Today (Friday) we have closed accepting server predictions for the first
target, T0283.

What should be done with T0283 WUs that are still on our machines?

Also. should the deadlines for the CASP7 WUs be just a bit ealier than the real deadlines.

Back to the T0283. One of them I still got running has a deadline of May 27. But if the CASP deadline was May 12, will those results be of any benefit?

Do Rosetta belong to the group 'server prediction' or 'human expert prediction'? The latter must be with computer assisted, of course.

A definition of what both these terms mean with regard to CLASP7 might be useful. Thanks!

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Regards,
Bob P.

Today (Friday) we have closed accepting server predictions for the first
target, T0283.

What should be done with T0283 WUs that are still on our machines?

I'm with Robert on this one... should we be aborting the unfinished 283s??

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Questions? Try the Wiki!
Take a look inside my brain

Today (Friday) we have closed accepting server predictions for the first
target, T0283.

What should be done with T0283 WUs that are still on our machines?

I'm with Robert on this one... should we be aborting the unfinished 283s??

I do not think you should abort these work units. There are opportunities for amending the server submissions after the cut off date for original submissions. In addition, the data is useful in other ways.

But Dr. Baker or Rhiju will post something on this soon, so I would recommend you wait on any aborts.

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Moderator9
ROSETTA@home FAQ
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Today (Friday) we have closed accepting server predictions for the first
target, T0283.

What should be done with T0283 WUs that are still on our machines?

I'm with Robert on this one... should we be aborting the unfinished 283s??

Sorry about the confusion!! each target has two deadlines. the first is for completely automated web servers, which is two days after the target is released. we do have a web server (robetta) but it is not using rosetta@home. the second deadline, which is for the more intensive computing and human assisted calculations depends on the target, and generally is around 3 weeks--these are the calculations running on rosetta@home. at the CASP7 web site you can see the list of targets and their submission deadlines. bottom line--don't abort any work units!!

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Today (Friday) we have closed accepting server predictions for the first
target, T0283.

What should be done with T0283 WUs that are still on our machines?

Also. should the deadlines for the CASP7 WUs be just a bit ealier than the real deadlines.

Back to the T0283. One of them I still got running has a deadline of May 27. But if the CASP deadline was May 12, will those results be of any benefit?

Do Rosetta belong to the group 'server prediction' or 'human expert prediction'? If the latter, than it should be called 'human expert prediction (computer assisted)'.

rosetta@home is in the second category; see my previous post

---

Today (Friday) we have closed accepting server predictions for the first
target, T0283.

What should be done with T0283 WUs that are still on our machines?

I'm with Robert on this one... should we be aborting the unfinished 283s??

Sorry about the confusion!! each target has two deadlines. the first is for completely automated web servers, which is two days after the target is released. we do have a web server (robetta) but it is not using rosetta@home. the second deadline, which is for the more intensive computing and human assisted calculations depends on the target, and generally is around 3 weeks--these are the calculations running on rosetta@home. at the CASP7 web site you can see the list of targets and their submission deadlines. bottom line--don't abort any work units!!

Roger that. Crunching on. :)

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...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! :)

---

Regards,
Bob P.

...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, you can assume that a message will be posted here. You may want to subscribe to this thread, as the plan is to post any information or request for user intervention to be posted there.

---

Moderator9
ROSETTA@home FAQ
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...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.

---

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

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!

---

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.

---

Moderator9
ROSETTA@home FAQ
Moderator Contact

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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With the permission of the user community, I would like to take the top few posts from this thread, and start a new thread with them. This one is getting very long now, and in consideration of the modem users, I think we should start chapter 2. I will cross link the threads to each other. I would also like to rename them to "DISCUSSION of Rosetta@home Journal" followed by (1), (2), (3) and so on.

Are there any objections?

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

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Moderator9
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