He doesn't believe that with the current technology a search for extraterrestrial life or gravitational waves is useful. He further believes that with the current stage of protein prediction capabilites no 'productive' search is useful, since the reliability is too low to draw any conclusions.

Yes! I could not possibly say better. The Einstein project is making sens in terms of testing software/current generation of hardware. But not with 75,000 active hosts. Rosetta for example got 55,000. Statistics: http://boinc.netsoft-online.com/

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TestPilot, AKA Administrator

according to a post by him on 22nd August in his journal, he appears to saying it is all ANYONE had at the time the HPF project started, not just WCG.

Yes! I totally agree - 3 years ago all they had is a technology that by now three years old! That was exactly my point - why would you spend enormous megawatts of electricity to generate results that would be useless/outdated by the time you will publish them?

He also also appears to be collaborating with WCG on the new HPF2 project, and producing manuscripts on the results of HPF1 - I would think it highly unlikely he would do so if the work is useless wouldn't you???

Yes, I personally think that hpf2 would be useless also- but that is speculations!
Why don't we think of what was done by now? We can operate using fact this way. Let simply look at HPF1.
The guys promised to generate structures of human proteins and make them publicly available. And not just available, but average project participant was assuming that data will be useful for scientific research. By the way, any one who follow that project - did they finally published that database with results? In two years from the beginning of the project, software/structure prediction methods advanced, database was not published, they run out of work, ppl was complaining of redundancy, all they come up to keep users quiete was generating structures for all known genomes... And the main question was - was any of thous results used in real researches? If results was not published - than it is rhetorical question. In case they was - then....
Think of scientist. He got protein sequence. He need to get 3d structure. First step he go protein data bank, and will check it. If not lucky, than search protein homology using BLAST, SIMAP, whatever. Then download similar protein and work with is. Only, in not so very likely event of the nearest similar protein is of pure quality researchers would be forced to use protein prediction software/ or databases with already predicted structures. What he most likely go for - will he use current generation of software or results of predictions of 3/4/5 years old methods?

As regards your request to "Do you own reserch for FightAIDS..." - surely if you make an unsubstantiated critism, then it is up to you to qualify it?

Oh I did answered part of your question to back my point. My original claim was that most projects out there useless. You disagree with that? It is totally ok. I got no time to go and discussion all those projects. I do have researched vast majority of them. If you would like to know something specifically - then i might help you. As to you question about fightaidsathome... You know, I got opinion on efficiency of autodock software they use, on scripp institute that run project... Not sure that it worth of discussing. So you think that project that don't have and never had forum for participants, pulled out statistic page from web site, just becouse it showed couple hundreds of active users after a year or so of project run is good and worth of helping? Ok, then go install that software and start crunching for them. I could not possible change such an attitude.

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TestPilot, AKA Administrator

Did you read my posts at all Testpilot/Administrator ? Yes? It is ok if you did'nt understand them BTW. That is not your fault really. You cant help that.

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@ TestPilot/Administrator:

Yes! I totally agree - 3 years ago all they had is a technology that by now three years old! That was exactly my point - why would you spend enormous megawatts of electricity to generate results that would be useless/outdated by the time you will publish them?

That would mean that Dr Bakers research/manuscripts are worthless then - I'll let you tell him...

Yes, I personally think that hpf2 would be useless also- but that is speculations!
Why don't we think of what was done by now? We can operate using fact this way. Let simply look at HPF1.
The guys promised to generate structures of human proteins and make them publicly available. And not just available, but average project participant was assuming that data will be useful for scientific research. By the way, any one who follow that project - did they finally published that database with results? In two years from the beginning of the project, software/structure prediction methods advanced, database was not published, they run out of work, ppl was complaining of redundancy, all they come up to keep users quiete was generating structures for all known genomes... And the main question was - was any of thous results used in real researches? If results was not published - than it is rhetorical question. In case they was - then....
Think of scientist. He got protein sequence. He need to get 3d structure. First step he go protein data bank, and will check it. If not lucky, than search protein homology using BLAST, SIMAP, whatever. Then download similar protein and work with is. Only, in not so very likely event of the nearest similar protein is of pure quality researchers would be forced to use protein prediction software/ or databases with already predicted structures. What he most likely go for - will he use current generation of software or results of predictions of 3/4/5 years old methods?

If you are correct, then this is all very depressing and means frankly that those at Rosetta and WCG are wasting their time with the current protein research.
But surely we are always going to be behind in our research? - you can't work with future methods that haven't been invented yet - old research and its success/failure leads to new research, no?

Oh I did answered part of your question to back my point. My original claim was that most projects out there useless. You disagree with that? It is totally ok. I got no time to go and discussion all those projects. I do have researched vast majority of them. If you would like to know something specifically - then i might help you. As to you question about fightaidsathome... You know, I got opinion on efficiency of autodock software they use, on scripp institute that run project... Not sure that it worth of discussing. So you think that project that don't have and never had forum for participants, pulled out statistic page from web site, just becouse it showed couple hundreds of active users after a year or so of project run is good and worth of helping? Ok, then go install that software and start crunching for them. I could not possible change such an attitude

I have no idea if 'most projects out there are useless' so I am not in a position to agree/disagree.

As regards FightAids@Home - the reason why they don't have a forum or stats website is because in November 2005 they joined as a project within WCG and all discussion and stats regarding the project are now within WCG's site/forums.
I would imagine that as a result the number of active users crunching Aids is now in the many thousands.

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Crunching In Memory Of My Dad

In the FWIW category:

1) The science that is being done by all the DC projects has merit. The very nature of supercomputing/DC is to harness the power of the here and now, such that the future is enabled. In the case of SETI, this is just fun as who wouldn't want to be the first to discover "the signal." Einstein is probably also in the "meaning of life, the universe, and everything else" category. Basic science pure and simple.

In the case of the protein structure projects, this has a more relevant implication - Rational Drug Design (RDD). RDD is to electronics as electricity is to "chemical/shotgun" drug design, but in its infancy (i.e. the transistor hasn't been invented yet?). I have spent some time with people that are trying to produce unknown-structure protein crystals in microgravity with some success. That top-down experimental process is very expensive and time consuming. I see this DC, bottom-up, refinement of protein structure as narrowing the gap between/pointing the way toward more productive analytical-to-empirical protein structure experiments.

This is a VERY good thing, and there is a REAL benefit to humanity in this (protein structure) research.

2) Some projects are better suited to the processing advantages of different platforms. I am a Mac user. Rosetta does not seem to be conducive to that effort. My results (viewed in terms of credits) are worth 40% of a comparable windows machine.

3) Windows is the vast majority of the DC target market and will get initial apps tailored to that platform. As a Mac user, I understand that. And I also understand that a project needs to cater to, and rely upon the familiarity with, that platform. This does not change my belief that a killer Mac worker is out of reach of the project. If a/this project wants that 10-20% increase in DC processing, they know where to look.

4) Back to RDD. Given the financial/business implications of success in this area, who owns the product of the DC results? If a protein goes on to be a source for a successful therapy (drug), who gets the financial reward? At least in SETI and Einstein and all other basic science projects, the answer to that question is simply the joy of contribution.

In the RDD area, while I realize that protein structure characterization is all basic science now, it is leading to [potentially, very] lucrative drug production. It would be my suggestion that a statement be made that some financial distribution construct be put forth so that people get some small, long-term return on their investment in these projects.

There may be ZERO financial benefit given the vagaries of drug design, but there may be some. That's the risk.

I believe that a lot of people have invested real money to support the goals of these projects, and deserve a real return -- IFF it is oriented to a commercial (however far in the future) outcome, and a return is in the offing.

-------

Personally, (and I know I have low credits just having started DC in March, 2006) I will support the projects that are conducive to my platform's capabilities and/or those that are non-profit, basic/diagnostic in nature (WCG: Fighting Cancer). I leave it to the protein structure folks to determine what is the right course for their project[s] and I will revisit (particularly Rosetta, because I believe that you all have made a great attempt at inclusion in support of your project.).

I know that much of what I have written above goes against the BOINC initial premise (non-profit), but at the same time the BOINC premise is being used for potentially for-profit activities. A clarification is in order.

Sorry for being long. Keep up the good work. Solve the problem!

I'll post this on Team MacNN forum.

Larry

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Hi Administrator and John,

please refrain from personal attacks against each other.

What would help is not allowing normal folks to use forum handles like "Administrator". It's confusing and disruptive - this is what John was saying prior to the verbal garbage that got directed at him and forced him to retire.

I fully agree.

Ignore this board.

Perhaps this is better advice. Count me in, good luck Rosetta. I'll still crunch for you (with a lower resource share), but I've had enough with the icor on the boards. For what it's worth, I don't blame the project or the forum mods for what has happened here over the last 2 weeks. I agree it would have been better if they had spent more time working with the community to prepare us and include us, but they are not responsible for what everyone else posts here.

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Team Starfire World BOINC

"administrator" had created the ID by mistake and now has it straightened out. They weren't intending to masquarade as an admin. Just made a simple error in setting up BOINC somewhere along the line and confused the Windows administrator user, with the BOINC user.

Now that it is straightened out, they won't be posting as Administrator anymore.

---

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/

those at Rosetta and WCG are wasting their time with the current protein research

Oh, have you read what I have wrote so far? OMG - point me where I say that Rosetta@home is not useful? My believes absolutely contrary - I think Rosetta is not just worthwhile, but definitely one of the best, and most likely best DC project around.

And you must be confusing Rosetta@home and HPF, those are different projects, with very different goals, run by different science teams, by different organizations with different sponsors/source of funding. Yes, Dr. Baker supportive of HPF - and I believe he will be supportive of any large scale efforts that will use his software. But that dose not mean that you can put equality mark when evaluating projects

As regards FightAids@Home - the reason why they don't have a forum or stats website is because in November 2005 they joined as a project within WCG and all discussion and stats regarding the project are now within WCG's site/forums

As far as I remember they did not had forum when they started and they used absolutely ugly java based client. But, I did not followed them recently and I missed that part that they joined WCG. They made definitely huge progress toward the enduser convenience by joining WCG. But according to there web site they keep using using AutoDock. By simply switching to pharmacophore-based methods of docking productivity of crunching would get boost from hundreds to thousands times. So you can still say, that whoever run fightaids now still do not care.

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TestPilot, AKA Administrator

those at Rosetta and WCG are wasting their time with the current protein research

Oh, have you read what I have wrote so far? OMG - point me where I say that Rosetta@home is not useful? My believes absolutely contrary - I think Rosetta is not just worthwhile, but definitely one of the best, and most likely best DC project around.

And you must be confusing Rosetta@home and HPF, those are different projects, with very different goals, run by different science teams, by different organizations with different sponsors/source of funding. Yes, Dr. Baker supportive of HPF - and I believe he will be supportive of any large scale efforts that will use his software. But that dose not mean that you can put equality mark when evaluating projects

As regards FightAids@Home - the reason why they don't have a forum or stats website is because in November 2005 they joined as a project within WCG and all discussion and stats regarding the project are now within WCG's site/forums

As far as I remember they did not had forum when they started and they used absolutely ugly java based client. But, I did not followed them recently and I missed that part that they joined WCG. They made definitely huge progress toward the enduser convenience by joining WCG. But according to there web site they keep using using AutoDock. By simply switching to pharmacophore-based methods of docking productivity of crunching would get boost from hundreds to thousands times. So you can still say, that whoever run fightaids now still do not care.

TestPilot, just for the info the AIDS@Home is what brought WCG to the BOINC platform, HPF came after then the Cancer one.

Also the chap doinf the HPF is an old student of Dr Baker etc...

I also don't believe AutoDock is particularly good either. Anyone know what target's they are going for? (from the PDB).

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Team mauisun.org

Hi TestPilot

I would suggest we leave our little discussion here as bouncing point to counter point is not productive and has little merit for anyone here.

When it comes down to opinions people rarely agree and it seems to be sliding away from the original points into the old 'my projects better than yours' arguements which benefit no-one.

Regards, Ady :)

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Crunching In Memory Of My Dad

Come back to our team and our boards, where sanity awaits, and the joy of team crunching can be re-experienced.

Phoenix: Let me take responsibility for this problem. I noticed someone requesting Administrator use another account and several were helping him recover his normal name. When that didn't help, I contacted the staff. Perhaps others did, too. It got changed. Pass on my apology to John for not choosing the correct path sooner, as it may have kept this from developing as far as it did. If his major problem wasn't Administrator's name, then I'll mention that a local resident of where I live passed away. He lived extremely frugally and cut corners by not having running water. He and his wife would carry water to the house from a public water faucet. The guy passed away with more than a million in the bank. The next week, his wife had water service installed..

People have opinions, and even if they don't make sense to us, we all need to respect each other's opinions. Especially if they seem illogical to us. If you're unable to convince others of the correctness of your position, I've been told that you shouldn't blame your opponent being as thick as a rock, but on your lack of skill in explaining your side. If you bore them, they won't listen. If you offend them, they won't listen. If they know you're wrong or they know you're lying, they won't listen.

Try and be positive. It speaks better of a project if you can describe it in positive terms, rather than point out all the failings of other projects by describing them in negative terms.

If WCG using an older version of Rosetta requires 1000 results be tested to find a potential cure; while WCG using a newer version of Rosetta two years from now would require 20 results be tested to find the same cure. Get 5 more scientists testing the results now. Waiting just gets you to the cure 2 years later.

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Rosetta Moderator: Mod.Tymbrimi
ROSETTA@home FAQ
Moderator Contact

People have opinions, and even if they don't make sense to us, we all need to respect each other's opinions. Especially if they seem illogical to us. If you're unable to convince others of the correctness of your position, I've been told that you shouldn't blame your opponent being as thick as a rock, but on your lack of skill in explaining your side. If you bore them, they won't listen. If you offend them, they won't listen. If they know you're wrong or they know you're lying, they won't listen.

Try and be positive. It speaks better of a project if you can describe it in positive terms, rather than point out all the failings of other projects by describing them in negative terms.

Very well put, and something I think we can perhaps ALL agree on.

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Crunching In Memory Of My Dad

They never solved this problem: Problems with download of WUs: Either no work or overcommitted

Now I only receive 8.2 credits/hour for Rosetta while I get a little over 20 credits/hour from SETI@Home and Einstein@Home. Not worth the trouble, time and electricity.

Detached from Rosetta.

You receive 8.2 credit per hour... lucky man you are, I receive 1.. yeah yeah, 1 credit per hour...
so me too Seti... here I come

Roll

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Mod.Tymbrimi
So, could you please explain what I did wrong? How could you say "Pass on my apology to John" referring to the guy who posted anmotivated attacking post with the whole point of bringing someone down? And it is clear that "Administrator" nickname were used by him just as a point of attack. I was not even talking to him priot to his post! You feel like it is Ok for someone to post stuff like that?

Let me publish my reply under my name so ppl do not read the whole post wondering who posted it untill the very end of the post where is signature, sure with your edit

Mod.Tymbrimi

I noticed someone requesting Administrator use another account and several were helping him recover his normal name.

Let me clarify this. I was the one who requested help to get my original credentials. The only reason why I did that is because I did wanted to change project settings on my home computer. No one at that point never ever requested me to change my name - and couple forum moderators replied to my posts having no problem with Administrator name.

When that didn't help, I contacted the staff. Perhaps others did, too. It got changed.

In fact the changes came after I wrote mail to Ethan (Forum moderator/Project administrator/Project developer). With his help I got credentials of TestPilot back. The reasons I switched my forum nickname was for my own convenience and because I do find nickname Administrator somewhat silly.

Pass on my apology to John for not choosing the correct path sooner, as it may have kept this from developing as far as it did.

The very first post that that John posted in this thread was personal assault against me. He tried to start flame by making personal attacks on the ground of my nickname, my status and mine imaginable behavior. I think such posts should not be tolerated on any forum. When the guy got pointed out on that - he decided to leave.

If his major problem wasn't Administrator's name, then I'll mention that a local resident of where I live passed away. He lived extremely frugally and cut corners by not having running water. He and his wife would carry water to the house from a public water faucet. The guy passed away with more than a million in the bank. The next week, his wife had water service installed..

I leave this parable on your conscience. Your don't know me, to draw such a primitive and offensive analogies. The whole reason about this paragraph is to show your personal preferences. You think you found indirect and “witty” way of doing that, but reasons behind it remains pretty much straightforward.

The rest of your post is set of sounding good banalities, in an effort to make your post looks like it was written in good faith.

As to nickname Administrator. It is not in any way offensive nickname. It not violates any rules. As to point that John or someone else might assume that person behind that nickname have something to do with staff/moderators – is complete nonsense. Do not think ppl are stupid – they see forum status. And John’s post clearly illustrate it – no one so far assumed me being somehow involved with the project other than crunching for it. I did create that account on my buddy’s computer just to show BOINC and Rosetta screensaver to illustrate what DC is about. I never had intentions to make forum post under that nickname or use it for crunching on the first place. But it happens to be that that was only nickname I can use to log in to the system and there is no way I can change or create other record without loosing my TestPilot status in BOINC client on home computer. And, yes, I am an administrator in real life. I still fill like using TestPilot for other posts on this forum – but since I started to post in this tread under Administrator – I think nothing prevents me from keep doing that.

On my side I was doing all I can not to go into pointless and unnecessarily flame, that John’s team members tried to start over and over in this tread. But you post make it sound like it is official point of view that I did something wrong and I’m should be blamed of John’s unmotivated anger about my nickname/status/etc. I did nothing I’m ashamed of, I did absolutely nothing wrong in this tread or in the project and I could not be blamed for anything bad. Furthermore I was trying to keep my posts as informative as I can, backing my points with facts and real arguments not switching to personalities, except for one time when I replied to John’s assault.

But yes, there is one “fault” on my side. I am trying to inspire people to think about projects and critically evaluate them, not just mindlessly go for good slogans and good declarative goals. Sure critics draw some resistance and negative reactions. If I be here to gain popularity I would make point of my posts something like “You guys doing such a grate work! Keep up doing it!” But that was my choice and I do realize consequences.

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Ok. Let me clarify a bit my point as to FightAIDSathome.
Here is the link to the most resent description of the project progress: http://fightaidsathome.scripps.edu/news/vol1.html
What they are basically saying there, is that they compute interaction of 1900 drug like molecules against 270 variation of one of AIDS protein. So they, lets open Excel, are trying to predict outcome of reaction of total 513,000 interaction. Not that many – but they mention some scary sounding quadrillions. I’ll address those a bit later.

There was another DC project Find-A-Drug. It actually over now – but lets take a look at it statistics. The project was running for ~3 years. Here is the link :
http://www.find-a-drug.org but you have to navigate stat page yourself.
31,320,743,182 total interaction calculated (I was using total from targets page). Kinda different number.
Number of proteins they were running against drug like molecules was ~280. Very similar. Number of drug like molecules checked against protein vary from 40,000,000 up to 500,000,000 with an average of ~100,000,000, a far cry from 2,000 of FightAIDS.

Lets try to estimate efficiency of software used by projects. Ok, Find-A-Drug was running for 3 years, it had more members, and that press release from FightAIDS most likely referring to very recent developments of FightAIDS project. Plus WCG running other projects, not solely FightAIDS. So I think it would be fair to reduce total number of Find-A-Drug calculation by 10 for above mentioned reasons in sake of comparation.

In this case we are getting that FightAIDS roughly 6,000 times slower when compared to Find-a-drug. Well within expected scope. That mean that for every hour your computer spent doing work for FAD the very same computer need to be ran for more then 8 months nonstop to calculate similar amount of interactions in FightAIDS project. If that is not impressive enough – think of in-house farm with 200 CPU that beat distributed project with 1,200,000 active CPU crunching nonstop.

Ok, let me explain how come the difference is so huge. The answer is fundamental difference between software used by above mentioned projects. When AutoDock try to predict interaction between target protein and a ligand, it “wrap up” protein with net, where in every point of net crossing AutoDock performs energy evaluation. The bigger the protein – the bigger net you need. And this way more energy calculations. And HIV protease used by FightAIDS relatively big one. The tighter the net – the higher chances to catch strong reaction. And net should contain at least dozens of thousands net squares, for most proteins. On the other hand to run THINK (software behind Find-A-Drug project) you have to know the active site. It is place on the surface of protein which is responsible for function that is carried out by protein. This way THINK eliminating need for the net, thus dramatically reducing amount of computation needed to be performed.

The obvious advantage of the AutoDock, is that you can feed it with just a 3dementional structure of a protein, without knowing anything else about protein you want to suppress. The disadvantages is huge. It is not only speed. A lot of molecules that will show strong interaction using computational simulation, and will confirm reaction in vitro, would have no effect or very weak effect in vivo – simply because even when they were bidding protein, they fail to actually block it function! Other advantage of having running protein against A LOT of compounds is that you can choose not only those ones that have strong predicted reaction, but select those ones that would have way higher chances to react ONLY with protein of interest. Which is very important in terms of limiting side effects.
As to active site. AIDS is very well studied and relatively good understood virus. And for most, if not all of it active sites are known. You can check FAD web site – they were running interactions against 30 AIDS targets, what sounds for me as FAD covered pretty much all viral pathway, and in every case they knew active sites. So this should not be a problem at all.
As to quadrillion number. Most of it comes from “net” calculations, performed by AutoDock. Plus it looks like they count all energies calculations against all atoms in HIV protease, some kind of “marketing” way of counting reactions for the sake of getting impressive number. Plus they included redundancy 5 time redundancy in that calculation:)

FluffyChicken

Anyone know what target's they are going for? (from the PDB).

Most likely they use different submission of HIV protease in PDB database made by different groups on different strains of HIV. Plus some sort of possible mutations. But that is my guess.

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TestPilot said:

So, could you please explain what I did wrong? How could you say "Pass on my apology to John" referring to the guy who posted anmotivated attacking post with the whole point of bringing someone down? And it is clear that "Administrator" nickname were used by him just as a point of attack. I was not even talking to him priot to his post! You feel like it is Ok for someone to post stuff like that?

Keep in mind the saying that "two wrongs don't make a right." More than one person seemed offended at the way you described other projects. John seemed under the impression that you chose the name "Administrator" for ulterior motives to present your opinions of the other projects. You posted your opinions about other projects as "facts". Those that have run those projects may see your opinions stated as "facts" as offensive. You don't have to insult someone directly when insulting the project they run.

Neither side of that interchange was right.
I'll go clean things up a bit.

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Rosetta Moderator: Mod.Tymbrimi
ROSETTA@home FAQ
Moderator Contact

TestPilot, did you crunch over at Find-a-Drug?

An open source science community are using some of the results, Malaria mainly (you can follow all the work, since their 'logs' are publiched to the web).
But they also have some of the HIV (if not all the 'anti' active ones).

Best to start reading here
http://usefulchem.wikispaces.com/
It expanded quite a bit from the initial blogspot blog.


P.S. The HIV part is stuck at this bit

HIV


Objective

Find, synthesize and test new anti-HIV compounds.


Progress

Need for new anti-HIV compounds found by this search and this search for: to find new
90 compounds predicted to show HIV protease inhibition provided by Find-a-Drug


Next Steps

Find a collaborator to test for HIV protease inhibition

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Team mauisun.org

TestPilot, did you crunch over at Find-a-Drug?

Yes! I never posted on FAD forum, but I definitely remember you form just reading it!:)

An open source science community are using some of the results, Malaria mainly (you can follow all the work, since their 'logs' are publiched to the web).

Wow! That is nice to hear. I remember it was somewhat disappointing when Keiht said there is a little interest from industry in results. And it really cool that ppl working on them. And I do remember it was some lab testing made in Europe based on academic grants - during course of project or closer to the end.
Plus, hopefully, there is way more activity/progress that is not made publically available.

But they also have some of the HIV (if not all the 'anti' active ones).

I think with all the commercial investments in HIV research open source almost have no chance to compete, but I'm wishing them luck!

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I wonder what ever happened to John.

If I remember right, this John in question was the founder of our team, Team-TNO originally (after the X-Files: Trust No One), then upon the demise of that original series with The Lone Gunmen and the young Mulder & Scully, the CSM (Cigarette Smoking Man) and all the rest, we morphed into Team-SciFi. Yeah, John founded our team back in the beginning of all of this mad DC stuff. Our team was certainly among the first teams, as it were. Aaaaaaand John was the founder. And I totally forgot about this whole sad affair.

John, you still out there?

......... I want to believe......

.....Alaska calls right?.....

.... or was it... Kari Wuhrur...? :D

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The Liver is EVIL. It must be PUNISHED!

Team-SciFi