Updated the Citizen Science Grid forums for DNA@Home  |
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I've made some updates to the Citizen Science Grid forums, adding new ones for DNA@Home and SubsetSum@Home. I've also made some progress on the Citizen Science Grid home page here:
http://volunteer.cs.und.edu/csg/
Let me know what you think and if you have any suggestions! Still under construction but at least you can get an idea of the look and feel for the new site once I get everything unified. I'll be shutting down these forums in a couple days, so please make an account over on wildlife@home so you can post over there.
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| Planned downtime on 2014-08-11 08:00-18:00 CET |
| There will be a downtime on 2014-08-11 (next monday) from 08:00-18:00 CET due to network maintenance. |
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| Planned downtime on 2014-08-11 08:00-18:00 CET |
| There will be a downtime on 2014-08-11 (next monday) from 08:00-18:00 CET due to network maintenance. |
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| more on project unification |
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Hi Everyone,
I've come up with what will hopefully be a good solution to the project unification. I've created a new project called Citizen Science Grid, which you can take a look at here (note it's very rough and i'm still working on a lot of the webpages to unify everything):
http://volunteer.cs.und.edu/csg/alpha/index.php
Since Wildlife@Home has been the most recently active project, I'm re-using the Wildlife@Home database for this project. Note that this project won't export statistics. Instead, credit earned by this project will be exported into the various sub projects.
So this means if you run Wildlife@Home only, you don't need to do anything. If you run any of the other projects, first make an account on Wildlife@Home (or on the Citizen Science Grid webpage) if you don't have one already.
I'm currently working on a webpage where you'll be able to link the account on Citizen Science Grid/Wildlife@Home to your accounts on DNA@Home or SubsetSum@Home. You'll need to enter in your user name and email for the account you want to link it to. Then when you generate credit it will be generated for that old account.
In a week or so I'm going to shut down the forums on SubsetSum@Home and DNA@Home, because they're going to just use the forum on Citizen Science Grid. That way all projects will be using the same forum.
Does that sound okay?
--Travis
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| Version 17.0 has been created |
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Just now the version 17.0 has been created. It is based on the vboxwrapper 26086. And I have updated some things:
1 improve the support for pause and resuming tasks
2 the vdi size will increase slower than previous versions
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| project unification |
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Hi Everyone,
So I want to try and start unifying the projects to simplify server updates, checking the forums, etc. Before I get going I want a little feedback as to what I'm planning so everyone is okay with it.
Basically, I'm going to create a new project (probably called "Citizen Science Grid") or something along those lines. Unfortunately, because people have different accounts on each project I can't do an automatic merge of the users and databases. So this means you'd have to create a new account on the new project (when the new project starts those will be the only forums for the site).
When the new project is up and going, I'll allow everyone to transfer their credit from their other accounts via a webpage (basically if you're logged in, you can enter in the user name and id of your account on citizen science grid, hit okay and it will transfer the credit over). So a couple questions about this approach:
1. will it break the credit trackers too badly? I'll subtract credit on the old project to 0, and then add the same amount of credit to the new account on citizen science grid.
2. I kind of want to keep credit for the different projects separate; if I keep different tables and export the stats of each project as it's own part of XML, will that cause any problems? Or would everyone rather just have one combined credit for each of the projects here (Wildlife@Home, DNA@Home, and SubsetSum@Home -- we'll probably be launching another one in the fall as well, so I want to get this done before we go doing that).
So, once I get some feedback, and if people don't have too many issues with this I'll set up the new project and get things started. Otherwise back to the drawing board. :P
Also, on a SubsetSum@Home note, I'm hoping to get a student to work on the project in the fall; but no guarantees yet (we're pretty busy with Wildlife@Home, and DNA@Home is booting back up).
thanks, hope to hear from you soon about this!
--Travis
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| Technical break |
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The OProject@Home System will be transferred to the new server. The system will be available after 10/08/2014.
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| New test set was launched! |
| It is need for the optimization of the solver smallexpx. |
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| Project fix |
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I have fixed the bugs related to 1) people not being able to send private messages and 2) people not being able to report a post as abusive.
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| New batches |
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You are currently helping us to distinguish between molecules who can bind a particular target from molecules who can't. This type of experiment is called virtual screening and is one of the main applications of molecular docking. It is of particular interests to pharmaceutical companies as it can truly accelerate the process of drug discovery as to quickly identify potential binders.
The batch IDs are used to represent the different targets:
856 - Heat-shock protein 90 (HSP90)
1549 - Fibroblast growth factor receptor kinase (FGFR1)
3144 - Enoyl ACP reductase
3610 - Thrombin
3836 - Retinoic X receptor alpha
5775 - Poly(ADP-ribose) polymerase
6094 - S-adenosyl-homocysteine hydrolase
6895 - Factor Xa
7671 - HIV protease
8922 - Aldose reductase
9119 - Trypsin
9644 - AmpC beta lactamase
9953 - Hydroxymethylglutaryl-CoA reductase
11723 - Antagonists of Estrogen receptor
11912 - P38 mitogen activated protein kinase
12216 - Adenosine deaminase
12404 - HIV reverse transcriptase
12978 - Epidermal growth factor receptor (EGFR)
13460 - Neuraminidase
16308 - Androgen receptor
16890 - Glucocorticoid receptor
17749 - Agonists of Estrogen receptor
19592 - Tyrosine kinase SRC
20110 - Glycogen phosphorylase beta
20493 - Glycinamide ribonucleotide transformylase
20568 - Acetylcholine esterase
21619 - Cyclooxygenase 2
22545 - Peroxisome proliferator activated receptor gamma
23713 - Vascular endothelial growth factor receptor kinase
26580 - Platlet derived growth factor receptor kinase
27139 - Cyclooxygenase 1
27680 - Angiotensin-converting enzym
27848 - Phosphodiesterase V
28485 - Catechol O-methyltransferase
29229 - Progesterone receptor
30398 - Purine nucleoside phosphorylase
31072 - Thymidine kinase
31492 - Cyclin dependent kinase 2 (CDK2)
32589 - Mineralcorticoid receptor
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| ATI OpenCL issues |
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It appears similar to the disaster of ntlm, that the md5 OpenCL may have the same issues. I *thought* we had run this algorithm before so it may not be the algorithm but issues with the hybrid2 code. In any case I have halted the production of new work for the GPU side, though there is still work already in the buffer.
I think in the immediate case we have the following to do ASAP:
1) find a way to continue Nvidia CUDA even if we have to disable OpenCL AMD/ATI (or vice/versa) so it isn't a 100% GPU shutdown
2) fix the OpenCL code
I am about to go pick up a new GPU that will let me directly attach vms in my server to the card, such as windows x64. On the GPU side PowerBlade has had the burden of all things windows related, and it is past time that I have a dev environment for both sides. I do have notes in the code for the ntlm side that has a very similar design on the md5 side that might be the issue in both, but I will know more as soon as I can test that directly.
*If* we could come up with a table construction for mysqlsha1 to keep work flowing in the meantime that would be great for crunchers, but we have exhausted the algorithm to a large extent with the code currently deployed. In the mean time work is likely to:
1) dry up
2) erroneously validate in some cases 2 OpenCL results agree (we still do limited checks on the server even with matching WUs)
3) result in a lot of inconclusive results
In any case further updates will be made in as timely a manner as possible. I do not see the time-frame to fix the OpenCL code bugs and get that code out to clients to be more than days.
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| Forum under spam attack |
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Hi there,
the ddm forums are currently under heavy spam attack.
I've just deleted the relevant posts. To prevent further spam, from now on users can only post new messages if they have at least one credit point.
Cheers,
Nico
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| Beal Engine ver. 1.0 for Linux 32-bit |
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Will there be a 64 bit Linux version?
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| Docking@Home is Retiring |
| With a heavy heart, we are announcing the retirement of the Docking@Home project. Unfortunately, we no longer have the resources to maintain the project. Starting on April 30, 2014 Docking@Home will no longer be distributing new jobs but will continue to collect results. On May 23, 2014 the server will stop accepting results as the project enters retirement. We hope that you can use this time to point your workers to new VC projects. (here is a link to active BOINC projects).
Over the past 9 years weâve had 98,512 Volunteers contribute computing power from 264,535 hosts. We have granted a total of 5,422,290,917 credits, which means our volunteers contributed roughly 159,398,584 Hours (18,196 years!) of computation. Back in Jan we made all of the result data public and we will keep that interface active. Thank you to everyone that made Docking@home a success over the years. Itâs been fun! Please join us on the forums to share your best and worst story from the project.
Over the past few months weâve been working on bringing the ExSciTecH project to life. We hope that you will join us in our adventure on this new project. Feel free to stop by the ExSciTecH forums and say âHiâ!.
Thanks for your support over the years!
The Docking@Home Team |
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| New application - Zeta-Search |
| EDGeS@Home has launched a new application called Zeta-Search. |
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| ExSciTech games beta version online! |
| Explore the molecules that make up the world around us! Challenge yourself to identify them using molecule flashcards game! Build your own question sets to challenge the rest of us! Join us in the ExSciTecH (Exercise, Science, Technology, and Health) project!ExSciTecH molecule flashcards are live and now in public beta. You can access ExSciTecH here!
You can play the flashcards game without an account, but you will need to register a new account to save your high scores and to build your own question sets. Your question sets will be public after we review them. In the forum, there is a tutorial on how to build question sets through this link. We look forward to having experienced volunteers with chemistry background to enrich our question sets. Please note that the account is separate from your Docking@Home account. |
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| New application - Zeta-Search |
| EDGeS@Home will launch a new application called Zeta-Search soon. |
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| Server maintenance |
| We are planning to migrate our database to another server on Thu, Feb 20, 2014. This will cause outages in our service between 8:00 AM and 5:00 PM UTC. Thank you for your patience. |
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| Project on hold |
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I have to pause the project at the moment for few reasons.
I'm quite busy now on my work, can't find enough time to work with project application to solve stability problems... Also, I found that with current way of how project work, we can search whole Internet in few hours which is great result but also this give back tons of results - proper way to clear this data is hard task for current server and I need to find way to sort this out as well.
I will inform you as soon as I solve this but that can takes months with current quantity of time I can spend on project...
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| Progress ... |
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Just very short report (I am still working, changing everything and don't have established results so far). I have almost 15 mln of positions at master level and 15 mln of positions from FISC database now. Each evaluated with ~5 sec Stockfish evaluations (thanks to BOINC community!). I introduced 66 basic numerical features from position. I divided my collection into 2 classes {safe, unsafe}. unsafe - positions where side on move is most probably losing (< -100 cp) and safe - positions where side on move is not losing (>= -100 cp). Then I applied some known methods of classification. The best results I received with neural networks with 2 hidden layers 33,10 (area under ROC 0.8755) relatively good results are also with simple logistic regression (area under ROC 0.8528). I developed small chess engine and put there this logistic regression as position evaluation function and played some games. Engine is weak for now - but it seems to play reasonable with some visible plan. That is good enough to continue. When I implement more features and game will be more pleasant to see I will present it here. This is the end of this short report. Please wait for more detailed reports later. Thanks.
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