Posts by Aaron Finney

21) Message boards : Rosetta@home Science : Problem with switching mid WU failing 90-100% of work (Message 8330)
Posted 4 Jan 2006 by Aaron Finney
Post:
Whenever BOINC switches between projects, and pauses a workunit, sometimes the WU gets a computation error. It's repeatable, but doesn't happen every time.

It will fail 90-100% of all workunits before they are complete.

This problem appears only with Rosetta on my machines.
22) Message boards : Cafe Rosetta : Can Teams merge? (Message 8296)
Posted 3 Jan 2006 by Aaron Finney
Post:
[/quote]
First off I don't think you can actually just Disband a Team, everybody can quit the Team but the Team name & Credits will still be there as far as I know. I tried all of this one time @ the Seti Project and in the end all the Credit were lost from the original Team. I can still go back and bring up the original Team & the Credits are still there even though nobodys on the Team.

The only way it might be possible would be to notify the Project by E-Mail of your intentions and maybe they could do something. But if the Project's allowed that then you would be opening up a whole new can of worms...IMO

Soon you would have 2 or 3 or more Teams wanting to Merge just to enhance their position in the Rankings. Thats why BOINC was set up the way it was, to keep the Credits where they were earned.
[/quote]

Nono.. there are management functions for the team leaders. You can completely disband the team. Although - You will not be able to apply the credits from one team to the other. Kinda sucks IMHO.

Technically, the project owners can do unlimited management of the credit and team system. Convincing them to do so.. is another story.

See the wiki.

http://boinc-doc.net/boinc-wiki/index.php?title=Team
23) Message boards : Cafe Rosetta : Can Teams merge? (Message 8295)
Posted 3 Jan 2006 by Aaron Finney
Post:
I've never switched teams, staying loyal to The Planetary Society, the team that STARTED IT ALL.

Um, since when has TPS been doing protein science?


If it weren't for TPS, SETI@Home would probably not have obtained it's funding.

Without SETI@Home, I doubt there would be a market for distributed computing powerful enough to drive what we now enjoy.

TPS, while completely unrelated, and unknowingly.. may have ignited something greater than just the Search for ET.

Now, because of BOINC, our machines are doing much more than just searching radia data for signs of intelligence.

David Anderson commented on this a few times, but his statements could be perceived as self-serving.

However, I don't think we would be here if it wasn't for TPS. Therefore - I shall always crunch for them.
24) Message boards : Cafe Rosetta : Can Teams merge? (Message 8215)
Posted 2 Jan 2006 by Aaron Finney
Post:
I really don't think so, you can always just create a new Team but the way BOINC is set up is that the Credits will stay with the Team that it was earned with.


IIRC, that was changed? I've never switched teams, staying loyal to The Planetary Society, the team that STARTED IT ALL.
25) Message boards : Cafe Rosetta : Can Teams merge? (Message 8213)
Posted 2 Jan 2006 by Aaron Finney
Post:
I was wondering if two like minded teams can merge into a new seperate team, and keep their past production intact.

Can somebody give me an accurate answer?

Scott


The answer is both yes, and no. (And Yes!)

These are the steps you would have to take in order to combine the teams.

1. Select a new "Team Leader".
2. Convince the existing Team Leaders to send out an E-Mail to all existing team members notifying them of the merge, and what to do about it. It would be wise to WRITE or print out the email addresses so that they are not lost in step 3.
3. Once all members have been notified, Disband BOTH teams completely.
4. Have the new "Team Leader" Create the new team. It's better to do this before step 2, unless the new Team Leader is an existing team leader, in which case this is impossible. In that case, please keep the time between step 2 and 4 as small as possible.
26) Message boards : Cafe Rosetta : Humor in the work? (Message 8211)
Posted 2 Jan 2006 by Aaron Finney
Post:
Thank-You All,
I get it,dohh,Now will crunch even more,good for a laugh!

Doug Worrall


Let's hope that there isn't some completely scientific reason for the names and we're not all cracked out of our minds making up reasons for the terminology.. Won't I feel silly!
27) Message boards : Cafe Rosetta : Personal Milestones (Message 8157)
Posted 2 Jan 2006 by Aaron Finney
Post:
Hmm..

SETI Classic WU total - 10,393
http://setiathome2.ssl.berkeley.edu/cgi-bin/cgi2?email=austinwichita@aol.com&cmd=print_cert&certnum=10000&size=0&color=1

BOINC World Rankings by project, (Format, "Project - Total Credit(rank) - RAC(rank)")
SETI@Home - 31,996 - 58,607
CPDN - 49,253 - 37,350
Predictor - 514 - 19,138
LHC@Home - 1,258 - 221
Einstein - 21,083 - 17,099
Rosetta - 882 - 538
COMBINED - 10,945 - 8,223

BOINC Totals per project..
SETI@Home - 23,286.71
CPDN - 945.00
Predictor - 49,241.00
LHC@Home - 11,252.70
Einstein - 7,020.96
Rosetta - 10,942.05

BOINC Combined project total - 102,520+

I guess I just passed 100k, so i'm stoked.

and in the combined total for all projects, I will have just leaped in under the top 10,000 also in another week.
28) Message boards : Cafe Rosetta : Humor in the work? (Message 8154)
Posted 2 Jan 2006 by Aaron Finney
Post:
In First Person Shooter (FPS) games - frags/fragging has to do with killing your opponents. (Examples of FPS are Counter Strike, BattleField 1942, etc) What's the "No Random WTS" refer to? Horrible to see abbreviations I'm not familar with. *grin*



Random WTS = Want To Sell.

Also akin to WTB = Want To Buy

There is a problem in MMORPG's where people will communicate with everyone randomly with "WTS - Holy Shield - 5000k interested?"

FFXI doesn't really have this problem, but most others do.
29) Message boards : Cafe Rosetta : Humor in the work? (Message 7857)
Posted 29 Dec 2005 by Aaron Finney
Post:

"NO RANDOM WTS OR FRAGS"

... being a MMORPG fan...


Any chance of a link for the as yet unenlightened?

Odd as it may seem to you fans, I would't know a MMORPG if I saw one.

Oh dear, there goes my mouse cred -- R~~


lol... MMORPG :) Massively Multiplayer Online Role Playing Games

http://en.wikipedia.org/wiki/MMORPG
30) Message boards : Cafe Rosetta : Humor in the work? (Message 7506)
Posted 24 Dec 2005 by Aaron Finney
Post:
I checked one of my machines today.. lol..

I noticed that the name to one of the workunits was..

"NO RANDOM WTS OR FRAGS"

I have to admit.. being a MMORPG fan.. I nearly fell on my ass when I finally let it set in.

funny stuff.

Check it out...

http://boinc.bakerlab.org/rosetta/workunit.php?wuid=4033965
31) Message boards : Number crunching : Rosetta alpha ?? (Message 7270)
Posted 22 Dec 2005 by Aaron Finney
Post:
If there is a beta (alpha, really) for this project.. I'd like to be a part of it also David :) pretty please
32) Message boards : Rosetta@home Science : Fighting malaria and HIV (Message 5770)
Posted 10 Dec 2005 by Aaron Finney
Post:


You are close. the outer surface of HIV is extremely variable, so when an infected person has an immune response to it, the antibodies don't do anything because the virus has already changed. but there are a few key "Achilles heel" regions where the virus can't change because it needs these regions to keep infecting people, get into cells, etc. Unfortunately, the immune system doesn't usually make antibodies to these regions, because the variable parts are much more noticeable to the immune system (this is one of the ways in which the virus is very tricky). Our idea is to take these "Achilles heel"
regions that are critical to the virus, and embed them into small stable proteins which could be sent all over the world very cheaply. The hope is that when vaccinated with these proteins, people will make antibodies to these Achilles heel regions (because in contrast to when on the real virus, on the vaccine they will be very conspicuous). So then people will have antibodies which can "neutralize" the virus (indeed, several "neutralizaing" antibodies have been found in patients, and they do recognize the Achilles heel regions, but they are normally either not made or made at very low levels).




It doesn't make sense to me why this would work.

If the body doesn't readily and frequently recognize these portions of the virus outer surface as portions that would instigate an auto-immune response, then what good would vaccinating someone against these proteins do?

Even if the body had been vaccinated, the antibodies wouldn't be released in force unless the body recognized a potential threat. - Which.. if it recognized HIV in this way, it would create the proper antibodies anyway. Or do I have the wrong impression of the immune system?

Or maybe I am just thinking too hard :)
33) Message boards : Rosetta@home Science : Dead in the water (Message 5768)
Posted 10 Dec 2005 by Aaron Finney
Post:
Actually, I also believe this MIGHT be because your cache size is too small. Increase your cache size (in small increments, unless you are extremely familiar with it's workings) and it might download a small amount of rosetta for you to crunch, while keeping a bit of the cache open for a possible successful contact with SETI.

IT MAY BE that your cache size is so low that by downloading any new work from anywhere, your client might consider that detrimental to your balancing your resource debt.

IIRC with a recent change, the more long term debt you incur, the larger the required available portion of your cache gets(as a percentage related to your PC's performance). Obviously, you'd need a larger cache if your PC is only moderate in it's performance, compared to something with all the latest hardware.
34) Message boards : Rosetta@home Science : BOINC a bit stupid?! (Message 5539)
Posted 8 Dec 2005 by Aaron Finney
Post:
Not that I'm trying to poke holes in your issue.....

But...

You DO know the difference between SETI Classic, the BOINC Infrastructure, SETI(current), and Rosetta, yes?

Because uhm.. it sounds like you kinda don't.

Also... Were you with SETI Classic before it hit golden status ? (Golden, means it is a FINAL release, meaning all bugs are fixed and the software is where it was intended to be)

SETI Classic had just as many problems before it went golden. Just as ALL other software. Now - I will say that SETIclassic enjoyed a long period where there was absolutely nothing wrong with the program, but absolutely nothing changed. BOINC will reach this point someitme in the near future, and it will be just as nice. However - The time for SETIClassic is over.

Le Roi est Mort, Vive le roi!
35) Message boards : Rosetta@home Science : Rosetta - The World AIDS Conference awaits you. (Message 5325)
Posted 6 Dec 2005 by Aaron Finney
Post:
Thanks Aaron--we should be running vaccine design calculations on rosetta@home well before the next conference, and will definitely plan to present our work at this meeting (maybe you can help!). thanks for the heads up!



I called one of the people involved with the project, and they want you to send in your data for a poster via an online form in an "abstract".

There is a retrovirus conference coming up in Denver, and the World AIDS Conference is in Toronto, Canada in this summer. Personally, I think you should shoot for the World Conference in Toronto. The abstract deadline is in March I think.. so if you could provide to them a small abstract, (assuming they approve it) they should let you attend.

Non-Officialy, I can guarantee you you would get approved for at least a poster presentation and registration of your staff. If you have the money you could build a booth, but I don't know if the U of W would foot that bill :)

Costs for Universities is MUCH less than that of major companies however. Major companies can spend over 300k, but non-for-profits and universities pay almost nothing. (probably 1500 per person or less, including airfare)
36) Message boards : Rosetta@home Science : Rosetta - The World AIDS Conference awaits you. (Message 5258)
Posted 6 Dec 2005 by Aaron Finney
Post:
I was at the European AIDS Conference in Dublin, and I talked specifically about the FAAH Project, Scripps/Olsen, and the Rosetta Project to just about everyone I met. The conference organizers were interested in hearing something from one of the major players in this "Screen Saver" that helps fight HIV. I did NOT speak of FAAH/Scripps/Olsen very favorably. If HIV related work becomes one of the central parts of the Rosetta Project, the conference would be extremely interested in having a person from this project come and speak / set up a booth.

The European AIDS Conference was attended by almost every major country, pharmaceutical company and labratory working on the HIV Virus. While I did not have alot of information at the time regarding Rosetta's relationship to HIV work, I did mention that the people here were at least working on it.

The general response I received from those involved (Even the Virology research scientists, and executive level entities from Merck, Boehringer, GlaxoSmithKline, BM-Squibb, and Roche) was that they had never heard of such a program. However, they were extremely interested in participating (one even suggested using company computing power.).

I think that if this is in fact a core portion of the rosetta program, it would be in your best interest to contact the World AIDS Conference organizers and attend the next conference.
37) Message boards : Rosetta@home Science : FightAids@Home (Message 5257)
Posted 6 Dec 2005 by Aaron Finney
Post:
Thats fine everyone has a reason to not run a project or two or several, I have got a few of the Genome project they are runing but am awaiting the porting over of the Aids Project on to BOINC one more worthwile project for me to slowly munch on


Well, given the past history of the FAAH project, and Scripps in general..

I'd much rather give my cycles to Rosetta, especially now that they have a vested interest in HIV research. See my post on the World AIDS Conference.
38) Message boards : Rosetta@home Science : Runtime Errors (Message 3976)
Posted 22 Nov 2005 by Aaron Finney
Post:
Today I got a string of like 10-20 Runtime Errors that each said..

"The application caused the program to terminate in an unusual way"

or something like that. I rebooted my machine and everything is running fine now I think. Wierd.

CORE:BOINC Version 5.2.7
APP:Rosetta Application 4.79
OS:Windows XP Pro SP2
CPU:Intel Pentium 4 Northwood 3.06/533/HT
MB:ASUS P4T-533 w/1007.002 BIOS
RAM:Samsung 1200Mhz 32-bit 232pin RIMM 2x256mb non-ECC
VIDEO:ATI Radeon 9800 Pro / Catalyst 5.11
PSU:Thermaltake 560w W0023
MOUSE:Logitech MX1000 Cordless Laser Mouse / Setpoint 2.46
KB:Logitech Cordless / Setpoint 2.46
MONITOR:Viewsonic P810
39) Message boards : Rosetta@home Science : AMD64 Support? (Message 3969)
Posted 22 Nov 2005 by Aaron Finney
Post:

It's not that FLOP calculations don't benefit, it's that the SETI program itself doesn't use the type of code to benefit from a 64 bit app.

Rosetta may or may not, it depends on the algorythms.



Most applications don't benefit from the 64 bit adress space, but from the ability to use more registers in the 64bit modus (for example media encoding) http://www.linuxhardware.org/article.pl?sid=05/02/24/1747228&mode=thread


I was mostly commenting that the logic of "Seti and Rosetta both are heavily FLOP based, hence - If SETI wouldn't benefit, neither would rosetta" doesn't really apply in all circumstances.
40) Message boards : Rosetta@home Science : Website suggestions and comments (Message 3906)
Posted 22 Nov 2005 by Aaron Finney
Post:
David, here is a cliche idea, To spark interest in rosetta@home.

Ok, think of the matrix code running down the screen but its amino acid sequences instead, there is some kind of hynototic moby sounding music playing. All seams preety cliche but then screen starts changing and music is more intense, The acid sequnece starts increasing speed and starts morping into a protein. It shows the protein develop and then anouther protein pops up and more and more. Next we fade into a sceen from baker labs and we see you guys doing stuff with test tubes and lab rats and then it fades into some kid taking a pill. It ends with a powerful message supporting the rosetta@home project.

It could be done in flash or anouther medium. I am sure there is room for that contest idea I had earlier for something like that.



Or better - User definable screen savers that get programmed via an output A-La "Winamp Style".


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