Can you help us make rosetta better?

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David Baker
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Message 575 - Posted: 27 Sep 2005, 5:39:15 UTC

All of your help is doing wonders for our research! We will be posting the results of the current round of computations in the top predictions section when David Kim returns from vacation in London early next week.

However, we obviously haven't been able to solve all of the problems that have come up. David and I were thinking that we might be able to enlist the coders among you to make things even better. We could make the rosetta c++ code available through this site, and you could help us resolve platform specific issues and maybe make the code even faster. For anybody who is seriously interested and becomes more involved, we have an annual rosetta developers meeting every summer in the washington cascades which is a lot of fun.

Would anybody be interested in seeing the code, and helping to track down problems? There would be a very simple click on license agreement which exists because the annual meeting and some of the code development is funded by licensing the software to industry, so we have to require that the code not be used for commercial purposes.

Also, are there suggestions of things we should add to the home page?

thanks again!

David

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Peter M. Nielsen

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Message 580 - Posted: 27 Sep 2005, 8:10:19 UTC - in response to Message 575.  

Would anybody be interested in seeing the code, and helping to track down problems? There would be a very simple click on license agreement which exists because the annual meeting and some of the code development is funded by licensing the software to industry, so we have to require that the code not be used for commercial purposes.

David

Hi David,

I would like to have a look on the code and help optimize it.

- Peter

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RDC

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Message 584 - Posted: 27 Sep 2005, 9:58:03 UTC - in response to Message 575.  
Last modified: 27 Sep 2005, 9:59:22 UTC

Also, are there suggestions of things we should add to the home page?



A few easy suggestions for additional features borrowed from other projects with links on the home page to the additional pages could include:


  • A technical news section to go into additional details of various project related issues.
  • A page that lists Rosetta@Home in the news where you can better archive the various articles regarding the project that are placed in the current news section.
  • A link to Paul D. Buck's BOINC-Wiki tutorial site at http://boinc-doc.net/boinc-wiki/ which is a fantastic resource for learning about how BOINC works and for answering many of the questions that come up that are BOINC related.





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Message 587 - Posted: 27 Sep 2005, 10:11:46 UTC
Last modified: 27 Sep 2005, 10:52:54 UTC

I'm a 20 year Fortran/C/C++ vet. I'll happily take a look at the Windows code line as I'm sure some of the "client errors" I've seen look to do with memory management, (possibly threading, but the client is not extensively MT'd). The thing is, how is the software line managed? Obviously, I don't want to fix my own client only to have the next version come down the pipe and replace my mods, there must be an overall versioning system/strategy. It would also be useful to know which compiler you are using to produce the production client, and if non-standard, what compiler options.

Feel free to e-mail me if you want.

I am not in the US, so the meeting is not really an option for me.
Wave upon wave of demented avengers march cheerfully out of obscurity into the dream.
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Message 588 - Posted: 27 Sep 2005, 10:33:46 UTC

as i am studying bioinformatics right now and worked as programmer and sysadmin in the industry before, i sure would be interested to look at the code, but as i done more .net development than c/c++ so far, i cannot promise any too big contributions in the near future.
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Profile Paul D. Buck

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Message 623 - Posted: 27 Sep 2005, 15:15:25 UTC - in response to Message 584.  


*A link to Paul D. Buck's BOINC-Wiki tutorial site at http://boinc-doc.net/boinc-wiki/ which is a fantastic resource for learning about how BOINC works and for answering many of the questions that come up that are BOINC related.

If you are waiting on permission to add a link, permission is granted.
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Message 632 - Posted: 27 Sep 2005, 15:56:06 UTC

I would like to see the server software updated to the latest version. That way my version 5 clients can connect.
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Message 715 - Posted: 28 Sep 2005, 19:52:58 UTC

Timestamps would be nice as well. :)
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Message 731 - Posted: 29 Sep 2005, 2:42:05 UTC
Last modified: 29 Sep 2005, 2:44:43 UTC

One thing I would like to see is how close each of my work units is to the target (in terms of score and RMSD) or to the best submitted prediction. This could perhaps be on a per user, per host or even per result basis, depending on the amount of computing power needed.

Another thing I'd like to see is how "my" finished predictions look. Of course, if that's going to take a lot of computing power, let the science come first.

Overall, I am very happy with this project - the amount of feedback, information and response from the project team is the best I've seen on any BOINC project I have participated in.

Keep up the good work and I'll keep my computers working for this interesting and worthwhile project.
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David Baker
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Message 733 - Posted: 29 Sep 2005, 3:31:42 UTC

We are planning to set something like this up soon after David K returns. When each calculation finishes, it will tell you the lowest energy structure it found, and you can compare to the lowest energy structure found overall which we will post on the web. Once the screenserver is up, the last image on the screen will be the lowest energy structure you found, or perhaps without the screensaver we can simply have the program generate a picture of this structure.
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Divide Overflow

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Message 737 - Posted: 29 Sep 2005, 3:55:19 UTC

Outstanding! Thanks David Baker, David Kim and the rest of the Rosetta@home team!
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Message 743 - Posted: 29 Sep 2005, 4:05:48 UTC - in response to Message 731.  
Last modified: 29 Sep 2005, 4:08:30 UTC

Another thing I'd like to see is how "my" finished predictions look. Of course, if that's going to take a lot of computing power, let the science come first.


Without getting into the mechanics, but rather as a momentary passing thought, this is perhaps something that could be passed off (at least in part) to the graphics card, hence leaving the CPU cycles saved for the science itself. Given that graphics cards for awhile (back to the GeForce 3, and I know the Radeon 9x00 series, and possibly the 8500) has shader support... The shaders in these more recent graphics cards include their own programming language of sorts with varying ability to be programmed to a degree. If it could be possible to offload some of the computing power that might be required to generate such images to the gfx card, and the CPU continues to process the actual science, then this would be less of an issue...
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Profile Paul D. Buck

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Message 781 - Posted: 29 Sep 2005, 20:05:15 UTC - in response to Message 733.  

We are planning to set something like this up soon after David K returns. When each calculation finishes, it will tell you the lowest energy structure it found, and you can compare to the lowest energy structure found overall which we will post on the web. Once the screenserver is up, the last image on the screen will be the lowest energy structure you found, or perhaps without the screensaver we can simply have the program generate a picture of this structure.

A "better" way to do this would be to allow the use of logging and external visulization. CPDN does this with their models. The old 3rd party apps for SETI@Home Classic also allowed you to do some of this ... in my case they were worthless as I had enough results that the screen turned pink so they were not so good from my standpoint.

What I am trying to say is that the ability for the participants to see the "reality" of their contribution is not well supported in most BOINC projects. I console myself with my "numbers" and a vague sense that I am somehow contributing, but, it is hard for me to say "Look what *I* did!", and have it be a positive statement ... :)

Not knowing as much as I would like about how this all hangs together for most projects I do have this question in my mind about just how valuable is what I am doing? For the project science I am pretty much at sea (being a retired sailor this is not as scary as it sounds) as my abiities are in another area. But, I do read Sci American, Discover Magazine, and occasional books (only 2-3 a year unfortunately, and usually biased towards non-bio subjects) ...

Since I can independently research BOINC and that *IS* in my area of expertise I usually confine myself there. Anyway, I guess I am rambling and I am not sure that I am succeeding in getting my point across ... does not supprise me, today is not going well ...sigh ...
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RDC

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Message 784 - Posted: 29 Sep 2005, 20:13:15 UTC - in response to Message 733.  

We are planning to set something like this up soon after David K returns. When each calculation finishes, it will tell you the lowest energy structure it found, and you can compare to the lowest energy structure found overall which we will post on the web. Once the screenserver is up, the last image on the screen will be the lowest energy structure you found, or perhaps without the screensaver we can simply have the program generate a picture of this structure.


BURP does similar when they issue work. When a completed WU is verified, an image of the rendering is available on the WU status page so you can see what you spent time on.

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Alex

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Message 1395 - Posted: 15 Oct 2005, 18:18:12 UTC

Perhaps have the visualisation bounce around in '3d' spinning and rotating and bouncing off the sides of the screen...

Might be a bit much to model the structure in the old fashioned stick and wooden ball model of molecules.


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Message boards : Number crunching : Can you help us make rosetta better?



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