Genome@Home

[Redlass]

I recently reinstalled the client on both my home and work machine. Still can't get either of them to work. Not that I've spent a whole lot of time on the computer, though. I'll try to fuss with it some more soon.

[jenninca]

I don't know what the deal is, but for the past day, my filter has been zipping along! Maybe I just got a small gene, but it's gone from sequence 19 to sequence 21 in the last hour, when usually I'm lucky to get from 19 to 22 overnight! I can handle this!

Cindy

[pageclot[$]]

How far across the page do the letters get, when you finish one of your 30 subloops?

There's news in the GAH site about some super genes being handed out to people, up to 150 positions. Those should take a while to process.

In other news, MandN have processed their first gene!

Yay!

p

[jenninca]

My letters are 72 letters long.

I think I spoke too soon. I left right when it was finishing 21, now it's eight hours later and it's only halfway through 24. More like normal speed.

Cindy

[emcphers]

There has been some really Odd sized genes coming through lately. Out of the 7 processors I have going, the WU's look like this:

23.76
10.9725
10.3125
23.2725
12
8.4525
20.4525

There for a while, they were all staying around 16, and now they are all over the board. I have been checking out all the forums for the top teams and seeing what they are doing to push such high numbers. If you haven't seen the Genome Spy program yet, you really must. Especially if you are running more than one instance of Genome, or running it across a network. I have 3 different computer running the 7 instances of Genome and this program allows me to see all of them and what their status is.

You can get the program here: Genome Spy

It's an easy installation and runs down in the task tray. I usually leave it closed, to free up the processor speed for Genome, and then open it every now and then to see what the status is.

Hope this is usefull to someone. There are a few other programs out there that do comparable things, but I haven't found one that looks or performs as good as this one.

Ok Genome people, I'm heading for the top!!

Erik

[Joubert[$]]

I got a big 'un going now too, Flame. Just counted 'em. On sequence 6 of an 88 variable gene. I'm hopeful that the reasons that the big ones are coming now is that they're able to start making compound proteins. You know, we've done the shorter strands, so what happens when you start combining two strands of protein you've already vetted -- that sort of thing.

BTW, removing for dupes (yes, I'm still ticked about that), our little team has created 2,385 sequences. Think about that for a minute. You know how long it takes for one of these to run. How much processing power did we lend this study? Figure an average P3 or P4 doing two a day -- we've added 3.2 machine years of time to the effort. That value has to be worth several thousand dollars that can now be diverted to other areas of the research effort since they don't have to buy 3 or 5 computers to do the processing work we've done.

And I think that's cool.

[hypotenuse]

Originally posted by joubert

And I think that's cool.

Me too George. Very cool.

:thumbs:

Lynne

[AdaDavis]

I just went back and read through this thread ...and discovered why my FIRST project is taking so long - It is now on sequence 26 of 30 ...of a protein with 144 variables.

Until I read this thread, I thought that was the norm.


Good thing I have DSL, or this could be a looooong project.

Ada

[magenta321]

Hey guys, I'm trying. My desktop was my work horse. The laptop is now the only one I am "allowed" to run the program on. The laptop only crunches when I am using it, otherwise it goes to sleep. So, all the genes I crunch now are a testament to my time on EA, mycoupons, or the times when I am shopping online.

So I haven't left, if I am one of the ones letting the team down. I am honestly crunching as often and as much as I can.

[Flamepillar]

I've been having a little trouble with my computer lately; turns out I just needed to defrag, 'cos it's been running just super since then. I've shut down the program a few times since then, because for a couple days there it was really swimming through mayonnaise, taking a half a day to do four sequences of a gene with 36 letters in it. Now everything seems to be back to normal.

[magenta321]

Yeah, I defragged recently too. Learned the hard way that you need to stop the filter program when you are defragging.

[pageclot[$]]

Originally posted by magenta321
Ug. First I get a teeny gene, then when I finish that one, I get one where the letter sequence goes all the way across the window and drops onto the next line! I don't even want to count the letters, I'll surely go cross-eyed!

Just count the second line's # of digits and add 80, Margaret.

pageclot

[murasaki]

Mine doesn't scroll either, but I usually catch the number when the filter is loading.

We're 54 this morning! But it looks like we'll be in this position for a few days. We're a few thousand units behind our next victim.

--naomi

[pageclot[$]]

Anyone heard about problems loading the client on machines with Windows XP?

One of our members, (MandN) is having problems getting the client to run and/or download on his new screaming fast machine. I don't know whether my instructions aren't good enough, or whether it's a problem with XP.

I do notice that the "download additional copies" screen does not refer to Windows XP.

P

[magenta321]

Ack, I just went to look at my stats and it tells me I am not found. Then I looked at Rubicon and Gracef, up at the top of the list. They are found. Then I went down to the people down near me, like File and Slick. They are not found either.

I wonder if we aren't big, bad and important enough to be found.

Hrumph.

[Joubert[$]]

It seems to happen every so often - probably during maintenance. I wouldn't be concerned. I periodically get the "User Cannot Be Found" message.

[jenninca]

Does anybody know a way to force an upload? I am having the worst time getting to my computer when it hits 30 to start my internet connection. I've probably got at least five genes to upload right now, but it started over again just before I woke up this morning.

Cindy

[jenninca]

Oh yeah, to answer a question from a couple of days ago--I originally had some trouble getting the program to load on my new computer, which has Windows XP. The way I got it to load was to copy it from my old computer onto a CD, load it on to my new hard drive, then go in through the "My Computer" icon and clicking on the "ghclient" icon. I can't get it to show up on my programs menu.

[pageclot[$]]

Originally posted by jenninca
Does anybody know a way to force an upload? I am having the worst time getting to my computer when it hits 30 to start my internet connection. I've probably got at least five genes to upload right now, but it started over again just before I woke up this morning.

Cindy

Here's what I do:

Shut down GAH client. (if you wait until it starts a sequence, you won't lose as much. If you shut it down when it's at 50%, it'll start that sequence over again when you start it up)
Go to the start button
Go to programs
Genome at home
Upload results.

If this doesn't work under Windows XP, (i.e. you don't have the program folder) you might have to do a run command. Under start, run, search for the gahclient, (it should be in Program files) and press Enter. When it comes back to the Run programs dialog, add "-upload" to the string. (no quotes). Then press enter. It should start uploading. If it doesn't, check to make sure you've left a space between gahclient.exe and -upload.

When it's finished uploading, you can start the client again as normal.

pageclot

[jenninca]

Thanks, Kevin, and thanks Tipu, too. I got it to work. So now I get to jump up a large amount again. Wa-hoo!

Cindy

[Joubert[$]]

I filched this message off their website. No need to have everyone go running over there:

Updates
Friday, December 21, 2001

Happy Holidays from Genome@home!

It's hard to believe that the project is almost one year old. We've come a long way since our initial release in January. The scientific work behind the Genome@home project is moving at a furious pace. Our first publication was submitted a few weeks ago, and it should appear in print in a few months (the peer review process can take seemingly forever!). This a major milestone for the project and is the result of a lot of hard work from everybody involved in the project, especially all the users.

Our plans for the New Year are very exciting. January will the see the introduction of Genome@home2.0, a snazzy graphical client similar to the current Folding@home client. I'll be putting together our next scientific paper, regarding the use of the large sequence libraries generated by Genome@home for homology modeling, protein structure prediction, and genome annotation. We'll be starting some exciting work on peptide and peptide-mimetic ligands, with very real applications in drug design. Finally, I'll be analyzing the data from the SH3 and SH3-ligand projects as part of a larger collaborative effort with Folding@home to computationally simulate how proteins bind ligands, the fundamental molecular action which imparts biological function to all proteins.

Some smaller notes: I've upgraded our web server, which has been having difficulty lately. There were a number of minor problems with it, which I fixed, so it should run smoothly now. I'll be away on holiday next week, but Vijay will likely be checking in on the Yahoo discussion group in case anything comes up.

Best wishes for a Happy Holiday and a Prosperous New Year. - Stefan & The G@h Team.

[nicholmere]

Originally posted by magenta321
They do seem like nice folks, but I am thinking they wouldn't join us.

Not to worry, t'was just a spot of humour.

[magenta321]

I got this from those Knights that say Ni! Ni! Ni! guys.

Increasing Processing Speed

Idle Sensitivity -- This is an often overlooked setting that can be adjusted in Windows 9x to increase the speed of work unit processing. In simple terms, "Idle Sensitivity" controls how sensitive Genome@home is to requests for CPU time from other applications, processes and services. By default, Genome@home is installed with a medium idle sensitivity setting. By lowering idle sensitivity (moving the slide bar to the left), Genome@home will run at a higher priority more frequently, thus processing work units more quickly. Most users won't notice an overall performance difference by running Genome@home at a lower idle sensitivity. To access this setting, go to c:\windows\system and find the file named conagent.exe (you will also see there an ms-dos icon called conagent, but you want the file conagent.exe). Right click on that file, choose "Properties", then "Miscellaneous". You will see the idle sensitivity setting in the column on the left. Note that changing this setting will affect all DOS programs that run on your computer. If that is an issue and you would like to adjust idle sensitivity for Genome@home only, copy the conagent.exe file to your Genome@home directory and make the changes to that file. It is then mandatory that you click on the MS-DOS icon at the top of the Genome@home program window, select "Properties", then the "Program" tab. Edit the Command line entry to point to the path of the conagent.exe file that was copied to your Genome@home directory.

I tried this. I am on Windows ME and I tried this trick (even though it says it is for 9x) and it seems to have made things go a little faster. I just thought I'd bring it to your attention, in case anyone else wanted to increase their productivity a little.

Margaret

[magenta321]

Hey gang, I found something cool.

A while ago I asked if there was a way to graph team EA members production rates. I wanted something like statsman's t