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Son Goku
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Joined: 13 Mar 2006
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 Posted: Mon Jun 19, 2006 2:31 am Post subject: Well, looks like Tanpaku about ready for BOINC 5.x upgrade |
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This on their main site...
http://issofty17.is.noda.tus.ac.jp/index_E.php
| Quote: | June 15, 2006
Important!
TANPAKU server will be down from 21 June to 22 June for upgrade and maintenance. You will use BOINC client version 5. |
When XML stats will get out for the other projects, is not yet known however... |
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Dagger
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Location: BC Canada
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| Posted: Mon Jun 19, 2006 7:16 am Post subject: |
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Then we can get out of 75th place.
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Killerrabbit
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Joined: 23 May 2002
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| Posted: Mon Jun 19, 2006 9:34 am Post subject: |
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Kind of difficult to get out of 7th place with no work, also it was a bit difficult to read the news as it loooked all funky and stuff.
Ni
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Son Goku
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| Posted: Tue Jun 20, 2006 4:26 am Post subject: |
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After it's upgraded to accept BOINC version 5 clients, the work shouldn't be such a problem, as long as there are WUs that is.
Umm, the link I gave was to the English page, at least on my browser here. If someone isn't getting English, just select the English language from the top of the page... |
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Killerrabbit
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| Posted: Tue Jun 20, 2006 9:09 am Post subject: |
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Who is on the team anyway?
Ni
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Dagger
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| Posted: Tue Jun 20, 2006 4:08 pm Post subject: |
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I'm on it. but i'm waiting for the 5x upgrade to be done so BOINC can recognize it.
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Killerrabbit
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| Posted: Tue Jun 20, 2006 5:16 pm Post subject: |
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We are all waiting for that upgrade to happen.
Ni
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Son Goku
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| Posted: Tue Jun 20, 2006 6:05 pm Post subject: |
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I'm on it, but have 0 credit thus far, until this upgrade's a done deal  |
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A Shrubbery
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| Posted: Tue Jun 20, 2006 9:14 pm Post subject: |
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Is it just yet another folding project? If so, other than the stats for our team, what advantage/difference is there?
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Son Goku
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| Posted: Wed Jun 21, 2006 12:03 am Post subject: |
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| It deals with protein folding... I doubt the method used is exactly like folding@home, as Rossetta doesn't go about it the same way. One would need to check their page for their specific methodology and how they're going about things/what specifcally their working on (target wise), etc... |
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Killerrabbit
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| Posted: Wed Jun 21, 2006 10:45 am Post subject: |
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I have tried to do that to find more information, but it all seems to be in Japanese.
Ni
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Son Goku
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| Posted: Wed Jun 21, 2006 10:26 pm Post subject: |
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Hmm, they have 2 languages... The link I gave is in English (at least here), the default link (which is also what goes into BOINC is in Japanese). Not sure what to say
Here's what I get at this URL
http://issofty17.is.noda.tus.ac.jp/doc/first_E.html
| Quote: | ...On the other hand, the DNA base sequence of a gene provides the amino acid sequence information of the protein it encodes. Therefore, gene is a blueprint to make a protein and genome, the complete set of genes in a living organism, is a blueprint of our body as a whole. Because genomic information provides us a lot of clues for solving secrets of life, hundreds of genome sequencing projects of many species are performed around the world. Today, the human genome has been also deciphered!
The relationship between protein structure and function
Given the genomic sequence information, do we understand the whole life? Unfortunately, although we know that a gene corresponds to one of the proteins, it is still difficult to deduce its function from the amino acid sequence.
Protein folds into its unique three-dimensional structure corresponding to its amino acid sequence and then works in our body. In other words, there is a deep relationship between structure of a protein and its function. Therefore, if we can predict a protein structure from its amino acid sequence, this structural information provides very useful information for deducing its protein function.
However, we don't have the method that predicts the folded structure of a protein from its amino acid sequence alone.
Protein structure prediction by computer simulation
There has been an interest in predicting protein structures by computer simulation. Although computational power has greatly increased now, it is still difficult to sample enough conformations directly in a reasonable time to find the folded structure with even state-of-the-art computers.
Under this situation, researchers have proposed various methods to overcome this difficulty. In our laboratory, "Brownian Dynamics (BD) method" that is based on the simulation of Brownian motion has been developed, giving some successful results up to now. This BD method enables us to simulate long time with less computational time compared with conventional simulation methods.
However, toward the final goal of predicting a protein structure from its amino acid sequence, more computational power is required. In order to achieve this requirement, we are improving computational algorithm and also we have paid attention to simulating BD on a more powerful computational resource.
So, we launch the "TANPAKU" project on the distributed computing. |
The first part suggests what it's doing, and in that sense the project looks to be very similar to both Folding and Rossetta. The second part mentions a bit of blurb about the specific methodology they are employing to accomplish this goal. It does look to be a bit of a different method then folding, though I'd have to look more into what the "Brownian Dynamics (BD) method" is. I'm gathering that by sampling enough conformations, they're relating to the folding@home way of doing things; and by this saying it is still not the most practical way to go about deducing this. Something that predictor@home, as well as Rossetta have suggested, with their alternative methods to deduce protein folding...
Hope this helps. |
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Killerrabbit
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| Posted: Wed Jun 21, 2006 10:58 pm Post subject: |
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Well if they are on schedule they should have upgraded their servers to version 5 soon.
Ni
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Dagger
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| Posted: Thu Jun 22, 2006 3:38 am Post subject: |
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It's upgraded as of this post.. Ie you can now attach the project to BOINC, but the servers are still down for maintence, and so it won't fully attach.
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Son Goku
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| Posted: Thu Jun 22, 2006 3:55 am Post subject: |
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Ah, OK... Well, I guess I mise well attach it. Does mean it shouldn't be long however, as things have pretty much come along...
Edit: Oh yeah, of course. Without a dBase, it can't find our accounts  |
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Dagger
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| Posted: Thu Jun 22, 2006 12:11 pm Post subject: |
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I can get to my account page, but still can't quite attach yet.
[Edit] I see what ya mean by the DB. [/Edit]
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Son Goku
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| Posted: Thu Jun 22, 2006 3:34 pm Post subject: |
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OK, you can attach to the project now, but still need to wait to get work.
However, to do so, first go into the account page on the web and set a password. After a new password is set, use that to attach... |
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Son Goku
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Posts: 426
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| Posted: Thu Jun 22, 2006 11:55 pm Post subject: |
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I came home from class and noticed several Tanpaku WUs in my cache, which it is now working on.
Only things to keep in mind:
- They have a very short deadline (must be < 12 hours)
- They're extremely short at this moment. It looks like they're crunching a bunch of test WUs (possibly) to make sure everything goes OK
- Perhaps in part as a consequence of the above, the max daily quota per CPU core is > 65,000 WUs (It looks like the max value that can fit in an unsigned 16-bit integer, aka 2 ^ 16th power...
There is some work currently however, though extremly short per WU... I doubt the actual units as we move further along in testing will remain so short... |
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Killerrabbit
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| Posted: Fri Jun 23, 2006 12:35 am Post subject: |
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I just got some as well as of a few minutes ago.
I am sure they will extend the deadlines when the WU's get longer.
Ni
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Son Goku
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| Posted: Fri Jun 23, 2006 4:48 am Post subject: |
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Yeah, I'm almost suspecting short test WUs at first to make sure everything is going OK... And once there's some confirmation of that, then longer WUs might be on the way. Course, I wasn't able to crunch on the earlier app, to compare lengths to what they were before.
For now however, it would be a rather good project for people's old projects, having WUs shorter then predictor@home, hech shorter then Xtreme lab, last time I got units for it |
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