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Message 18023 - Posted: 7 Jun 2006, 22:42:14 UTC

Q: How can I add a picture to my user ID when I post messages.

A: It is called an \"Avatar\". And how to set it up is described in the BOINC Wiki.
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Message 18024 - Posted: 7 Jun 2006, 22:44:56 UTC

Q: How do I get one of those nifty boxes showing my BOINC credits at the bottom of my message posts?
A: There are some statistics sites that will generate these for you. You set up a profile there, identify your projects, and then modify your signiture line. The details are described in this thread.
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Message 18025 - Posted: 7 Jun 2006, 22:49:45 UTC

Q: All of the work units are for CASP. What will Rosetta do after CASP7 is over?

A: CASP is a contest of sorts. Different teams of scientists take on the challenge of offering their best predictions for a set of proteins where their structural shape is not yet known. It is a blind prediction. In other words noone yet knows the \"correct\" answer. But we will soon. And at that point the answers can be \"graded\" if you will, and the most accurate prediction can be determined. CASP runs every 2 years, and is basically a test to demonstrait the scientific advancements of the past 2 years.

But once CASP is over, Rosetta will go back to developing the science further, and coding new techniques and approaches to attacking the protein mystery. They will test their techniques against known protein structures and continue to refine the models and methods of producing them.
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Message 18026 - Posted: 7 Jun 2006, 23:01:29 UTC

Q: What\'s the big deal? What difference does it make what shape a protein takes?

A: If that protein is from the avian flu virus, or HIV, or linked to Alzheimer\'s or anthrax, then knowing the shape it takes will give researchers the information they need to design new proteins that can attack these diseases.

Present methods of discovering the true 3D structure take many weeks and 10s of thousands of dollars each to complete. That wouldn\'t be so bad if you just needed information about the 4 proteins I mentioned, but in order to design a cure, you need a technique of determining the shape computationally. This is because you can\'t experimentally try enough combinations to find an appropriate treatment. Also, there are literally 100s of thousands of proteins that serve various functions in the human body. So spending a few weeks on each one is not possible.

When Rosetta\'s models are refined to the point that they are highly accurate, a whole new field of biological science will be born. It will make it possible to design vaccines to treat emerging threats such as avian flu, and to do so in time to vaccinate people before the virus has mutated and effects humans. It means a detailed understanding of enzyme messagers in the body will become possible and this will help eliminate undesirable side effects from drug therapies.

It IS a big deal. And you are helping by crunching more Rosetta.
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Message 18029 - Posted: 7 Jun 2006, 23:25:32 UTC

Q: How do I create, or join a team?

A: Be sure you login to the Rosetta website. The team area of the Rosetta website has the details. You can create a new team there, or search for the team you want to join. Once you click on the team and view it\'s members, you will see a link after the phrase \"Join this team\".

Teams are specific to each BOINC project. So if you want a team for both Rosetta and SETI for example, you would have to follow the corresponding steps for each project.
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Message 18106 - Posted: 8 Jun 2006, 11:12:42 UTC
Last modified: 8 Jun 2006, 11:22:18 UTC

Q: How do you add links to a post on the message boards?

A: When you create a post and are in the entry screen, you will see a link to the left for \"Use BBCode tags to format your text\". BBCode tags are bulletin board tags. So, for example if I wanted to give you a direct link for the BBCode information, I would enter the following:

[ url=http://boinc.bakerlab.org/rosetta/bbcode.php ]BBCode tags[ /url ]


and it would look like this:
BBCode tags

When in doubt, find a post that has a link, click on the \"reply to this post\" link, and the link the person used will be shown with the BBCodes. You can then copy from that, click the bulletin board link at the top again to exit that reply, and then paste the link where you\'d like, not fogetting to modify the actual http:// address that it points to.
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Message 18107 - Posted: 8 Jun 2006, 11:23:47 UTC

Q: How can I add a link to a specific thread elsewhere in the forums?

A: It\'s always helpful if you add links to the specific post you are talking about. First review the information on adding links. Then, note that when you view a post, every person\'s message has a unique message ID. For example the message ID of how to add links is 18106. You can right click on that \"Message 18106\" text, and select \"Copy Shortcut\". Then you can paste that URL into your BBCode tags. This will link the reader of your post directly to the specific message within the thread that you copied.

For example:
to link to the specific message the URL in my BBCode tag would be
http://boinc.bakerlab.org/rosetta/forum_reply.php?thread=1755#18106

to link to the whole thread
http://boinc.bakerlab.org/rosetta/forum_reply.php?thread=1755
(keep in mind threads have a way of changing over time, and every has their own preference for viewing either the oldest posts first or the newest, so don\'t assume that the post that WAS on \"top\" will be when someone else follows your link).
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Message 18108 - Posted: 8 Jun 2006, 11:29:01 UTC

Q: How can I revise the text of my post after I\'ve posted it?

A: If you display the thread your post is in, there will be a link beside your post\'s message ID number that says \"Edit this post\". This only displays for you, based on the user ID you login to the Rosetta website with. Click the link, make your changes, and then click OK. You can only edit for an hour after you post, to review it right away and assure your BBCodes came out properly etc.

You may note some people note their changes with text like:
[edit] ...and it tastes great too! [/edit]

This isn\'t an actual BBCode tag, it is just a courtesy to other users that may have read their original post before revision, so they can see that they are not losing their mind about what the post USED to say.
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Message 18109 - Posted: 8 Jun 2006, 11:37:11 UTC
Last modified: 8 Jun 2006, 11:51:43 UTC

Q: How to include an image in my post?

A: If you want to include your statistics, then see the Q&A about showing the nifty box.

If you want to post an icon, such as a depressed smile:
You can go to a website that has lists of smilies and copy their BBCode tags into your post. In this case the smilies website is actually serving the image for you.

But how do I post my own image? Perhaps a captured screen image.

You must first get that image to a website. Perhaps one where you share photos. Upload the image there. Then display the albumn it is in and right click on the link to display the image and select \"copy as link\". (Sometimes it\'s difficult to get the link right, if you are using a photo sharing website, then you might \"share this photo\" with yourself to EMail yourself the link. Then you paste that into an [ img] tag. For example:
[ img]http://www.geocities.com/feet1st/DrDB.jpg[ /img]
will show this way when you remove the spaces:



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Message 18122 - Posted: 8 Jun 2006, 13:22:28 UTC - in response to Message 18109.  
Last modified: 8 Jun 2006, 13:25:00 UTC

Q: How to include an image in my post?

A: If you want to include your statistics, then see the Q&A about showing the nifty box.

If you want to post an icon, such as a depressed smile:
You can go to a website that has lists of smilies and copy their BBCode tags into your post. In this case the smilies website is actually serving the image for you.

But how do I post my own image? Perhaps a captured screen image.

You must first get that image to a website. Perhaps one where you share photos. Upload the image there. Then display the albumn it is in and right click on the link to display the image and select \"copy as link\". (Sometimes it\'s difficult to get the link right, if you are using a photo sharing website, then you might \"share this photo\" with yourself to EMail yourself the link. Then you paste that into an [ img] tag. For example:
[ img]http://www.geocities.com/feet1st/DrDB.jpg[ /img]
will show this way when you remove the spaces:



Posted screen captures (which should be discouraged due to the number of modem users) should be reduced in size (dimensions) prior to posting. If this is not done, it forces the width of the forum thread to be displayed to the width of the image. This then requires people to scroll right and left to read the text of other posts. Many people find this to be quite annoying. When other users report this as an issue, the image may be deleted to solve the problem. In some cases people have used wide images in their signatures, and this resulted in the deletions of all of their posts to solve the problem.
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Message 18126 - Posted: 8 Jun 2006, 14:10:26 UTC - in response to Message 18109.  

Q: How to include an image without making the message boards cumbersome to use?[/b]

A: You can always include a url tag that links to an image, rather than an img tag. Upload the image to a website, \"copy as link\", and then use a url tag as described here. And it would be helpful if you would indentify in your description what the image displays so people can decide if they need to click the link and go look at it.

This way it doesn\'t distort the width of the message board, and doesn\'t require any additional bandwidth unless the viewer of the post decides to click on the link. And even then they may view it, understand what you are illustraiting and then chose not to click on it in future views of the post.
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Message 18139 - Posted: 8 Jun 2006, 15:53:19 UTC

Q: I\'d like to do something more than just run my computer for Rosetta, how might I help?

A: The main thing the project continues to need is more computing power. But whether it is yours, or one of your friend\'s is all the same to the numbers. So the main way you can help is to enlist the help of your friends and coworkers.

Some ideas on how to bring more people to the project are posted. Add to the list if you have some other ideas on how we can all bring in more computing power.

If you encounter resistence, please post a description in this thread so others can possibly point you to existing answers to resolve concerns that you run in to.

There are some other ways you might help. The main one being to help post answers to people\'s questions on the message boards. If you feel you understand the problem being reported or have seen it mentioned before or know the resolution, go ahead and post a reply. Others, perhaps with more experience than you presently have, will see your reply and correct it or elaborate on it if they feel it will further help the person asking the question. But, otherwise, the sooner a good reply is posted the better. And if a good reply is already posted, it saves time for the moderators and other reviewers of the boards.
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Message 18814 - Posted: 16 Jun 2006, 16:19:23 UTC

Q: Can I perform new application downloads on a scheduled basis?

A: If you subscribe to the Rosetta Application Version Release Log thread, and see an update that a new application version is available, it will mean a larger download for your next work units, because it must download the new application version in addition to the work units.

You can perform this download of the application in advance if you like. This might help you perform the download when your schedule allows, or during off-peak time or during times of day when internet access is free or surcharges.

To do this, go to the Rosetta downloads website, and the applications are down at the bottom. Download the application for your operating system (Windows, Linux, or one of the Apple versions) and \"Save\" it in the Project\'s folder. For example, on Windows, by default, this would be the folder called:
C:\\Program Files\\BOINC\\projects\\boinc.bakerlab.org_rosetta

Now the next time you update to the project and more work units are requested, the new application version will already be found and this will save you from downloading it later. You can confirm this by looking at your messages tab. You will see a message such as the following when those first work units of the new version are download:
File rosetta_5.22_windows_intelx86.exe exists already, skipping download

If you keep a larger cache of work ready to process, this will help you have time to determine a new application version is released and perform the above steps. The way to do this is to increase the setting in your General Preferences for \"Connect to network about every... days\". Once you make such a change, you must update to the project for the change to take effect.

If your network access is limited you might also want to increase your runtime preference on work units.

Caution: don\'t increase both the runtime preference and the cache size at the same time. Instead, change the runtime Rosetta preference first and then run for a week before changing the \"connect to network\" General preference. This will give BOINC some time to learn the work units will take longer to run before changing the cache size. And this will help assure you get the correct amount of work to fill the cache, reflecting the new runtime preference.


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Message 19808 - Posted: 5 Jul 2006, 22:42:57 UTC - in response to Message 18814.  

Q: Can I perform new application downloads on a scheduled basis?

A: There was a bad link in the original post:
...go to the Rosetta downloads website, and the applications are down at the bottom.

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Message 28191 - Posted: 22 Sep 2006, 17:38:34 UTC

Do the plots on the top predictions page show all energy structures predicted or only the best decoy from each WU? It seems like they should show all decoys but it just dawned on me that this isn\'t necessarily true.
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Message 28222 - Posted: 22 Sep 2006, 22:34:40 UTC

I\'m not positive, but I\'m pretty sure that the points plotted represent each completed model. That\'s part of the point of the chart is the number of poor models we had to crunch to find a few gems. I mean you could view the work of 1,000 machines as all being the same \"work unit\" because they all originated from the same protein and the same searching approach. Just different random number seed. This solidifys my thought that it\'s showing all completed models. Not just the best model of each machine\'s crunching.
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Message 30487 - Posted: 2 Nov 2006, 5:14:03 UTC

Just getting past being a newbie so I guess this belongs here.
I have 2 chasis I want to put new motherboards in. Normally I won\'t be using these for work, just when I want to do testing. So I was wondering about what people think about my options.
Basically it seems to come down to 3 choices.
1. High end dual core systems (too expensive for part time use)
2. Something like I have today (celeron 3.2ghz with .5 GB of memory)
3. Low end, a motherboard that uses the old 133Mhz memories that are dirt cheap.

opinions?

Also thinking about adding another .5GB of memory to my current machine. Right now when I run Rosetta (without other apps), I am not memory constrained. What effect will adding memory have WRT Rosetta? Will I get WUs that can use the memory? Or will the memory be idle?

Thanks,

Al

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Message 30488 - Posted: 2 Nov 2006, 5:24:44 UTC

That depends on your budget. More current dual core processors like the AMD64 X2 4400 cost roughly $250 add a MOBO with built in video $60. Add case, PSU, HD, Ram, and OS and you can get a decent system for under 700. Subtract 40 for your existing case, and if you use linux subtract another 100.

512 Mram is generally enough for most boinc projects (per core).
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Message 30501 - Posted: 2 Nov 2006, 12:35:19 UTC - in response to Message 30488.  

That depends on your budget. More current dual core processors like the AMD64 X2 4400 cost roughly $250 add a MOBO with built in video $60. Add case, PSU, HD, Ram, and OS and you can get a decent system for under 700. Subtract 40 for your existing case, and if you use linux subtract another 100.

512 Mram is generally enough for most boinc projects (per core).


Thanks, that\'s some good input. Suspect I\'ll wait will after christmas and look for a dual core w 1GB of memory. Are Rosetta apps designed to utilize the extra cpu/memory, or is it a function of the OS (XP in my case)? When I was more active in coding we needed to let the compiler know what functions could be run in a multi-CPU environment. Or am I showing my age? ;)

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Message 30502 - Posted: 2 Nov 2006, 12:47:38 UTC - in response to Message 30501.  

That depends on your budget. More current dual core processors like the AMD64 X2 4400 cost roughly $250 add a MOBO with built in video $60. Add case, PSU, HD, Ram, and OS and you can get a decent system for under 700. Subtract 40 for your existing case, and if you use linux subtract another 100.

512 Mram is generally enough for most boinc projects (per core).


Thanks, that\'s some good input. Suspect I\'ll wait will after christmas and look for a dual core w 1GB of memory. Are Rosetta apps designed to utilize the extra cpu/memory, or is it a function of the OS (XP in my case)? When I was more active in coding we needed to let the compiler know what functions could be run in a multi-CPU environment. Or am I showing my age? ;)


Rosetta just runs one copy of itself per CPU (core) [that you allow it to use - if you got more than one, you can set it so that it only uses X number of the processor(cores)].

Memory usage is added per copy of Rosetta you run, so 2 x 512MB if you have a dual core CPU, 4 x 512MB if you have a quad-core or two dual cores, etc, etc.

The OS will sort out running the two Rosetta on the available cores, so Rosetta don\'t need to know about that fact.

And in fact, BOINC is the part that figures out that you\'ve got two CPU\'s and have that you need to run two copies of Rosetta to fully load the system. Rosetta just knows about itself in each of the copies, and there\'s no co-operation or communication between them.

--
Mats
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