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11)
Message boards
:
Docking@Home Science
:
What is the main goal of Docking@home ?
(
Message 4557
)
Posted 3200 days ago by
j2satx
Thanks for explanation, very appreaciated.
It may be of interest to participants:
- how will be results used, their availability etc.
- can you summarize differences and similar aspect of Docking@Home and other life-science projects already running on BOINC (Rosetta, SIMAP, Tanpaku, Predictor).
With regards to our immediate scientific goal, our results will be used
to improve our protein-ligand docking methodology and to validate
our models. Developing and validating our methods will improve
the effectiveness of our application of protein-ligand docking to
real-world scientific problems and future collaborations with
experimentalists.
As a policy, I would prefer to not summarize what is done on other
life-science BOINC projects, and I would direct you all to look at
the pages explaining the science of each individual project for
specific details. However, because we are a new site, I will provide
a brief comparison of the general types of work that is done on
each site.
Rosetta@Home, Folding@Home, Tanpaku, and Predictor@Home all perform predictions about protein structure and protein folding.
Rosetta@Home also performs predictions for protein design and
protein-protein interactions. Dr. David Baker does an excellent job
of explaining the potential applications of protein folding, protein
design and protein-protein interactions to fighting disease here:
http://boinc.bakerlab.org/rosetta/rah_medical_relevance.php
SIMAP@Home uses sequence information to determine protein
similarities and protein domains. The prediction of domains is also
used for the functional annotation of proteins.
FightAIDS@Home performs protein-ligand docking predictions
using AutoDock. Their site specifically targets important HIV virus
proteins. They are currently investigating the structural basis for
the evolution of drug resistance in important HIV drug targets,
with the goal of identifying new drug-like small molecules that
are less susceptible to drug resistance.
Our site Docking@Home will also perform protein-ligand docking
predictions, but we are using a CHARMM based approach to
docking, not AutoDock. Our immediate scientific goals are to
improve and validate our docking methodology, and then to
apply it to specific scientific problems. In the initial stages of our
site, we will work on a large "test set" of protein-ligand complexes
that includes important protein drug targets for HIV/AIDS,
cancer and other diseases. During the initial stages of our
project we intend to use these examples because they are
of high interest to the biomedical community, well-studied,
and have lots of excellent experimental data that we can compare
to and validate our methods.
I urge all of you to participate in as many of the life-science BOINC
projects as possible as they each provide an important and unique
contribution to the rapidly progressing field of computational biology.
Thank You,
Dr. Roger S. Armen PhD
Please provide the same type of comments for POEM@home. Thank you.
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12)
Message boards
:
Number crunching
:
Not getting work
(
Message 4555
)
Posted 3200 days ago by
j2satx
Some puters running dry.
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13)
Message boards
:
Number crunching
:
Cobblestones
(
Message 4499
)
Posted 3225 days ago by
j2satx
I agree with the issue of modifying the software application. If the project starts allowing or promoting "optimized" apps without project testing and acceptance, then I will leave. I do not run any projects that allow optimized apps that are not under project control.
Hi j2satx,
Users cannot recompile our application, so, they cannot run an optimized version of it. About your resources, we haven't had any complain with your results, when we get invalid results we usually send an email to the owner of the host.
I'm sure j2satx was talking about optimized BOINC application, not your project app... Optimizing BOINC can indeed increase the amount of credits received when using the Benchmark criteria...
I was talking about the project app. I don't think it is possible for the project to have any control over the BOINC Client, but someone has to monitor that WUs are processed within reasonable boundaries, to prevent getting excessive credits if someone has modified the BOINC Client.
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14)
Message boards
:
Number crunching
:
Cobblestones
(
Message 4494
)
Posted 3225 days ago by
j2satx
Hi All, we are discussing about this item (increasing the credit), but we have some concerns. One is that if we increase the credit much, we will attract the kind of volunteers that do crazy things with the code or with the machines (sw modifications or overclocking) just to gain more credit, even to the price of returning us bad results. Although we are using a strategy to validate, we don't want to go back to the use of HR and things like that, because as you know it results in longer times to get the credit and discrepancies between the claimed credit of one user and other, which ultimately means less credit for many users.
We need to find a value for the credit that is beneficial for you but does not attract those users, as I just told you, we are trying to find a solution, so keep tuned, I'll let you know as soon as we have an agreement
I have reduced my resources by 50%, while you check to see if the results from my over-clocked computers are bad .
edit: I changed my mind...no need to have 50% of my computers giving you bad results. I have suspended all WUs until you verify that my computers are giving you good results.
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15)
Message boards
:
Number crunching
:
Cobblestones
(
Message 4493
)
Posted 3225 days ago by
j2satx
Hi All, we are discussing about this item (increasing the credit), but we have some concerns. One is that if we increase the credit much, we will attract the kind of volunteers that do crazy things with the code or with the machines (sw modifications or overclocking) just to gain more credit, even to the price of returning us bad results. Although we are using a strategy to validate, we don't want to go back to the use of HR and things like that, because as you know it results in longer times to get the credit and discrepancies between the claimed credit of one user and other, which ultimately means less credit for many users.
We need to find a value for the credit that is beneficial for you but does not attract those users, as I just told you, we are trying to find a solution, so keep tuned, I'll let you know as soon as we have an agreement
All my computers are over-clocked. My results must be good if your system validates them.
I agree with the issue of modifying the software application. If the project starts allowing or promoting "optimized" apps without project testing and acceptance, then I will leave. I do not run any projects that allow optimized apps that are not under project control.
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16)
Message boards
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Number crunching
:
Zero Progress
(
Message 4456
)
Posted 3233 days ago by
j2satx
Have not had one of these in two days now. Maybe they are finally out of the system.
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17)
Message boards
:
Number crunching
:
Zero Progress
(
Message 4448
)
Posted 3235 days ago by
j2satx
20/day??
Wow, I've seen 4 across my 3 quads, 3 duals, and 3 singles (since the initial onslaught was over. They're 50/50 docking/primegrid)and the last was on/about
the 25th and they were resends.
Guess you're just lucky.
And there I was thinking we were past those nasty things (from my vantage point anyway). Hmmm, I've set a </= 2 day cache(was 2 day, but lowered to .33
in preparation for Simap run), so maybe yours is higher and just managed to grab a bunch of bad ones during a stocking up period??
tony
I was running about 90% Docking for a week, so picked up more than usual. By the time I see them in the morning, the core running those WUs has wasted 2-4 hours. Only had one this morning, so maybe they are being flushed out of the system.
You need three three-core CPUs and you'll have a real nice set....LOL
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18)
Message boards
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Number crunching
:
Zero Progress
(
Message 4442
)
Posted 3236 days ago by
j2satx
Same here! Had 2 of those jobs, cancelled them, the next two show the same problem. All of them are 1dh4* jobs
Right now we are solving the problem with the download partition. The work-unit generator suddenly generated a lot of work-units some days ago that we erased but the result collector did not properly erased the files from the download partition that got full. Now the result collector is erasing the old workunits, the download is getting the space back, and we are monitoring the system. Once the daemons have gained our trust once again, we will move on to this challenge below.
Please stay tune!
Michela
Still get 20 or so of these per day.
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19)
Message boards
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Number crunching
:
The WORK queue is empty
(
Message 4440
)
Posted 3236 days ago by
j2satx
No new WUs to crunch and pending is rapidly building up again.
Fixed!
Thanks,
Michela
Thanks for the quick response.
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20)
Message boards
:
Number crunching
:
The WORK queue is empty
(
Message 4433
)
Posted 3237 days ago by
j2satx
No new WUs to crunch and pending is rapidly building up again.
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