SIMAP Project

[Buga1]

Anything related to SIMAP.

SIMAP Homepage

Description:
Today, protein sequence comparison is the most powerful tool in computational biology for characterizing protein sequences because of the enormous amount of information that is preserved throughout the evolutionary process. SIMAP is a public database of pre-calculated protein similarities that plays a key role in many bioinformatics methods. It contains about all currently published protein sequences and is continuously updated. The computational effort for keeping SIMAP up-to-date is constantly increasing. Please help to update SIMAP by calculating protein similarities on your computer. The computing power you donate supports manifold biological research projects that make use of SIMAP data.

Team attach: Calm Chaos
SIMAP - BoincStats

Project = Active | WU Availability = First of Month | WU Time = Medium


Rick

[Astro]

Simap to release 250000 tomorrow evening (in central Europe).

I'll be backing up the truck.

Last month they released 350000 which lasted all of 2 days 23 hours or there about, so this month, they should go even faster.

If I'm real lucky perhaps I can even pass my Einstein total, now that would be something, given that they only give out work once a month (note: a couple months ago they did have continuous work for a month or so, but that's really unusual)

[AC]

I was taking a look at SIMAP these past few days. But since you say it doesn't have a steady flow of work...

[Astro]

Simap has started dishing out work. As usual, it a little hit/miss getting a connection to actually get work, but 6 of my 8 have a decent cache. This sketchyness shouldn't last more than a few hours.

[Astro]

looking at my numbers I got 97K Simap last month, but this month they only half 2/3rd the work available. That means I can hope to get 50K in the next several days (5 maybe). If anyone out there can help out for the first 5 days of May, i think we can get Simap into the 6 digits.

thanks for your consideration.

[AC]

Ah, you have a plan. Hmm, SIMAP. Right now I'm mostly working on TANPAKU but I've been trying some of the other projects too. My goal is a maximum of four projects going on my system. AI System is one I'm still trying to get more information on.

Okay, since I supended Milkyway to work on TANPAKU I'll give SIMAP some resource share.

[danielmid]

I've been working SIMAP since you said they were gonna release some wu's.

[Astro]

Great,

I have tried a few schemes to maximize participation. They have limits, the boinc client has EDF (kind of). Where if it thinks you'll run into trouble meeting deadlines it won't get new work. Anyway, I start out setting my cache well below the deadline (like 2.5 days so it'll keep refreshing the cache). Then when the batch monitor (at simap) shows about 28% complete, I bump it up to 6 days. After about 32% they will run out of work. That seems to get me an additional day or two out of them. It seems about 4-5 actual days worth is about the max you can get, so I had an evil thought last nite. Since all my puters are Dual Boot, I would just wait until tonite(when I suspect they'll be near 28% complete), then reboot into windows and get a couple days worth, then switch back to linux and set my cache to 6 days and finish loading up. That way, when I run out on Linux I'll still have a couple days worth on Windows I can run without running past the deadline. lol

Oh yeah, and if you are one of those who likes more credit/hour, then Simap isn't too bad. They're better than Rosetta and Malaria, but worse than MW and Einstein (with power users app).

Here's a liink to the batch monitor where you can see the % of batch progress.

[Astro]

First, I'm not sure I posted these last few posts in the right spot. Looking at the title of the thread, It appears this conversation is out of place (off topic), so if some mod wants to move it to the right spot, then that's OK.

We're starting off with:

43932 credits
81 as BSRac
and 220th position as a team at Simap

will be interesting to see how fast we rise.

Frankly, I'm hoping we displace CPDN on the CC Boincstats totals signature to move from 16th to 11th position.

[AC]

Thanks for giving that info Astro

The batch monitor now shows 14.2%. I'm already over there and I saw that Dan is too.

[Astro]

Thanks for giving that info Astro

The batch monitor now shows 14.2%. I'm already over there and I saw that Dan is too.

I'm working 10-12 hour days starting at 5 am so if it's in the twenties tomorrow morning, I'll be boosting it to 6 days, then loading up, then changing to 2.5 days, and rebooting to windows to load up windows as late as possible so I don't miss any deadlines.

They have a 100 wu/core/day restriction that has to be massaged.

Thanks for participating.

Much of the work done today will be granted tomorrow too, so hopefully our rac will rise markedly (along with the TC).

tony

[Dark Angel]

First, I'm not sure I posted these last few posts in the right spot. Looking at the title of the thread, It appears this conversation is out of place (off topic), so if some mod wants to move it to the right spot, then that's OK.

We're starting off with:

43932 credits
81 as BSRac
and 220th position as a team at Simap

will be interesting to see how fast we rise.

Frankly, I'm hoping we displace CPDN on the CC Boincstats totals signature to move from 16th to 11th position.

Nothing wrong that I can see Tony...the topic is for anything SIMAP so post away.

[danielmid]

Dan is having computer issues at the moment related to mobo upgrade. Reinstalling Windows at the moment, but I lost my cache from simap :(

[Knightmare]

Ok. I attached to SIMAP.

50% MilkyWay and 50% Simap. Let's see how much help I can give us there.

[Astro]

eeek,,, say it ain't so.

I awoke, checked the batchmonitor, saw it was up to 21.8%, changed my cache to 2 days. Rebooted two machines to windows, and waited and waited, but no work. I checked their front page and it says that they're already out of work. Grrrrrr. So much for the 30% theory. So, all I have is 4 days worth on linux(if my boinc actually has the cache properly determined and filled).

Seems I need to rework my scheme for 250K issuances of work.

[edit] during my post mortem, I see they only sent out 168K's worth, not the 250 mentioned on the front page. Must be some initial fill percentage I'm not fully aware of yet.

[AC]

Aaah! And I almost had a new 5 day cache! What happened was, I increased my network settings but I was getting continuous downloads from SIMAP and TANPAKU both and it looked like my bandwidth was being choked. So I aborted everything and figured there's plenty of time till the batch monitor gets to 28% and I'll just mess around with some of my network settings to see what the best of the two options are ("Connect about every" and "Additional work buffer"). By the time I set the later to 5 and updated it was too late and I couldn't get any new tasks. Now I'm on my last SIMAP WU.

Sorry about that :(

[Astro]

I understand the bandwidth issue. If you notice, I only rebooted 2 of the machines. I knew if I did all of them at once then bandwidth would have ground to a halt. LOL


Well, there's always the June 1st wus.

thanks for trying.

[danielmid]

Crunching away on about a days worth on the laptop, new machine had about 2.5 days and decided to go kaput on me, so it had to be reformatted and killed.

[Astro]

Looking this morning I see that our team is in 23rd place by RAC and 15th place by "credit/day". Oh I wish they had more work.

[Astro]

After the last Boincstats update, we're now in 18th place by RAC (+5 spots), and 14th by credit/day. Simap has also been raised 3 positions on the CC boinstats team signature.

[Buga1]

Nice going. Wondered why I seemed to never get any Simap WU's. Will keep that in mind for next month.

Rick

[AC]

Well, I did get a little over 800 in about a day

[AC]

After the last Boincstats update, we're now in 18th place by RAC (+5 spots), and 14th by credit/day. Simap has also been raised 3 positions on the CC boinstats team signature.

At 16th now.

[Astro]

I've let WCG onto the "allow work" catagory with a 50/50 share with Boincsimap (still have a days worth running full time), so my credits/day will droop for the next two days and then drop right off at Simap. my Simap RAC should stop ascending after todays update. Still have 4800+ credits pending at Simap.

[Astro]

We still might make the 100,000 goal, even with the abreviated amount of work. Currently Boincstats says we have 93,550. I still have some work and 2,950 pending. <crossing fingers for luck>

[Buga1]

Kool,, Nice little hop over there at SIMAP. Thanks for the help there Astro.

Rick

[Bird-Dog]

CC passed the 100,000 and I`ve about 2000 pending credit and work left. Nice to have others on simap, I felt quite lonely on my own each month lol

[Astro]

Silly me, I forgot to check the team stats at the site, which are updated very frequently. We ARE at 100,097.73. Woo Hooo, I can stop worrying now.

Thanks everyone for participating.

tony

[Astro]

OK, ladies and gentlemen. The Simap front page says:

Calculation of SIMAP updates is starting soon.
The calculation of new simap workunits containing the novel proteins from may 2008 (simap app) and their domains (hmmer app) will start on june 1st in the evening (UTC).

Let's see what happens this month.

[Astro]

wow, they're going to have even less this time than last (180K new sequences), so we may as well load up with the max right off the git/go.


We're starting off in 177th place with 120,219 cobblestones.(this is a place marker for later reference)

[Astro]

Less than 24 hours till they start handing out the good stuff. I have a .5 day cache and will be setting Einstein and other projects to NNT tomorrow morning in preparation.

Here's a record of the starting spots:
Astro 370,597
Bird-Dog 73,280
Dances with Werewolves 2,256
Daniel 2,114
Buga1 1,543
Krunching Kajun 1,135
A/C 993
Knightmare 937
yeababy 393

[AC]

Thanks for the update Astro. This time I won't make the same mistakes with my cache. If I do I should be banned, again.

[Buga1]

About what time would that be, when they start releasing the next batch? CDT if possible. Buga and Timezones don't work well together. LOL

Thanks Astro for the reminder.

Rick

[Astro]

News from the staff:

During last days we got another 400.000 new sequences. So I guess we will get work for approx. two weeks now. We're going to start now.

Best regards
Thomas

I have to assume they mean two weeks receiving work, not sending out work. I does appear they'll have work to send for 3-4 days.

So, I'm setting a 4 day cache and only loading up one OS ATM.

OH yeah, I'm getting work now. the servers are being hammered so getting work is sketchy.

[Buga1]

Well I have 2 systems waiting for some. Hopefully will get some this round.

Rick