...bottom line--don't abort any work units!!

Can we safely assume for the future, that should we be past deadlines and/or workunits are no longer useful for processing, etc. etc., that the Project people would post an Announcement to abort the work units in question? It seems like it would be in the Project's self-interest to focus volunteer computing resources on those units that will yield a valued result, and not wish to waste volunteer resources/time with computing results that have no use....

Seems sort of self-evident, I know, but some reassurance that this issue will be monitored closely by the Project may reassure the volunteers! :)

Yes of course! We will need every second that is available for these challenges, and will cancel any jobs on targets that have expired. But given the pace at which targets are released, I don't think there will be any jobs remaining in the queue for targets by the time the deadlines come along.

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The first CASP 7 target was released today!

Here is its amino acid sequence:

MSFIEKMIGSLNDKREWKAMEARAKALPKEYHHAYKAIQKYMWTSGGPTDWQDTKRIFGG
ILDLFEEGAAEGKKVTDLTGEDVAAFCDELMKDTKTWMDKYRTKLNDSIGRD

can you tell from this what the three dimensional structure and function
of this protein are?

The problem with proteins, of course, is that you can't
read off directly from the sequence what the structure and function are, although
both are completely determined by the sequence (the genetic blueprint, quite literally).

We are excited because this protein looks unrelated to any protein of known structure, and is
not too much bigger than most of the proteins we've running tests on these many months, so it
is a perfect challenge for the methods we've been developing. After some quick runs on RALPH to
make sure work units behave properly, you should see work units for this protein by the end of tomorrow!

I think first two target are easy but third one is really hard. Any manual luck for this sequence template.. T0287

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GeneCard
This lists the amino acid chain as "BHA3980", states it has an unknown function, and lists one fewer AA chain when it's mature.
Whole genome sequence
description of what this bacteria can do..

When I see the term "alkaline" - I think of Sundews and Venus Fly Traps.

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Just wondering if you could comment more on how you were able to reduce the memory requirements by over 2x? What kind of tricks did you use to accomplish this?

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Just wondering if you could comment more on how you were able to reduce the memory requirements by over 2x? What kind of tricks did you use to accomplish this?

Most of my experience in this arena (reducing the memory footprint of software) comes from PS/2 game development. You've got 32 megs on a PS/2, no virtual memory, and the rule is really simple. If your game doesn't fit, it doesn't run. Period.

That said, two comments of David's struck a tremendous chord with me, because they're the exact same things as I've done in the past.

1. There's no "magic" you do. It's just plain old legwork, going over and over the code. Trimming a couple of percent here, and a couple of percent there. "Does that array really need to have 256 members, or could we get by with 64?" Do that over and over, and in the long term it adds up.

2. "Does that array need to be permanent? Or can we allocate it from the heap, effectively sharing it with some other array at some other time?" This also adds up, albeit with a price: that of memory management. On a PS/2 this is far worse, since there's no Vmem system, so memory fragmentation can be a real nightmare. With the Vmem present on Win32, that's a lot less of a problem. Memory leaks are, of course, fatal. Far more on PS/2 because no Vmem to cover for your errors. :)

But you get the idea.

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I have encouraged all of the researchers leaving my group for faculty positions at other universities to continue working with and developing rosetta, and now there are six research groups in addition to mine actively developing the code.

It would be great if some of those Rosetta researchers would participate (occasionally) in the "Science" forum here and talk about how they use Rosetta, or comment on threads, like https://boinc.bakerlab.org/rosetta/forum_thread.php?id=1631, on the route taken by the various protein-study projects, or one of you could forward "internal" discussions here.

---

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It would be great if some of those Rosetta researchers would participate (occasionally) in the "Science" forum here and talk about how they use Rosetta, or comment on threads, like https://boinc.bakerlab.org/rosetta/forum_thread.php?id=1631, on the route taken by the various protein-study projects, or one of you could forward "internal" discussions here.

That would be way cool, which I think would not only provide a great public educational outreach benefit, but also perhaps attract more BOINC volunteers to partipate in Rosetta because it has such a first-hand, community forum/discussion/educational interaction from outside scientists who are also "making it happen" at the basic research level.

Outside researchers that do post could perhaps identify themselves/their affiliation via their signature block.

Thinking out loud, a thread might perhaps be set-up where some of the outside researchers could discuss the kind of research they are pursuing, as time and temperament permits.

Just some thoughts, but exciting ones!

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Regards,
Bob P.

I have encouraged all of the researchers leaving my group for faculty positions at other universities to continue working with and developing rosetta, and now there are six research groups in addition to mine actively developing the code.

It would be great if some of those Rosetta researchers would participate (occasionally) in the "Science" forum here and talk about how they use Rosetta, or comment on threads, like https://boinc.bakerlab.org/rosetta/forum_thread.php?id=1631, on the route taken by the various protein-study projects, or one of you could forward "internal" discussions here.

I agree, we should encourage R@H user to discuss these issues and how we can contribute. I am sure some of the dedicated users even don't know how rosetta works.

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I have encouraged all of the researchers leaving my group for faculty positions at other universities to continue working with and developing rosetta, and now there are six research groups in addition to mine actively developing the code.

It would be great if some of those Rosetta researchers would participate (occasionally) in the "Science" forum here and talk about how they use Rosetta, or comment on threads, like https://boinc.bakerlab.org/rosetta/forum_thread.php?id=1631, on the route taken by the various protein-study projects, or one of you could forward "internal" discussions here.

I agree, we should encourage R@H user to discuss these issues and how we can contribute. I am sure some of the dedicated users even don't know how rosetta works.

They post all the time, you just have to know who to look for.

sound good. thanks

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A side benefit to some of the memory use reductions is that it should be relatively easy to reduce the sizes of some of the input files we send out with each work unit. Would a 30% reduction make a significant difference to dialup users?

Yes, anything that you can do to reduce bandwidth usage would be much appreciated.

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Are there any objections?

If I hear none prior to 3 hours from the date stamp on this message, I will proceed.

A fine idea. Takes too long to display and reply to this thread now. Perhaps do the same with Dr. Baker's thread? Or even color code his posts interspersed within the same "archieved", read-only thread??

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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/

The 5.16 release log says "...new feature where at the end of a simulation, Rosetta compares its fold to the predictions made by a dozen other algorithms." I can see that if several methods of prediction agree, it tends to strengthen the validity of the results. How are the results of all the other methods already known? Is this a CASP thing to try and get the best model? Is Rosetta making adjustments to bias some of it's decisions based on the other results (i.e. changing it's prediction slightly to yield something that more closely matches)? Or is it just comparing and scoring the fit with the other predictions and returning the scores?

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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/

I had an e-mail from CASP this morning that said the results of the robots would be made available after something like 3 days of issuing the protein. Perhaps these results are being collated and bundled with the wu's? Should be straight forward toi do, the result files are very small.

Of course, I could be entirely wrong.

I am always wary of using homologs and other predictions. I can see cases of, "we all made the same mistake", or, "we searched the wrong domain because the other models pointed to the wrong place", this kind of thing.

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Wave upon wave of demented avengers march cheerfully out of obscurity into the dream.

In response to some of the recent discussions on the science boards, today I'd like to tell you about how Rosetta is being used to help understand diseases caused by protein misfolding.

A significant fraction of human diseases are caused by proteins misfolding to form long "amyloid fibrils". These diseases range from Alzheimer's disease to infectious diseases from amyloid forming prion proteins. A huge breakthrough in the understanding of the process of protein misfolding to form amyloid fibrils was published in Nature last year from David Eisenberg's research group at UCLA. They reported the first high resolution structure of an amyloid forming peptide. It revealed a set of interactions which seem very likely to be general to most if not all amyloid structures.

We have been collaborating with Eisenberg's group to try to predict the portions of proteins known to form amyloid structures responsible for amyloid fiber formation. We use the rosetta-design method to identify sequences compatible with a generalized model of their amyloid structure. You can read about the promising results of this work in the collaborative paper with Eisenberg's group that is posted on the "2006" portion of our home page publication list mentioned in my previous post. The next challenge which we are collaborating on is to design "caps" that will add on to fibers and prevent them from growing further. This is a good example of how basic research development can have applications to pressing medical problems that were entirely unanticipated.

On a different note, Rhiju asked me to request that users with computers with remaining problems sign up for ralph@home--the error rate is significantly lower on ralph perhaps because there are a larger fraction of high end machines, and this makes it harder to track down the remaining issues on rosetta@home.

Dear Dr Baker,
One quick question. I am still wondering if Rosetta is working parallel to protein misfolding cyclic amplification techniques!
thanks

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Refering to my comment above, here is the e-mail I received from CASP.

Next week we are planning to release 8-10 targets again (based
on their availability and difficulty).

We want to remind all the participants that server predictions
are being made available 3 days after the target is released.
They can be accessed from the main casp7 web page by following
the link "Server Models". Note, that tarballs of all 3D models
(with AL predictions already converted into coordinates) are
posted at the same place usually with a short delay (1/2-1 day).

I'd have included it above, but at the time, I was re-installing Windows on the machine that has my e-mail client on it!!!

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Wave upon wave of demented avengers march cheerfully out of obscurity into the dream.

Refering to my comment above, here is the e-mail I received from CASP.

Next week we are planning to release 8-10 targets again (based
on their availability and difficulty).

We want to remind all the participants that server predictions
are being made available 3 days after the target is released.
They can be accessed from the main casp7 web page by following
the link "Server Models". Note, that tarballs of all 3D models
(with AL predictions already converted into coordinates) are
posted at the same place usually with a short delay (1/2-1 day).

I'd have included it above, but at the time, I was re-installing Windows on the machine that has my e-mail client on it!!!

if all the automated methods such as robetta agree on the rough outlines, we do make use of this information--this is the "comparative modeling problem". Bin has developed some neat new approaches to this problem that I described last month (basically, the searching problem is similar to what you have been seeing all along, except that instead of starting with a fully extended chain we start with a variation on the starting model) that he is testing out on these cases (the challenge is to go from the rough and usually inaccurate starting model to an accurate high resolution structure). Rhiju is focusing on the case where the automated methods all disagree (like T283, 285 and 287) and for these the automated methods do not provide any useful information.

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On the AP article:

Donna from the AP sent me a draft of her article; it is great! Thanks to all who helped her with it! She says the AP reaches half a billion people each day--hard to beat that for publicity!

Just a reminder to create a "landing page" specifically designed for this (a la BBC-CPDN's 1-2-3 join page and ideally an installer of BOINC+Rosetta), i.e. instructions for "regular", non-computer-savvy people.

PS: The LiveScience article -Rosetta@home in the news (republished on YahooNews!, FoxNews, MSNBC) must have been read by many people, but had minimal impact on TeraFLOPS (why, your guess is as good as mine).

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On the AP article:

Donna from the AP sent me a draft of her article; it is great! Thanks to all who helped her with it! She says the AP reaches half a billion people each day--hard to beat that for publicity!

Just a reminder to create a "landing page" specifically designed for this (a la BBC-CPDN's 1-2-3 join page and ideally an installer of BOINC+Rosetta), i.e. instructions for "regular", non-computer-savvy people.

PS: The LiveScience article -Rosetta@home in the news (republished on YahooNews!, FoxNews, MSNBC) must have been read by many people, but had minimal impact on TeraFLOPS (why, your guess is as good as mine).

we don't have a special landing page--does the volunteer team have ideas for this?

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Many of the targets are very closely related to proteins of already known structure; in fact I'm not sure why the experimentalists bothered to determine their structures! The search is pretty easy in this case, and we are not putting too much effort into these predictioins (they are not so exciting).

...perhaps for some of the other teams these are to help them gauge their progress since the last CASP.

Hope to see some T296's on Ralph soon.

For those that were wondering, here is a thread from the AP reporter.

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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/

One of the Rosetta team mentioned running 10k decoys, and using that data to create another WU to run 10k more decoys; in the hopes that the approach would result in better results than our running 100k decoys on a single WU. Are we going to try this approach on the 445 AA behemoth that you announced?
Have we got to try out the 10k, analyze, create a new WU and create 10k more decoy approach yet? (How well did it do?)

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