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Message 9620 - Posted 23 Jan 2006 7:00:57 UTC
Last modified: 12 May 2006 3:06:27 UTC

END OF FAQs


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Message 9685 - Posted 24 Jan 2006 6:27:21 UTC - in response to Message ID 9620.
Last modified: 16 May 2006 1:23:46 UTC

Q. Is there an anonymous reporting system for obscene or threatening forum posts?


Yes, the function can be used as follows-

In the bottom left corner of every post in the forums there is a series of small icons (buttons) that can be used to "Rate" each post. The last of these buttons is a small red box with an "X" in it that looks like this - .

If you click on that box, you will be provided with a reporting form. Fill in the requested information and submit the form by clicking on the "OK" button.

This will generate a report to a Forum Moderator who will then review the report and take appropriate action.

{NOTE: No user specific information relating to the reporting user is provided to the Moderator when using this function.}


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Message 9713 - Posted 24 Jan 2006 16:05:19 UTC
Last modified: 16 May 2006 1:25:49 UTC

Q. Can I contact the forum moderators directly by e-mail?

At the request of the user community a method of contacting forum Moderators "off forum" has been established. David Baker has decided to leave it up to the Moderators as to how they wish to handle the matter. Based on this decision, each Moderator will decide for themselves if they wish to provide "off forum" communications to the user community. To that end, Moderators may establish an email account that will allow off line contact, but they are not required to do so.
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However, before sending mail to a Moderator account, it must be clearly understood that the address of the senders account will be revealed to the Moderator. In addition, certain kinds of requests that are sent to the project team, may be forwarded to these Moderator accounts to be handled as a moderation function, and when that happens, it will be necessary for the project to provide contact information to the Moderator so the issue can be addressed.

To send to a private message to a moderator account, send an e-mail to

Moderator9 - Rosettamod9 at yahoo dot com (replace the "at" and the "dot" with the correct symbols to properly format the address)

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Message 9763 - Posted 25 Jan 2006 4:27:24 UTC
Last modified: 16 May 2006 1:27:40 UTC

Q. Do the forum Moderators have access to my personal information?

Typically volunteer Moderators do NOT have access to personal information such as e-mail addresses and other information related to users. However Moderators who are also project administrators DO have access to this information.

In the event that a user contacts a Moderator using any form of e-mail, the users return e-mail address will become available to the Moderator. Not all Moderators have provided a means for users to contact them directly. The few that have, may have questions referred to them by the Project Team, and in those cases the Moderator would be provided the necessary contact information to assist the user.

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Message 9765 - Posted 25 Jan 2006 4:50:56 UTC
Last modified: 16 May 2006 1:28:51 UTC

Q. Who are the Forum Moderators and what is their function?

The Rosetta@home project uses a mixture of full time project team members and volunteers from the user community to Monitor posting activity in the forums. These individuals are called "Moderators" and whenever they post a message, that titles will appear beneath their user ID. In some cases the actual user ID will be "Moderator" followed by a number (IE. Moderator1, Moderator2, etc). These IDs are provided to the volunteer Moderators so that there is no confusion when they act in an official capacity.

Moderators are responsible for organizing the forums, assisting users with problems and issues, removal of unacceptable materials and postings, and maintaining the decorum of exchanges between users by enforcing the forums rules.

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Message 9768 - Posted 25 Jan 2006 5:54:21 UTC
Last modified: 16 May 2006 2:00:34 UTC

Q. Can I appeal a Moderators decision to delete my posts?

Yes. But Moderators have a great deal of individual latitude with regard to the actions they take to preserve a proper forum environment. If you feel the action taken was not appropriate, you should first appeal directly to the Moderator who first took action in your case.

If you still feel that the action was not appropriate in your situation, you can appeal directly to the project team using the links from the Rosetta@home home page.

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Message 10279 - Posted 31 Jan 2006 20:01:15 UTC
Last modified: 16 May 2006 2:02:09 UTC

Q. I received an e-mail telling me that one of my forum posts has been moved/deleted. What does this mean?

Deletions
Generally speaking receipt of an email indicating that a post has been removed is an indication that the post was determined to be unacceptable for one or more of the following reasons.

    1) It contained profane or obscene language, or quoted a post that contained such language.
    2) It contained obscene imagery, or quoted a post that contained such images.
    3) It contained a threat against another user or the project or quoted a post that contained such threats.
    4) It was of such a personally inflammatory or insulting nature that it incited a series of rebuttals of the nature of personal attacks ("flaming").

(in some cases these violations of forum policy may result in the deletion of the entire thread)

Moving of posts
If one of your posts has been moved, this would generally indicate that there is nothing wrong with the content of the post itself, but that it was perhaps off topic for the thread where it was posted, and was moved to another thread appropriate to the topic. In some cases, a particular thread may be available for a specific purpose. One example would be the gathering of information related to error data, These threads are generally not open for discussions but instead are intended for posting very specific kinds of data. In this case posts that do not provide the type of information sought will be moved to a thread for the discussion of the issue.

For a discussion of the criteria that might be used to evaluate the appropriateness of posts and their removal see this thread

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Message 10281 - Posted 31 Jan 2006 20:05:29 UTC
Last modified: 16 May 2006 2:05:44 UTC

Q. Are there any rules at Rosetta@home for using the forums?

The Rosetta@home forums are provided as a place for open exchange of ideas within the Rosetta user community. Users are encouraged to post their ideas, exchange information with one another, assist each other, and bring issues to the attention of the Rosetta Project team.

The Rosetta user community is international, and open to people from all walks of life. For this reason communications between users in the forums is expected to be polite, and suitable for all possible audiences. Threats and profanity are unacceptable, as are language and images of an obscene nature. So called "flaming" is not acceptable.

This concept has been distilled into a simple statement displayed each time a user posts in any of the Rosetta@home forums.

"Don't use obscene language or images, and don't threaten other participants; otherwise we may delete your messages."

Forum Moderators have the authority to determine if a posting falls within the acceptable guidelines established for use of the forum. If in the estimation of a Moderator a particular post or group of posts is unacceptable, they can act to move or delete such posts. Usually when this occurs the author of the post will be notified by e-mail of the action taken.

Moderators also have thee responsibility of keeping the forums organized so that the project team and the larger user community can locate information of interest to them. As a result, on occasion Moderators may start new threads for discussion or gathering of information, move posts that are not topically correct for a particular thread, or highlight a thread topic by anchoring it at the top of the forum thread list.

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Message 10343 - Posted 2 Feb 2006 14:55:48 UTC
Last modified: 16 May 2006 2:09:00 UTC

Q Exited with zero status but no 'finished' file?

A. This is a BOINC problem, it's harmless, just ignore it.

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Message 10345 - Posted 2 Feb 2006 15:03:47 UTC
Last modified: 16 May 2006 2:10:59 UTC

Q. Master file fetch failed?

There are two possibilities when you get this error,

A1. This means the Rosetta@Home 's server is down. Give it a few hours and then try again.

A2. Your internet connectivity may not be working properly. Try to browse the Rosetta@Home web site, and have a look at the server status page, the link is on the Rosetta@Home home page.

To fix your internet connectivity (generally shut down everything including your router (if you have one), modem, DHCP server (if you have one) etc... start every thing up in the correct order and and try again).

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Message 10347 - Posted 2 Feb 2006 15:13:22 UTC
Last modified: 16 May 2006 2:13:55 UTC

Q. Why am I getting a 'Reason: Access Violation (0xc0000005) error'? *

A. An error occurred somewhere on the computer, it could have been BOINC or Rosetta@Home or any programme that your computer was doing at the time. This is not a Rosetta@Home specific error, as far as I am aware it happens, on occasion, in all of the BOINC applications. Keep Rosetta@Home in memory and ignore this problem if it's not getting out of hand.

If you get one of these errors you can report it Here

Thanks to hugothehermit for his work on this FAQ.

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Message 10349 - Posted 2 Feb 2006 15:15:39 UTC
Last modified: 16 May 2006 2:21:26 UTC

Q. What does the error "Maximum Time Exceeded" mean?

A. The Maximum time exceed error occurs when a work unit requires more time to complete processing than was anticipated by the project at the time the work unit was created by the project server. The maximum time allocated for a particular work unit is measured in CPU cycles. If the system requires more that the predetermined number of cycles to complete processing then the BOINC client software is designed to abort the processing and notify the user that the maximum time for the work unit was exceeded. This feature is designed into the BOIC software to prevent a work unit from entering into an endless loop where it might continue processing indefinitely.

There are very few things that can be done on the users computer that will reduce or eliminate maximum time exceeded errors. The project team will have to make an adjustment to the work units before they are sent out to permanently solve the problem. If you are seeing these errors frequently, you should notify the project by posting a message on the appropriate forum, so they know that an adjustment is required.

If you get a Max Time Exceeded Error, you should report it Here

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Message 10352 - Posted 2 Feb 2006 15:20:40 UTC
Last modified: 16 May 2006 2:22:52 UTC

Rosetta generates an error telling me that I must free xxx.x MB. I don't understand, there's gigs of free space on this system....

Example from message log -

Fri 20 Jan 2006 10:05:32 AM EST|rosetta@home|Message from server: No work sent
Fri 20 Jan 2006 10:05:32 AM EST|rosetta@home|Message from server: (there was work but you don't have enough disk space allocated)
Fri 20 Jan 2006 10:05:32 AM EST|rosetta@home|Message from server: No disk space (YOU must free xxx.x MB before BOINC gets space). Review preferences for minimum disk free space allowed.
Fri 20 Jan 2006 10:05:32 AM EST|rosetta@home|No work from project


Your problem is not the actual hard drive space on your disk, but the amount of space that is allowed to be used on your hard drive for Rosetta, which is specified by your online account settings.

-Go to the Rosetta home-page, then click on the link to 'Your Account' under returning participants heading.

-Once logged in, go to edit general preferences, and once there, adjust the settings for the disk and memory usage.

-Once you save the settings, open Boinc Manager, and on the 'Projects' tab, click the update button. This will load your saved preferences onto the PC, and this should solve the issue.

In the prefs it is not really clear what all these settings actually do. A few things are not intuitive about the space settings.

1) First the "use no more than xxx GB" applies to BOINC space used. Everything for BOINC not just rosetta or rosetta slot space. You are unlikely to violate this one with any normal size queue.

2) "Leave at least xxx.xx GB" refers to the total space that must be left on the disk before BOINC will be allowed to run the project but it is not a BOINC space use number. If loading anything from a project would violate that value BOINC will not allow that to happen. You can also violate it outside of BOINC and stop BOINC from running.

3) "Use no more than xx%" refers to the total FREE space on the disk no matter what is using it, it is not a BOINC space use number. But if loading something for BOINC would violate it BOINC will not allow that to happen. And it too can be violated outside of BOINC and stop BOINC from running.

So in practical terms, these all play against each other as "OR' factors not "AND" factors. But you can force an "AND" condition. Violate any one or more of them in any combination and BOINC will give you the not enough space space error.

If BOINC would use more than XXX GB of space (1) it will not run (or load work). OR if you have less than XXX.XX GB of total free space (2) on the disk if BOINC added new data BOINC will not run. OR If your total use of a disks FREE space exceeds xx% (3) no matter how much is BOINC or anything else then BOINC will not run.

Part of the problem is the difference between these values as calculated by the system. To most people 1Kb is 1000B, but to the disk system it is 1024B. So the system thinks it has more data that the person reading the numbers unless you take that difference into account. And for BOINC there is no gray area on this. Go over the parameter by so much as a single byte and it will fail.

So the first setting at 100GB should work fine, you can set this to a value bigger than your total disk space and it will usually not hurt anything. Set parameter 2 to something small like .001GB. For the third setting try something like 80% or less. you will have to balance these numbers for your system until you find what works.

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Message 10353 - Posted 2 Feb 2006 15:23:15 UTC
Last modified: 17 May 2006 1:06:29 UTC

My results page says I had a "Client Error", will I get credit for the time my computer worked on this work unit?

Yes. The Rosetta project runs a process every night that awards credits for work units that are reported with client errors or fail for any reason. These usually appear in your "Results" list as "Client error" and show that no credit was granted.

However, if you click on the actual "Result Details" link on the left in the listing, the awarded credits will be shown as credits granted at the bottom of the Result Details. The credit is added to your total credit count as well, just as normal credit awards would be. The Maximum credit award for errors is 300 points, but typically the awards match the claimed credit for the work unit.

You must allow at least 24 hours for the credit award process to run after the work unit is reported back to the server.

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Message 10354 - Posted 2 Feb 2006 15:29:20 UTC
Last modified: 4 Mar 2006 4:50:11 UTC

Q. Why do I have Work Units assigned to me that I don't have?

A. This seems to be caused by BOINC and the Rosetta@Home server losing the ability to communicate properly, and it can safely be ignored.

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Message 10356 - Posted 2 Feb 2006 15:32:21 UTC
Last modified: 16 May 2006 2:35:24 UTC

Q. Why is it reported that I have more computers than I actually do? / How do I merge my computers?

A. When you detach and then re-attach to the same project, BOINC assumes that it's a different computer, You can merge these computers so they are one again, Your computers click on the computer you would like merge click Merge this computer (down the bottom of the page).

NOTE: This function is temporarily disabled. It will be functional with the next server software upgrade.

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Message 10357 - Posted 2 Feb 2006 15:37:00 UTC
Last modified: 4 Mar 2006 4:49:27 UTC

Q. Why can't I get new Work Units from Rosetta@Home ?

A. If your computer is doing more than one science application (Seti@Home and Rosetta@Home for example) BOINC decides how much work you can have so that that the Work Unit deadlines are not reached. Either allow BOINC to do this or if you are more interested in one of the science applications you can change the resource share Rosetta@Home preferences ->Edit Rosetta@Home preferences and change the resource share. Alternatively you can suspend the other application(s), BOINC Manager -> Projects (tab) click on the application you would like to suspend and either click on the Suspend button or the No New Work button (to allow BOINC to finish the Work Units it has on hand but not to get new ones), on the left hand side.

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Message 10359 - Posted 2 Feb 2006 19:12:35 UTC
Last modified: 6 Mar 2006 0:26:09 UTC

Q. Should I use Hyper Threading?

A. Yes, it gets you a small gain over not using it. If you are very low on memory and don't want to use more than x CPUs then Log in (if your not already) -> Edit Preferences (down the bottom) -> On multiprocessors, use at most N CPUs.

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Message 10360 - Posted 2 Feb 2006 19:15:19 UTC
Last modified: 4 Mar 2006 4:48:44 UTC

Q. Can I move work from one computer to another?

A. The short answer is, yes it is possible. BUT, the true answer is that moving work from one machine to another is neither recommended or supported by the Rosetta@home project team. One major problem with moving the work between systems occurs when the work is finished and ready to upload. The entire BOINC system is designed such that the computer that originally downloaded a work unit must also return the work unit. So systems statistics, credit claims and many other elements of the BOINC system would no longer operate as they were designed.

In addition, some work is actually customized to some degree based on the processor to which it will be send. Even if the work is successfully downloaded to a machine, moved to another machine and processed, and then moved back such that it is returned by the correct machine, the process could still adversely affect the results that are returned in unpredictable ways.

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Message 10365 - Posted 2 Feb 2006 20:28:57 UTC
Last modified: 4 Mar 2006 4:48:24 UTC

Q. Why am I getting an error every time BOINC runs a benchmark?*


A. Update your BOINC version to 5.2.13 or higher as it no longer removes applications from memory when doing a benchmark.


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Message 10366 - Posted 2 Feb 2006 20:32:30 UTC
Last modified: 28 Apr 2006 3:24:43 UTC

Q. Why is my computer stuck on 1% ? *


A. This is a known BOINC and Rosetta@Home issue, Starting with Rosetta Version 5.06, a number of new features were added to Rosetta to prevent this problem. The first of these is a new "WatchDog" thread. The watchdog monitors progress made on the workunit, and if it appears to be "Hung" it will terminate processing and return any results produced. Work Units terminated in this way ARE awarded credits in a separate process run on the server data base on Friday of each week. In addition the automatic terminate feature is enguaged if a work unit exceess 4 times the user selectable "Time" setting.

If however you feel there is a problem there are a couple of things you can do about it, they should be done in the order here:

First make certain the work unit is actually stuck or hung =

Depending on how the Wu is configured, some may have over 1,500,000 steps in the first model and still not reach 1%. This can take over 5 hours of CPU time. There are a few even larger ones.

Between checkpoints (Saves to disk, which occur when the percent complete changes) the time to completion in the BOINC work tab, will increase instead of decreasing. This is because BOINC calculates the time to completion based on the number of CPU seconds that have passed and the percent complete. So if the CPU time rises and the percent remains the same, the time to completion will increase. When the running Wu checkpoints, the percent complete will suddenly jump up, and the time to completion will suddenly drop. Then the entire process will repeat until the next checkpoint, or the WUs finishes.

The time settings in your preferences have a lot to do with what the jumps will be as the WU progresses. If you have your time set to say 2 hours, and one of the large Wus comes along, it is possible for it to run for over five hours showing 1%, and suddenly jump to 100% and finish. If the Wu is one of the smaller ones, running with the same settings, it might only run 5 min or less, doing about 35,000 steps for each model, and the percent will jump to something like 5% and keep rising until it hits about 1 hour and 55 mins and finishes.

So look at the graphic display and see what is going on every so often on these longer ones.

The project has said they are working on "leveling" all of this out so there is not so much variation. Those Wu should start appearing soon.

If the Work Unit is really Hung -


    1. suspend the Work Unit, BOINC Manager -> Work (tab) -> click on the Work Unit click the Suspend button (on the left hand side) then Resume button, wait for the computer to re-start the Work Unit (it will need to finish the new Work Unit it started, if it had another available) and see if it's still stuck, give it about 20min.
    2. Shutdown BOINC, restart BOINC see if the Work Unit is still stuck, give it about 20min.
    3. Reboot your computer. See if the Work Unit is still stuck, give it about 20min.
    4. Abort the Work Unit, BOINC Manager -> Work (tab) -> click on the Work Unit that's stuck click the Abort button (on the left hand side).



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Message 10368 - Posted 2 Feb 2006 20:35:53 UTC
Last modified: 4 Mar 2006 4:47:47 UTC

Q. Why am I getting an error every time BOINC switches tasks?

In some cases interrupting the work in progress can cause the work unit to abort with a client error. Interruptions can include pausing or suspending either the Rosetta application, or the running work unit, shutting down BOINC, restarting your system during work unit processing, and updating a project. Updating a project may cause an application switch to occur at a time prior to when it normally would occur.

The way to prevent this error is to set your preferences located in your account information to "Leave applications in memory during application switching = YES".

This problem is a know issue for the Rosetta project and work is being done to adjust the system so this will not be necessary at some future date.


{Note: This setting will keep applications for all projects to which your system is attached in memory. On systems with marginal amounts of memory this may case system performance problems.}

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Message 10369 - Posted 2 Feb 2006 20:42:00 UTC
Last modified: 5 Mar 2006 0:46:14 UTC

Q. What is project "Swapping" and how should I have it set?

Project swapping occurs if a particular computer is doing work for more than one project. This would be the case if you were running Rosetta@home, and any other BOINC project such as Protein Predictor@home, Einstein@home, or Climate predictor to name a few. The BOINC software installed on your machine regulates how much of your computers time is devoted to the work for each projects to which your machine is attached. When it is time for one project to allow another to project some computer time, the currently running application will stop and the one requiring processing time will start. This is call an "application swap".

There is an option in the user preferences to either keep applications (like Rosetta) that are inactive due to application swapping loaded in the memory of the computer while they are inactive, or remove them from memory. The default setting for this preference is to remove applications from memory during swaps.

For most projects this preference can be set either way. However, due to the way in which Rosetta stores data as processing proceeds, much processing time can be lost if the applications are not kept in memory during applications swaps. Moreover, when the BOINC software activates Rosetta to continue processing a partially processed work unit, an error can result during the reloading process. For this reason you should set your preferences to keep applications in memory during swaps.

Once set, this preference will apply to all active projects on your machine. For this reason you may see some performance issues on your system, such as slower operation, or the inability to load and run memory intensive programs. This would include things like video and image editing software, some audio and streaming video functions, Games, and multi media presentation packages.

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Message 10371 - Posted 2 Feb 2006 20:49:42 UTC
Last modified: 4 Mar 2006 4:47:11 UTC

Q. I am not connected to the internet all the time and Rosetta@home runs out of work, What can I do?

You should determine how often you will be connected to the internet, and adjust your project preferences to the number of days (up to 10) that you plan to be disconnected. By doing this your system will try to download enough work to keep the system busy for the period of time between connections.

There is an issue related to the loading of large queues of work beyond 7 days. In some cases the project may require processed data in a short time frame. When this happens the reporting deadlines for the work units may be less than 10 days in length. If you time between connections to the internet, is longer than the reporting deadlines for the work units on your system, you will not be able to return the results before the deadline and you will not receive credit for the processing you have done. Moreover this will have an adverse effect on the science project itself.

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Message 10373 - Posted 2 Feb 2006 20:54:59 UTC
Last modified: 4 Mar 2006 4:46:52 UTC

Q. How do I set Rosetta@Home to stay in memory?

A. To change your preferences to leave Rosetta@Home in memory, General Preferences Log in (if your not already) -> Edit Preferences (down the bottom) -> Leave applications in memory while preempted? Check yes and click the update preferences button, also remember to update BOINC. BOINC Manager and select "Projects"(tab) , select "Rosetta@home", and click "Update"

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Message 10374 - Posted 2 Feb 2006 20:56:29 UTC
Last modified: 28 Apr 2006 3:37:30 UTC

Why should I set BOINC to keep application in Memory?

This is less of a problem now that "Checkpointing" is more frequent for the Rosetta application.

However, If the application is removed from memory during an application swap, it will loose the work performed since the last checkpoint. In the case of Rosetta the checkpoints occur each time the percentage advances. If you do not keep the application in memory, and you set the swap interval to less than the time it takes your machine to reach a checkpoint, the work units can appear to be 'hung".

This is why the recommended configuration is to set "Keep applications in memory" to "YES". As an added protection, it is also recommended to set a value of nominally 120 min between application swaps. Either of these settings alone has been shown to reduce the problem, but they can be used togeather for better results

It should be noted that ALL BOINC projects suffer from loss of CPU cycles if the applications are not kept in memory. Any work that is not saved at a checkpoint before a swap, is lost when a swap occurs. On applications like Rosetta and Climate prediction this loss is significant (15 to 30 min). On projects like Predictor, SETI and Einstein, the loss is less but it is still there (usually 60 seconds using the default setting for writing to disk). People who wish to squeeze every cycle out of their machine, usually keep applications in memory for this reason.

It is important to note that the memory we are talking about is not actual RAM but in fact is virtual memory (on disk), so the actual impact of this is not that significant. In addition you can adjust how much memory is used by the application in this regard.


Question submitted by:
Dimitris Hatzopoulos
Team:
Greece United

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Message 10375 - Posted 2 Feb 2006 21:05:14 UTC
Last modified: 5 Mar 2006 0:44:29 UTC

How do I set the adjustable Work Unit time parameter in my Preferences ? What should I set it to ?

This parameter is adjusted by going to your "Account Page". On the Account page, there is a link to "View or edit Rosetta@home preferences". If you clink on the link to "Edit Rosetta@home preferences", you will find a Pull Down menu called "Target CPU run time". If you do not change this setting, all of your Rosetta@home Work Units will run in approximately 8 hours. This time will vary slightly but should be fairly consistent for a particular machine.

If you pull the menu down, you will be presented with options for times ranging from 2 hours to 4 days. Select the option that best meets the needs of your system. The project would prefer you select times from 8 hours and up to reduce the load on the servers, but this setting is totally up to you. If you have bandwidth concerns a longer setting will help reduce the bandwidth required to run Rosetta. It is best to allow your work queue to drain completely before making the adjustment and then allow Rosetta to resume work and download fresh work units under the new setting. This will allow the BOINC client to accommodate the new setting for project time management purposes.

Once you have made the change you must either update the project from the BOINC manager manually or wait for the system to contact the server in the regular course of processing before the change will take effect.

While the Rosetta application will attempt to respect this setting and process work units within the time selected, there will be some variation. This is because the software must adjust in increments of one complete model run. For some work units one model may represent a relatively short amount of processing time, on the order of a few minuets. For other Work unit types a single model can take a significant amount of time, on the order of a few hours. Each work unit will always complete at least one model before reporting results. In practical terms this means that if you have selected a short time setting, some work units may take significantly more time to process than your setting.

{EDIT: The following combines the information from a number of FAQs to present a more complete picture of how the "Time" setting works overall}

All of the new format WUs are generally physically (number of bits) the same size. The time factor tells the system how long you would "like" your system to work on a single WU creating different models as it goes. Based on the benchmarks done for that class of WU when they were created, the server knows how many models can be run for that WU in the time you asked for. In every case the WU will run at least one model no matter what you set the time to be. In any case your computer will be told how many models to run before returning the result as a part of the data that comes with the work unit. For small proteins this could be 30 models in 4 hours, for large proteins it might only be 1. In some cases it might take 9 hours to run a single model, and your system will spent 9 hours on the WU no matter what your time setting is, because all WUs run at least 1 model.

You can judge for your self if the protein you are working on is large or small by looking at the graphic. If there are a lot of "joints' in the protein, long strings, and it looks complex, it is large. Obviously small would be the opposite of that.

From a user stats point of view each WU represents a single result when it is turned in. The longer it runs the more credit it will claim. But from a science point of view each "model" represents a single result so each of your turned in results can represent anywhere from 1 - 100+ science results. That is why the default time is set to 8 hours (more science per WU). In most cases this will return between 1 and about 100 results depending on protein size. The faster the system the more models it can run in the alloted time. Because the models differ in size there is no way to calculate the number of credits per model. It is possible to make an estimate of credits per hour per system. The work unit itself has no bearing on this at all.

All of this means simply this. The project used to be based on having each WU produce a specified number of models for each protein run, no matter how long that took. say 60 models per WU. Now the system is set up to run for a certain length of time, no matter how many protein models that might produce per Work Unit, but it will always complete at least one model for each WU no matter how long that takes.

Now this can lead people to think they have a WU stuck when they don't. Depending on how the Wu is configured, some may have over 1,750,000 steps in the first model and still not reach 1%. This can take over 5 hours of CPU time. There are a few even larger ones.

Between checkpoints (Saves to disk, which occur when the percent complete changes) the time to completion in the BOINC work tab, will increase instead of decreasing. This is because BOINC calculates the time to completion based on the number of CPU seconds that have passed and the percent complete. So if the CPU time rises and the percent remains the same, the time to completion will increase. When the running Wu checkpoints, the percent complete will suddenly jump up, and the time to completion will suddenly drop. Then the entire process will repeat until the next checkpoint, or the WUs finishes.

The time settings in your preferences have a lot to do with what the jumps in percent complete will be as the WU progresses. If you have your time set to say 2 hours, and one of the large WUs comes along, it is possible for it to run for well over five hours showing 1%, and suddenly jump all at once to 100% and finish. If the Wu is one of the smaller ones, running with the same settings, it might only run 5 min or less, doing about 35,000 steps for each model, and the percent will jump to something like 5% and keep rising until it hits about 1 hour and 55 mins and finishes. By the way, that first 1% is the set up at the begining of the WU run. You can see that in the grafic display if you have it up when a WU first starts.

As a result of this behavior a number of people have asked how many checkpoint occur during the processing of a Work Unit?

There is no set number of checkpoints for a Rosetta Work Unit. All Rosetta Work Units will checkpoint when ever they complete a model. This will advance the percent complete counter in the BOINC manager. There is no connection between any particular percent complete and a checkpoint event because the length of a single model is variable. The persent complete is calculated using the length of time it takes to run a single model, divided into the run time set in the user preferences. So if you have a Work Unit set to run for 2 hours, and a single model will take 1 hour, the first checkpoint will occur at 50% complete. If the same Work Unit is set to run for 4 hours, the first checkpoint will occur at 25% complete. It is possible to have a Work Unit that only has sufficient time to run a single model, in which case the first checkpoint will occur at 100% complete, and the Work Unit will be ready to report.

So look at the graphic display and see what is going on every so often on these longer ones.

The project has said they are working on "leveling" all of this out so there is not so much variation. Those WUs should start appearing soon.

So now we get to the problem of forcing the system into a work deficit when you use the new Rosetta time feature.

BOINC does not know anything about any of what I just described. A lot of people who are used to the normal way BOINC controls the loading of the work Queue still have their systems set to a long connect time to get more WUs. But for the new Rosetta system this can cause you trouble, and it is unnecessary.

BOINC will ask for a certain amount of work (number of seconds of work) based on how much time you have left in your work queue. But it does not know that you can download what seems like a very small number of rosetta WUs, that in fact are large in terms of time because you have set the time for rosetta to a large number.

BOINC just downloads the WUs and suddenly they are taking a lot longer than BOINC expected. Now to be fair BOINC will adjust a little for this as it runs. And for short connection times (small work queues) it will adjust fairly well over a day or so, because it will figure out that the WUs are all about the same size and it will adjust the DCF to make things work But this does take a period of time where you should not make adjustments to the system so it can stabilize.

So, For Rosetta it might be best for farmers and people on low bandwidth, or modems who run only rosetta to readjust the system for a small queue. Say .1 days. Then set the time factor for a long runtime say 2-4 days. This will allow BOINC to think it should just get a few seconds of work to keep your system going, but it is really getting one or two WUs that will run for 2-4 days each. BOINC of course will try to connect about every 2 hours or so all day long, but if you are not connected (turn off network activity) or turn off your modem, it will just hold the results until you do connect. BOINC will take care of holding the results until then.

Now if you are on a constant internet connection with these same settings, BOINC will be connecting nominally the same 10 times a day, but it will just keep crunching rosetta for the same 2-4 days per WU until they are done. If you are running other projects under these conditions, they will be feeding and reporting all day long on the shorter queue using the standard BOINC reporting and queueing system.

So basically you have to play with the two parameters of Times to connect per day (queue size) and run length of the WU (Rosetta time setting) until you find the balance that fits your particular system requirements.

One caution of people who pay connection time by the packet is that if your connect time is set to a short length, it will send a few packet every time it tries to connect, but this should not be a large number. For people interested in local credit monitoring with the BOINC GUI stats tab, the stats will be more current.

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Message 10376 - Posted 2 Feb 2006 21:06:37 UTC
Last modified: 16 May 2006 2:39:14 UTC

A. I want to change my association with a team but how will this affect my credits?

Teams are part of the competitive aspect of running BOINC projects. All users of Rosetta@Home are free to create teams, joins teams, move from team to team, or run Rosetta as individuals. While the project may recognize the efforts of teams and their contributions to the proejct, Rosetta does not endorse any particular teem. Association with a team will not affect your individual credit count or score in any way, but you should be aware of the following factors related to teams.


    1) When a member joins a team, he will show up under "team management" to the founder, but will not show up on the "active members" list until they are granted credit for a result.
    2) Previous user credits are not applied to the teams total when he joins a team, except for CPDN sponsored projects (see wiki definition).
    3) When a member leaves a team voluntarily, the credit he earned for the team stays with the team.
    4) User credit is not affected by either joining or leaving a team.
    5) If the founder removes a member then the members credit will be removed from the team score.
    6) When a user quits a team, he's immediately removed from the founders "management functions screen". This means he'll no longer have access to your email addy, and can't kick you from the team.
    7) Team founders have access to all team members email addresses
    8) It can take up to a day for the username to be removed from the "active members" list after he leaves a team.
    9) The line "Members(with and without credit" didn't add members who had no credit when I tested this.
    10) The team founder shows on the "Active Members" list whether he has returned results or not while on the team.
    11) The credit shown on the team statistics view http://boinc.bakerlab.org/rosetta/team_display.php?teamid=xxx is a members overall credit score, not necesseraly what they have contributed towards the team.



BOINC-wiki says the following about "team credit":

"The accumulation of Credit in your own account will never change regardless of membership on a Team. You will always accumulate the appropriate Granted Credit if you are on a team, you will accumulate the same Credit as if you are not on a Team.

When you join a Team, you join it with a zero balance. After you have joined a Team, the Granted Credit is added to your Total Credit balance and to the Team's Total Credit balance.

When you leave the Team, the Credit you earned while a member of that Team will stay with that Team. You do not take it with you to add to another Team's Total Credit balance; except for Climateprediction.net which uses the old SETI@Home Classic rule where the Team's Total Credit is a simple summation of the Total Credit earned by the Participants that are a member of that Team.


There is a special "Team Recruitment Thread" located in the Rosetta Cafe where teams may post information about their team and how you can reach them.


Information for this FAQ was provided by-
mmciastro - BOINC Synergy
Rollo
FluffyChicken - mauisun.org

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Message 10377 - Posted 2 Feb 2006 21:10:06 UTC
Last modified: 9 May 2006 15:19:41 UTC

How do I set the adjustable Work Unit time parameter in my Preferences ? What should I set it to ?

This parameter is adjusted by going to your "Account Page". On the Account page, there is a link to "View or edit Rosetta@home preferences". If you clink on the link to "Edit Rosetta@home preferences", you will find a Pull Down menu called "Target CPU run time". If you do not change this setting, all of your Rosetta@home Work Units will run in approximately 8 hours. This time will vary slightly but should be fairly consistent for a particular machine.

If you pull the menu down, you will be presented with options for times ranging from 2 hours to 4 days. Select the option that best meets the needs of your system. The project would prefer you select times from 8 hours and up to reduce the load on the servers, but this setting is totally up to you. If you have bandwidth concerns a longer setting will help reduce the bandwidth required to run Rosetta. It is best to allow your work queue to drain completely before making the adjustment and then allow Rosetta to resume work and download fresh work units under the new setting. This will allow the BOINC client to accommodate the new setting for project time management purposes.

Once you have made the change you must either update the project from the BOINC manager manually or wait for the system to contact the server in the regular course of processing before the change will take effect.

While the Rosetta application will attempt to respect this setting and process work units within the time selected, there will be some variation. This is because the software must adjust in increments of one complete model run. For some work units one model may represent a relatively short amount of processing time, on the order of a few minuets. For other Work unit types a single model can take a significant amount of time, on the order of a few hours. Each work unit will always complete at least one model before reporting results. In practical terms this means that if you have selected a short time setting, some work units may take significantly more time to process than your setting.

{EDIT: The following combines the information from a number of FAQs to present a more complete picture of how the "Time" setting works overall}

All of the new format WUs are generally physically (number of bits) the same size. The time factor tells the system how long you would "like" your system to work on a single WU creating different models as it goes. Based on the benchmarks done for that class of WU when they were created, the server knows how many models can be run for that WU in the time you asked for. In every case the WU will run at least one model no matter what you set the time to be. In any case your computer will be told how many models to run before returning the result as a part of the data that comes with the work unit. For small proteins this could be 30 models in 4 hours, for large proteins it might only be 1. In some cases it might take 9 hours to run a single model, and your system will spent 9 hours on the WU no matter what your time setting is, because all WUs run at least 1 model.

You can judge for your self if the protein you are working on is large or small by looking at the graphic. If there are a lot of "joints' in the protein, long strings, and it looks complex, it is large. Obviously small would be the opposite of that.

From a user stats point of view each WU represents a single result when it is turned in. The longer it runs the more credit it will claim. But from a science point of view each "model" represents a single result so each of your turned in results can represent anywhere from 1 - 100+ science results. That is why the default time is set to 8 hours (more science per WU). In most cases this will return between 1 and about 100 results depending on protein size. The faster the system the more models it can run in the alloted time. Because the models differ in size there is no way to calculate the number of credits per model. It is possible to make an estimate of credits per hour per system. The work unit itself has no bearing on this at all.

All of this means simply this. The project used to be based on having each WU produce a specified number of models for each protein run, no matter how long that took. say 60 models per WU. Now the system is set up to run for a certain length of time, no matter how many protein models that might produce per Work Unit, but it will always complete at least one model for each WU no matter how long that takes.

Now this can lead people to think they have a WU stuck when they don't. Depending on how the Wu is configured, some may have over 1,750,000 steps in the first model and still not reach 1%. This can take over 5 hours of CPU time. There are a few even larger ones.

Between checkpoints (Saves to disk, which occur when the percent complete changes) the time to completion in the BOINC work tab, will increase instead of decreasing. This is because BOINC calculates the time to completion based on the number of CPU seconds that have passed and the percent complete. So if the CPU time rises and the percent remains the same, the time to completion will increase. When the running Wu checkpoints, the percent complete will suddenly jump up, and the time to completion will suddenly drop. Then the entire process will repeat until the next checkpoint, or the WUs finishes.

The time settings in your preferences have a lot to do with what the jumps in percent complete will be as the WU progresses. If you have your time set to say 2 hours, and one of the large WUs comes along, it is possible for it to run for well over five hours showing 1%, and suddenly jump all at once to 100% and finish. If the Wu is one of the smaller ones, running with the same settings, it might only run 5 min or less, doing about 35,000 steps for each model, and the percent will jump to something like 5% and keep rising until it hits about 1 hour and 55 mins and finishes. By the way, that first 1% is the set up at the begining of the WU run. You can see that in the grafic display if you have it up when a WU first starts.

As a result of this behavior a number of people have asked how many checkpoint occur during the processing of a Work Unit?

There is no set number of checkpoints for a Rosetta Work Unit. All Rosetta Work Units will checkpoint when ever they complete a model. This will advance the percent complete counter in the BOINC manager. There is no connection between any particular percent complete and a checkpoint event because the length of a single model is variable. The persent complete is calculated using the length of time it takes to run a single model, divided into the run time set in the user preferences. So if you have a Work Unit set to run for 2 hours, and a single model will take 1 hour, the first checkpoint will occur at 50% complete. If the same Work Unit is set to run for 4 hours, the first checkpoint will occur at 25% complete. It is possible to have a Work Unit that only has sufficient time to run a single model, in which case the first checkpoint will occur at 100% complete, and the Work Unit will be ready to report.

So look at the graphic display and see what is going on every so often on these longer ones.

The project has said they are working on "leveling" all of this out so there is not so much variation. Those WUs should start appearing soon.

So now we get to the problem of forcing the system into a work deficit when you use the new Rosetta time feature.

BOINC does not know anything about any of what I just described. A lot of people who are used to the normal way BOINC controls the loading of the work Queue still have their systems set to a long connect time to get more WUs. But for the new Rosetta system this can cause you trouble, and it is unnecessary.

BOINC will ask for a certain amount of work (number of seconds of work) based on how much time you have left in your work queue. But it does not know that you can download what seems like a very small number of rosetta WUs, that in fact are large in terms of time because you have set the time for rosetta to a large number.

BOINC just downloads the WUs and suddenly they are taking a lot longer than BOINC expected. Now to be fair BOINC will adjust a little for this as it runs. And for short connection times (small work queues) it will adjust fairly well over a day or so, because it will figure out that the WUs are all about the same size and it will adjust the DCF to make things work But this does take a period of time where you should not make adjustments to the system so it can stabilize.

So, For Rosetta it might be best for farmers and people on low bandwidth, or modems who run only rosetta to readjust the system for a small queue. Say .1 days. Then set the time factor for a long runtime say 2-4 days. This will allow BOINC to think it should just get a few seconds of work to keep your system going, but it is really getting one or two WUs that will run for 2-4 days each. BOINC of course will try to connect about every 2 hours or so all day long, but if you are not connected (turn off network activity) or turn off your modem, it will just hold the results until you do connect. BOINC will take care of holding the results until then.

Now if you are on a constant internet connection with these same settings, BOINC will be connecting nominally the same 10 times a day, but it will just keep crunching rosetta for the same 2-4 days per WU until they are done. If you are running other projects under these conditions, they will be feeding and reporting all day long on the shorter queue using the standard BOINC reporting and queueing system.

So basically you have to play with the two parameters of Times to connect per day (queue size) and run length of the WU (Rosetta time setting) until you find the balance that fits your particular system requirements.

One caution of people who pay connection time by the packet is that if your connect time is set to a short length, it will send a few packet every time it tries to connect, but this should not be a large number. For people interested in local credit monitoring with the BOINC GUI stats tab, the stats will be more current.

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Message 10382 - Posted 2 Feb 2006 21:51:33 UTC
Last modified: 9 May 2006 15:11:39 UTC

I lost my password and can't log back into my BOINC account?

Your Rosetta account information will only work for the Rosetta project. If you wish to attach to another project, you must use the account information for that project.

There is no way to recover passwords.

You can reattach to an existing Rosetta project account using your project key. You can obtain the project key from the original e-mail sent to you when you set up your Rosetta account. If you have lost this e-mail you can recover the account key from your system in the following way -

1) Inside the BOINC directory on your system you will find a file named "account_boinc.bakerlab.org_rosetta.xml"

2) Using a text editor such as wordpad open the file named "account_boinc.bakerlab.org_rosetta.xml"

3) On about the third line of the file you will see something like "<authenticator>56Ca362e06cafffc701fg7s1fxxxxxxx</authenticator>"

4) Highlight the portion of this line that I have highlighted in color above.

5) Using the copy function (Windows = control-C, Mac = apple-C) copy that text, and close the text editor.

6) Using your browser navigate back to the login page of the project and instead of using the password login, use the account key login and "Paste" (Windows = Control-V, Mac = apple-V) the account key in the account key field.

7) Click ok and that should log you back into the project.

This will work for any project assuming you have been attached to that project with your system and have simply logged out. Simply use the account file for that project in the instructions above instead of the Rosetta account file.

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Message 10908 - Posted 18 Feb 2006 22:02:04 UTC
Last modified: 9 May 2006 15:06:00 UTC

Q. I don't receive an E-mail? / My ISP is blocking my E-mail from Rosetta@Home?

A. This is usually caused by your ISP blocking the E-mail as spam, Even though you can join up without it I would suggest that you get a free E-mail account and use that, remembering that if you don't log on to these free E-mail accounts every so often then some of them will delete your account. I also as a general suggestion that I give to everybody (no inference that Rosetta@home could or would contribute to this should be taken) that you never use you ISP E-mail account for anything else than talking to your ISP as it's not funny being spammed on an account that you actually need.

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Message 10910 - Posted 18 Feb 2006 22:09:46 UTC
Last modified: 9 May 2006 15:04:23 UTC

Q. Which ports does Rosetta@Home need open?


A. Port 80 (http) is used for most communications with the project servers. Port 443 (https) is used if the password is being exchanged . Ports 1043 and 31416 are used for local control as well as for remote control of a BOINC client. 1043 is preferred and 31416 is a fall back. Unless you are RPC'ing over the Internet don't open 1043 and 31416 in your non-local firewall specifically for BOINC.

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Message 11192 - Posted 22 Feb 2006 5:34:15 UTC
Last modified: 27 May 2006 6:06:57 UTC

I am getting errors on some of my Work Units, What should I do ?

If ALL of your work units are getting errors, there may be something wrong with your BOINC set up. Read all the FAQs in this list to see if you can determine and fix the cause.

If you are only having a few errors during the normal course of running Rosetta, then you should look up the type of error under the BOINC "Message" tab, and report it on one of the following links in the Forum;


    For errors related to Rosetta Version 5.16 - Go Here (Part II)

    Retired threads
    For errors related to Rosetta Version 5.16 (part I)- Go Here
    For Errors related to Rosetta Version 5.13 - Go Here
    For Errors related to Rosetta Version 5.12 - Go Here
    For Errors related to Rosetta Version 5.07 - Go Here
    For Errors related to Rosetta Version 5.06 - Go Here
    For Errors related to Rosetta Version 5.01 or earlier- Go here



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Message 11662 - Posted 5 Mar 2006 0:54:57 UTC
Last modified: 9 May 2006 14:56:04 UTC

Q. What is the URL of Rosetta@Home?

A. http://boinc.bakerlab.org/rosetta

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gothehermit for his work on this FAQ.
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Message 11663 - Posted 5 Mar 2006 0:57:00 UTC
Last modified: 13 May 2006 0:09:53 UTC

Q. Where can I find statistical information about Rosetta@home?

There are many sources of statistics for BOINC projects. One of the most widely used is BOINCStats..

The information for Rosetta can be found at the following links -



You can also obtain your own user statistics from this site.

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Message 11666 - Posted 5 Mar 2006 0:57:01 UTC
Last modified: 9 May 2006 14:53:06 UTC

Q. What is RALPH@home?

RALPH is an acronym which stands for Rosetta ALPHa test project. RALPH@home is the official alpha test project for Rosetta@home. New application versions, work units, and updates in general will be tested here before being used for production. The goal for RALPH@home is to improve Rosetta@home.

Please consider the following before deciding to join:


    1) Since this project is a testing environment, applications and work units may be unstable at times.
    2) Credits and other competitive statistics do not mean anything in this test project. Credits may be lost due to instabilities and may be reset at any time for testing.
    3) There will not be a continual flow of work units. Work units will be issued only when necessary for testing.
    4) We urge participants to not abort work units during testing.
    5) Please set the resource share low for this project compared to other production projects in your RALPH@home preferences.


Please join us in our efforts over at RALPH@Home!

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Message 11667 - Posted 5 Mar 2006 0:59:01 UTC
Last modified: 9 May 2006 14:50:18 UTC

Q. Is Rosetta@Home concentrating on a particular disease?

A. Dr David Baker "My research group is involved both in fundamental methods development research and in trying to fight disease more directly...

Malaria: We are part of a collaborative project headed by Austin Burt at Imperial College in London that is one of the Gates Foundation "Grand Challenge Projects in Global Health". Malaria is caused by a parasite that spends part of its life cycle inside the mosquito, and is passed along to humans by mosquito bites. The idea behind the project is to make mosquitos resistant to the parasite by eliminating genes required in the mosquito for the parasite to live. Our part of the project is to use our computer based design methods (rosetta) to engineer new enzymes that will specifically target and inactivate these genes.

Anthrax: We are helping a research group at Harvard build models of anthrax toxin that should contribute to the development of treatments. You can read the abstract of a paper describing some of this work at this link

HIV: One of the reasons that HIV is such a deadly virus is that it has evolved to trick the immune system. We are collaborating with researchers in Seattle and at the NIH to try to develop a vaccine for HIV. Our role in this project is central--we are using rosetta to design small proteins that display the small number of critical regions of the HIV coat protein in a way that the immune system can easily recognize and generate antibodies to. Our goal is to create small stable protein vaccines that can be made very cheaply and shipped all over the world "

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Thanks to hugothehermit for his work on this FAQ.
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Message 11669 - Posted 5 Mar 2006 0:59:04 UTC
Last modified: 9 May 2006 14:43:05 UTC

Q. Where can I learn more about Rosetta@home from the point of view of the project leaders ?


A. Dr David Baker has established a "Rosetta@home journal" Where he will add regular commentary about the project, its progress and many other "insider" aspects of Rosetta@home.

While it is the intent that the journal thread itself be kept clear of posts from users, there is a second thread for Comments and Questions related to the postings in the journal. If you are interested in the researchers perspective on the progress of Rosetta, and asking a question, please take a look as this unique feature of Rosetta@home.

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Message 11671 - Posted 5 Mar 2006 0:59:06 UTC
Last modified: 9 May 2006 14:41:04 UTC

Q. What is the difference between Rosetta@Home and Folding@Home or Predictor@home ?

A. Dr David Baker "The goal of Folding@home is to determine how proteins fold given the sequence of the protein, and to apply this knowledge to study protein folding related diseases."

David Kim "Our project is similar to Predictor@home, in that we are trying to improve our methods by conducting research that is only possible with the computing power that a grid computing project can provide."

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Message 14820 - Posted 28 Apr 2006 3:44:47 UTC
Last modified: 16 May 2006 18:42:51 UTC

Q. Is there a list of information links for Rosetta@home all in one place?

Please explore our website freely, but the following links will provide a detailed understanding of Rosetta@home and make your time here more enjoyable.


* NOTE: Threads listed above with an "*" are reserved for posting by project team members only. All other threads are open to topical user posts.
** NOTE: RALPH@home is NOT a production environment. Software testing is not for everyone. Please read the information provided here and here BEFORE attaching.

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Message 16353 - Posted 16 May 2006 2:31:16 UTC - in response to Message ID 10356.
Last modified: 27 May 2006 6:08:47 UTC

Index of Frequently Asked Questions (FAQ) for Rosetta@Home
(Click on the links below for answers)

Questions about rosetta@home


Problems getting started


Project preferences Settings


Running Rossetta@home


Common Error messages


Forums



For additional information or more detailed answers to your questions about Rosseta@home, the BOINC client software or other BOINC projects visit the Unofficial BOINC WIKI.

For information about some of the teams working on the Rosetta project vist the Teams thread in the Rosetta Cafe.

Be advised: Some of the links posted on this website may take you other websites. The listing of those links on does not constitute an endorsement of any of those sites, the content of the sites or the teams represented in the listings, by the Rosetta@home project, the University of Washington, or their researchers and staff. Your use of these offsite links is at your own risk, the Rosetta@home project and the University of Washington are not responsible for off site content or management of any information they may gather from your connection to their site

----
Thanks to Bill Michael for his work on R@H FAQs
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