Using BOINC in Nebula to Advance UW Rosetta Research
How can Nebula users advance UW research?
Nebula users can help to advance the goals of a successful UW research team by allowing them access to idle central processing unit (CPU) time on their computers. The UW administration believes this is a great way to support research done at the UW, as well as a new and effective way to leverage the power of Nebula workstations.
What are BOINC and Rosetta?
Berkeley Open Infrastructure for Network Computing (BOINC) is a program that lets you donate idle computer time to science projects. Nebula now has available a version of BOINC configured to donate your computer's extra central processing unit (CPU) cycles to the UW-sponsored ROSETTA@home project. Rosetta is a biomedical project to determine the 3-dimensional shapes of proteins in research that ultimately could lead to cures for major human diseases.
Why is this research effort important?
Dr. David Baker and his colleagues believe they could unlock the mysteries of structural biology by being able to better predict and design macromolecular structures and interactions. Associate Professor Baker, a Hughes Medical Institute investigator in the Department of Biochemistry, says “All of biology and medicine are being understood in molecular terms—how the body works, what goes on with diseases, how pathogens work.” Understanding this would allow scientists to design better drugs and treatments for major diseases such as AIDS and malaria and invent enzymes that could catalyze novel chemical reactions, allowing, for example, development of new methods for detoxifying poisonous substances in the environment.
Predicting how a protein folds or designing new protein molecules for medicine and industry are two of the “big questions” that researchers in computational molecular biology are seeking to answer. Rosetta is a UW-designed suite of software tools that sorts through the possibilities to come up the right answers. As Baker and his team continue to work on the problem, one thing stands in their way: insufficient computing power. “For a long time, the problem was not having accurate descriptions of proteins and their interactions,” explains Baker. “But now the problem is that we don’t have enough computer power to run the simulations.”
For more information on the project, see:
- http://depts.washington.edu/ventures/Portfolio_Highlights/Rosetta.php
- http://boinc.bakerlab.org/rosetta/, including a message of welcome from Dr. Baker
- http://boinc.berkeley.edu/
What does the software setup look like?
The current default Nebula BOINC/Rosetta package:
- Is configured to only compute data for the UW's Rosetta Project
- Only runs from 6 P.M. to 7 A.M.
- Only runs after the system is idle for 20 minutes
- Uses a maximum of 60% of CPU (to keep heat and fan noise low)
- Writes to disk once every 10 minutes
- Uses the network once every two days
- Within the list of Rosetta user accounts defined at
the Rosetta site, uses a generic user account named
"Nebula" that is read only.
Also, by using the Activity tab in the BOINC manager ('B' in the tool tray) you can:
- Set the program to be able to run 24 hours a day on your computer if you want to increase your level of participation (idle time requirement and other resource parameters above will all still apply.)
- Disable the program on the PC if you decide the application isn't appropriate for your PC.
Advanced users can also reconfigure the package once it is installed and switch to a personal account they control and/or to provide computing cycles for other BOINC projects.
Does running this program create any problems?
There are no problems that we know of. The program has been set up so it will not slow down a computer, use significant electricity, or make noise by causing a computer’s fans to come on. Minor problems encountered years ago when the program began have been corrected. Individual computer users are in control of their machines and can permanently turn off the program any time they choose.
What changes will I notice when the program is running?
Changes that you will notice are minimal. There are no slowdowns, sounds, or interruptions. The program only runs after hours, when you have not used your computer for 10-20 minutes. When you return to using the machine, the program quickly gets out of the way. You will see two differences when the program is running on your computer:
- A small icon resembling a gold circle with 4 blue rays in the tray in lower right of the computer.
- A new screen saver. You can change the screen saver any time you like. If you don’t know how, you can ask Nebula support staff for help.
Once the BOINC program is installed by UW Technology, it runs automatically and you can just forget it. If you want more information about how BOINC is working, you can open it by right-clicking on the icon in the lower right corner and choosing Open BOINC Manager.
Can I see statistics that show my computer’s contribution?
Yes! You can see your own Nebula statistics plus your contribution to the University of Washington team's statistics. Both Rosetta and BOINC statistics are available.
Rosetta rankings are based on the number of work units done / day (rate of work).
- Rosetta stats for team University of Washington
http://boinc.bakerlab.org/rosetta/team_display.php?teamid=2612 - Rosetta stats for Nebula user
http://boinc.bakerlab.org/rosetta/show_user.php?userid=164960
BOINC statistics rank users based on TOTAL number of work units done (baseball fans will love these pages):
- BOINC stats for team University of Washington
http://www.boincstats.com/stats/team_graph.php?pr=rosetta&id=2612 - BOINC stats for Nebula user
http://www.boincstats.com/stats/user_graph.php?pr=rosetta&id=164960
This site shows both Nebula and UW rankings, as well as the fact that it’s computing 100% for the Rosetta project:
If you have questions about BOINC or Rosetta statistics, please see Rosetta@home at http://boinc.bakerlab.org/rosetta/
Should I leave my Nebula computer turned on all the time?
Yes. Your Nebula computer should always be left on so that updates can automatically be made and so the BOINC program can run. Although the UW administration is encouraging people to save energy by turning off their computers when they are not in use, this request does not apply to Nebula computers or anyone who wants to participate in the BOINC/Rosetta@home program.
Who can I contact if I have questions?
If you have questions about BOINC or how is is working on your compuer, please send email to nebula@u.washington.edu
