Hello. I just got a BOINC client on my Kubuntu system. I'm not sure what to do with it. I would like to join Rosetta and the team, but I don't know how.

Nice to see another Kubuntu user!

First you have to go to http://boinc.bakerlab.org/rosetta/ and make an account. Then join the betterhumans.com team. (link on the first post of this thread)

Then, when you load up the boinc client, put http://boinc.bakerlab.org/rosetta/ as your server and sign in with your username.

That's it. It is remarkably easy. Folding@home and other projects turned out to be much harder to set up, in my opinion.
 

I'm not sure where am I suposed to sign up for an account. The site sugests that I first get the client (i have), and then sign up, but I can't find anything remotely looking like a sign-up form.

urchinstar47:

I'm not sure where am I suposed to sign up for an account. The site sugests that I first get the client (i have), and then sign up, but I can't find anything remotely looking like a sign-up form.

Hey, it's great the team still attracts new participants, with just six weeks to go to complete it's first year of existence (April 13th). I think you need to start up boincmgr and click on 'tools' and then 'account manager'. Things should be self-explanatory from there (the procedure was still somewhat different when I signed up...),

-H. 

It's still not working. I tried it, but when it tries to contact the server it just stops.

Are you using Kubuntu 64 bit? If so, you cannot use the BOINC 64 bit client program. The reason is that Rosetta servers don't allow 64 bit connections, unlike some other BOINC projects.

Although, when I tried to use the 64 bit client, it at least let me log in, but it wouldn't do any calculation.

If that isn't your problem, I don't know what to tell you.
 

I haven't ever had any trouble with sign up in Linux under Vector or Gentoo. However, most of my recent windows sign ups have hung when I tried to connect to the server. I had to manually kill the process. When I reopened boincmgr though the project was functional. If you don't mind typing up everything you've done to this point, I'd be happy to pursue this in the Rosetta forums until we get a solution.

Sorry you're having so much trouble, the project usually runs quite smoothly (shhh!).

Hoelderlin, I noticed you are spending some cycles on Ralph@home
and was wondering if I should do the same.  I don't know a lot
about what they test with Ralph before it goes into Rosetta and 
thought I might pick your brain on the subject.

AidanSonoda:

Hoelderlin, I noticed you are spending some cycles on Ralph@home and was wondering if I should do the same. I don't know a lot about what they test with Ralph before it goes into Rosetta and thought I might pick your brain on the subject.

Hi Aidan, well actually is is quite some time since I last contributed to Ralph. It seemed sort of pointless after a while, since, the way I am running the software (Linux background job, no graphics), I never had any errors that I could have reported on Ralph. The main purpose of Ralph is to catch errors in new software versions or new WUs early, before they are deployed on Rosetta. I think the idea to set up a testing server originated after a particularly bad incident in December 2005, when they sent out a batch of bad WUs that would crash immediately after downloading and then the whole Rosetta team went on holiday and could not be reached till January 1st. Also, I think they had not yet figured out at that time, how to cancel bad WU batches on the server. On top of that, the server settings were such that each failed WU was cycled through 10 computers before being cancelled. Well, it wasn't too bad for me, since I was on holiday myself and had my computer turned off. ;-) -H.

Check out this interesting new development at Rosetta@home: 

As of last week the Rosetta@home software which participants run on their computers also includes the functionality to fold and determine the 3D structure of RNA, in addition to its protein folding and design capabilities. Here is some background info on RNA posted by project scientist Rhiju Das in the Rosetta@home forum.

Readers of the Betterhumans news section will know that RNA plays an increasingly important roll in many areas of medical research that are close to the heart of the Betterhumans community:

RNA In Aging Research

Restoring Mitochondrial Function

Gene genius: Are scientists closing in on the holy grail?

Isn't it great to be able to participate in such cutting edge research by simply running a program on your computer while you don't need it ?

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hoelder1in.org

Now that I've finally given up on Linux, I should be able to run boinc properly.

I'm afraid I do not posses Hoelder1in's gift for words nor, indeed, even half of his infectious enthusiasm. But seeing as the team has recently reached 1 Million in total credit, I am compelled to offer congratulations to all! And also my heartfelt appreciation for everyone's effort and continued support thus far (client/application/OS conflicts not withstanding) for this important research.

For myself, being able to participate in a project doing real science with pertinent trans-humanist implications has been exceptionally rewarding. Thanks to Baker Lab's unparalleled level of interaction with the distributed computing community I've not only been able to donate processor cycles, but have been able to actually follow and appreciate the effects of the effort; substantially broadening my understanding of protein simulation science and computational biology as a whole in the process. That I have been able to do all this as part of a team that is now contributing in the top 3% of all Rosetta@home teams is truly remarkable.

Again, many thanks to all involved and here's hoping this project continues to gain support within our forward thinking community.

gnawing at the bars of our biological cage

I borrowed this from Nick Bostrom's Letter from Utopia which I think beautifully expresses the transhumanist world view as I see it.

It has been quite some time since I last posted in this thread, one of the reasons being that it also has been somewhat quiet over at Rosetta@home and in David Baker's Journal - which I think means they are busy getting on with their work, i.e., improving their protein folding methodology and designing proteins for medical (HIV vaccine, cancer related, etc.) and other (Carbon sequestration) applications. Here are some recent developments:

Rosetta: the game

There has been some progress with the Rosetta game which will allow users to interact with their computer and other players (!) to solve difficult protein folding problems. The above link is a first prototype with limited functionality. Also see the related Rosetta@home forum thread.

And just an hour ago David Baker posted this enthusiastic update in the Rosetta@home journal:

The results of the last few days of computations of Rosetta@home on your computers have been pretty amazing! In collaboration with a group at the NIH, we experimented with adding a very small amount of information about protein structures from nuclear magnetic resonance experiments to the rosetta structure prediction process. this information is fairly easily obtainable, and doesn't seem like it would have much effect, but the results show quite contrary--the models produced are extremely accurate! this has the potential to revolutionize how scientists determine protein 3D structures using NMR data. We would never have been able to test the idea, which came up in a phone conversation several months ago, without all of your contributions.

Today I spoke at the AidsVaccine07 meeting about our work on designing vaccines. Scientists who have been working on this very challenging problem for many years are I think excited about our approach as it is something that hasn't been tried before and makes sense conceptually. While we are still far from a vaccine, our initial results with collaborators at the NIH are promising. I spoke to a reporter from the Wall Street Journal after my talk, and I think she is interested in writing an article on rosetta@home and HIV vaccine design.

So let's keep on gnawing at those bars by running Rosetta@home on our computers...

Those who are new to Rosetta@home and consider to join will find lots of interesting material on the Rosetta@home website. Also have a look at the first post of this thread and follow the links (Simon: it seems the links to individual forum posts don't work anymore since the Betterhumans relaunch - they all point to the top of the respective forum page. Is there a way to fix this on your side ??).

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Hoelder1in

I just want to bump up this thread and encourage more BetterHumans.com readers/members to join our Rosetta team. It's really useful and cutting-edge stuff that the Baker lab is doing and they need all the CPU cycles they can get.

See this new article on Nature News discussing recent Rosetta@home result
published in the journal Nature. Here is David Baker's entry in the Rosatta@home journal (from August), commenting on this exciting work:

Congratulations! Your collective results on structure prediction, protein structure refinement, and solving the X-ray crystallographic phase problem with rosetta@home were just yesterday accepted for publication as a research article in the journal Nature which many of you can find at your local newstands. ... As those of you familar with scientific publishing are certainly aware, Nature is probably the most widely read journal in the natural sciences, and only one or two research articles are published in any issue (almost all are shorter letters), so your work will reach a very broad audience and have exceptionally wide impact.

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Hoelder1in