Yes indeed, thanks for the updates!!!

Proud member of AMDUSERS www.amdusers.com

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So will each scientist ... provide feedback on the message boards ?

yes, that is the plan. also, we will be able to divide up the other tasks, such as posting updated results on the site, etc.

I was wondering whether it wouldn't perhaps make sense to place the team member's project/science updates on a web page (sort of blog-style), instead of in the forum - or perhaps they could be placed in a separate forum section where only the team members have write privileges. There would of course still be the opportunity for the participants to ask questions in the regular forum. It seems to me that separating the project/science updates from the interactive part where participants can ask questions might have a number of advantages. For one thing the project updates wouldn't get burried under lots of other, partly off-topic messages (like this one ;-) which mostly don't add to the information provided by the team members. And I can also think of reasons why the proposed format might be preferrable (easier to maintain) for the team members. Just a suggestion which I didn't yet see discussed in any of the other threads ...

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I'll be away from the message boards until the 31st, and just wanted to say a few more words about what you will be seeing over the next ten days.

We will be systematically testing the most promising strategies for searching the energy landscape. Each strategy will be tested on the following proteins:

1di2
1dtj
1dcj
1ogw
2reb
2tif
1mky
1b72
1r69
1n0u
1hz6

You have seen many of these before on the screensaver; if you would like to look at the final native structure in more detail (and find out a little about what the protein does), go to

http://www.rcsb.org/pdb/

and type the name of the protein into the search box. then click on "view structure" on the left, and you will get a number of options for viewing. the "quickpdb" option at the bottom does not require downloading any software. in some cases, we are only folding one "domain" of a larger protein, so what you see will be bigger than what will be appearing on your screensaver.

We've given the different strategies names like INCREASE_CYCLES_10 (which means do 10x more searching at the low resolution stage) and MORE_FRAGS_W_BARCODE (which means give each computer specific but different instructions on the building blocks to use in the low resolution structure). There are ten different strategies being tested. I won't know which are the best methods until the new year, but you might be able to guess by looking at the course of the folding runs on the screensaver.

Once this test is complete (around Jan 1), we will be able to determine from the results the most effective ways of searching the landscape, and I will give you a report shortly afterwards.

Happy Holidays everyone!

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Once this test is complete (around Jan 1), we will be able to determine from the results the most effective ways of searching the landscape, and I will give you a report shortly afterwards.

I would not be surprised to see that more than one strategy is needed ... or that most of them will have to be used ...

In other words, one size fits none ...

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I have been getting W/U named like this

No_Rand_WTS
BARCOAD_FRAG
INCREAS_CYCLES
MORE_FRAG
NO_MORE_RELAXED_CYCLES
I Have beem aborting then as I did not like the way the sounded

Sound more like a Virus then a wook unit to me

And I see the W/U clock stoped on 20 or so Nodes here
I have to reboot to get then going again Whats is going on here

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If You Want The Best You Must forget The Rest
---------------And Join Free-DC----------------

I have been getting W/U named like this

No_Rand_WTS
BARCOAD_FRAG
INCREAS_CYCLES
MORE_FRAG
NO_MORE_RELAXED_CYCLES
I Have beem aborting then as I did not like the way the sounded

Sound more like a Virus then a wook unit to me.

These are valid, they are testing various strategies, as discussed three posts below by David Baker. ;)

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Regards,
Bob P.

I have been getting W/U named like this

No_Rand_WTS
BARCOAD_FRAG
INCREAS_CYCLES
MORE_FRAG
NO_MORE_RELAXED_CYCLES
I Have beem aborting then as I did not like the way the sounded

Sound more like a Virus then a wook unit to me

And I see the W/U clock stoped on 20 or so Nodes here
I have to reboot to get then going again Whats is going on here

Yes, as a project scientist, I can confirm that these are valid WU names.

I have been getting W/U named like this

No_Rand_WTS
BARCOAD_FRAG
INCREAS_CYCLES
MORE_FRAG
NO_MORE_RELAXED_CYCLES
I Have beem aborting then as I did not like the way the sounded

Sound more like a Virus then a wook unit to me

And I see the W/U clock stoped on 20 or so Nodes here
I have to reboot to get then going again Whats is going on here

Yes, as a project scientist, I can confirm that these are valid WU names.

But with this WU's I have tons of errors all over my systems. From NT4, W2K, XP to Linux....

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Teddies....

Unfortunately we sent out a batch of faulty Work Units. They are not a virus. But they are often crashing after 30 seconds or so.

Please see this thread for a discussion of the problem.

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Click signature for global team stats

The post by Carlos Pfitzner seems to show that the shape of a protein also depends on its environment: first the virus envelope then the envelope + the harpooned cell.
In each case does the F protein adopts the lowest energy configuration in the environment?
Do we know all the parameters that cause a protein to fold into a given shape?
Besides modeling and simulation as practiced here in a pragmatic fashion, is there any reason to believe that a theoretical approach could work for finding the shape of a protein?
If all the determinants of a shape are known, if their interactions are known, would it be possible to deduce a rule, a formula to find this shape?
Finally I read somewhere here and from an academic that such a distributed project as Rosetta would appreciate outside people to contribute to the research which requires a multidisciplinary approach. If this is an option can we expect to see a working description of the problem?

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The structure of a protein does indeed depend on its environment (e.g. solvent ...)
The proteins about which most is known are the water soluble proteins, and so far all the proteins on rosetta@home have been water-soluble proteins. Several people in the baker lab (and other labs) have been working on devising methods to predict the structure (shape) of membrane proteins. This is a more difficult problem (partly because less experimental data is available) and as such it has taken longer to make progress. Some recent progress has been made in the Baker lab:

Multipass membrane protein structure prediction using Rosetta by Vladimir Yarov-Yarovoy, Jack Schonbrun, David Baker

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So will each scientist ... provide feedback on the message boards ?

yes, that is the plan. also, we will be able to divide up the other tasks, such as posting updated results on the site, etc.

I was wondering whether it wouldn't perhaps make sense to place the team member's project/science updates on a web page (sort of blog-style), instead of in the forum - or perhaps they could be placed in a separate forum section where only the team members have write privileges. There would of course still be the opportunity for the participants to ask questions in the regular forum. It seems to me that separating the project/science updates from the interactive part where participants can ask questions might have a number of advantages. For one thing the project updates wouldn't get burried under lots of other, partly off-topic messages (like this one ;-) which mostly don't add to the information provided by the team members. And I can also think of reasons why the proposed format might be preferrable (easier to maintain) for the team members. Just a suggestion which I didn't yet see discussed in any of the other threads ...

Fully agree with this suggestion. By eliminating a lot of "noise" in communications (such as credit scoreboards...) and improving access by making it direct, a separate forum would markedly enhance the value of information provided by the scientists as to where all this computing is going.

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So will each scientist ... provide feedback on the message boards ?

yes, that is the plan. also, we will be able to divide up the other tasks, such as posting updated results on the site, etc.

I was wondering whether it wouldn't perhaps make sense to place the team member's project/science updates on a web page (sort of blog-style), instead of in the forum - or perhaps they could be placed in a separate forum section where only the team members have write privileges. There would of course still be the opportunity for the participants to ask questions in the regular forum. It seems to me that separating the project/science updates from the interactive part where participants can ask questions might have a number of advantages. For one thing the project updates wouldn't get burried under lots of other, partly off-topic messages (like this one ;-) which mostly don't add to the information provided by the team members. And I can also think of reasons why the proposed format might be preferrable (easier to maintain) for the team members. Just a suggestion which I didn't yet see discussed in any of the other threads ...

Fully agree with this suggestion. By eliminating a lot of "noise" in communications (such as credit scoreboards...) and improving access by making it direct, a separate forum would markedly enhance the value of information provided by the scientists as to where all this computing is going.

Hi,

If you decide to do so, may I ask you to put in this thread a link to the place where we, dumb non-scientists, can read these updates and try to make something out of them ?

Thnak you,

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Anne

© anne schmidt

Weblog - PublicView

Bonjour Anne, we try to interpret Dr. Baker's journal, where a lot of the hard science is mentioned, in the thread about discussion of Dr. Baker's Journal.

I believe I found this article from one of the links from the homepage that referenced it. I found it most helpful in understanding more about the "big picture" here.

If you have specific questions, the Science forum would be the place to ask. And don't hesitate to ask in layperson's language. It is hard enough for native English speakers to understand Dr. Baker sometimes. Even if you do know about the science, I would think it gets considerably harder when interpreting into another language. We are all interested in improving our understanding of what it all means, and how it all works, so your question will help others as well.

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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/

It shall be great if the Rosetta interface also tells us which native protein structure we are trying the arrive at, u can relate much more to what is happening in that case esp if u have a background in biology.
I shall much appreciate this addition!

You can find more information about the protein computed in your WUs by entering the identifier of the protein in the search box on the website of the RCSB PDB.
The identifier is always included in the WU name. For example:
FRA_a009_STRUCTURAL_GENOMICS_hom001_4_a009_4_1o6eA_IGNORE_THE_REST_190_1637_14
Hope that helps.

yes it does! thanks for letting me know!

from all this, which is the actual protein that I can use to look up what this is about? I've done this once before, but i have forgoten.

FRA_a009_STRUCTURAL_GENOMICS_hom001_4_a009_4_1o6eA_IGNORE_THE_REST_190_1637_14

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