increase the resolution of a select subset of Human proteins. Better reso-lution is important for a number of applications including but not limited to virtual screening of drug targets with docking procedures and protein design. The second phase of the pro-ject will also serve to improve our understanding of the physics of protein structure and ad-vance the state of the art in protein structure prediction (help us to further develop our program, Rosetta).

The two main objectives are to: 1) obtain higher resolution structures for specific hu-man proteins and pathogen proteins and 2) further explore the limits of protein structure prediction by further developing Rosetta structure prediction. Thus, the project would ad-dress two very important parallel imperatives, one biological and one biophysical.

The Human Proteome Folding Project Phase-2 will use the computer power of millions of computers to predict the shape of Human proteins for which researchers currently know little. From this detailed shape scientists hope to learn about the function of these proteins, as the shape of proteins is inherently related to how they function in our bodies. This data-base of protein structures and putative functions will let scientists take the next steps un-derstanding how diseases that involve these proteins work. Proteins are the most important molecules in living beings. Just about everything in your body involves or is made out of pro-teins. Protein structure is key to understanding the functions of this diverse class of bio-molecule. Thus we hope that our work on HPF 1 and HPF 2 will contribute to critical pub-lic infrastructure to the biological and biomedical community."

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Best UFO Resources
Wikipedia R@h
How-To: Join Distributed Computing projects that benefit humanity