Posted on 04/15/2007 7:39:44 PM PDT by texas booster
Inner Life of the Cell: Animation conception and scientific content by Alain Viel and Robert A. Lue.
Animation by John Liebler/XVIVO.
SIGGRAPH Award Winning Video
It is geared toward training doctors and researchers, and gets pretty heavy into the organized structure of cells.
In Folding@home the goal is to simulate the actual atoms and molecular forces that force a protein to fold in a particular manner. When the molecules of a protein unzip to replicate or to contact another protein is the focus of our research. F@H looks at the folds a protein makes and the forces that allow/disallow a particular bond.
F@H concerns itself with the molecules that make up the structures in the video.
Extremely fascinating. Please have a look!
And when done viewing the video, please consider downloading the F@H program and getting a protein to fold for yourself.
New Folding thread ping!
This is a great video. While not connected to the Pande Group at Stanford, it is a state-of-the-art animation of actions within a cell.
Really worth a moment of your time!
New Folding thread ping!
This is a great video. While not connected to the Pande Group at Stanford, it is a state-of-the-art animation of actions within a cell.
Really worth a moment of your time!
And most likely the simulation only touches the tip of the mountain.
The choreography and timing depicted in the cell are stunning, mindiboggling.
These are not random, chaotic, happenstance physical actions and reactions. This is a trillion cell dance of stupefying complexity and uncanny coordination.
Some of the shorter words sounded very much like English. :=) It made me glad that I took up something as simple as computer programming.
How does it work?: You download a safe, tested program (see link below) that is certified by Stanford University. It gets work from Stanford, runs calculations using your spare computer power, and sends the results back to the University.
Is it safe? Yes! Folding@Home rarely effects computer performance in any way and won't compromise your privacy in any way. It only uses the computing power you aren't using so it doesn't slow down other programs.
How do I get started folding for Team FreeRepublic?:
1.) Download the folding program from Stanford University's folding download page (Folding@home Client Download). Type in your desired username.
2.) Type in 36120 for the team number. THIS IS VERY IMPORTANT - if you get the number wrong, you won't be folding for team FreeRepublic!
3.) The third question asks, "Launch automatically at machine startup, installing this as a service?" - We recommend you answer YES. Otherwise you will have to manually start the program after every reboot.
How can my computer help? Even if they were given exclusive access to all of the world's supercomputers, Stanford still wouldn't have as much processing power as they get from the supercluster of people's desktop systems Folding@home relies on. Modern supercomputers are essentially a cluster of hundreds of processors linked by fast networking. But Stanford needed the power of hundreds of thousands of processors, not just hundreds.
There's no reason to not get involved! It's free, easy, and you can know you're helping every minute without lifting a finger.
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I was hoping that they would react with glee at how wonderfully our bodies are made.
Lets just say that the eyes started glazing over with the first “leukocytes” and never unglazed.
I hope that FReepers will give it more of a chance, despite the language.
Or at least look at the pretty pictures ...
Bingo!
The deeper that we delve into the biology of life the more the mystery grows.
While I don’t have a time scale on the video, if there is one, most of these reactions occur in microseconds.
Millions of times in each cell, times trillions of cells in a body, times millions of seconds in a life, times the vast diversity of life that exists from a whale to an underwater bacteria living at the bottom of the ocean.
Its a little more than a coincidence.
Remember:
Mac, MacTel, PS3, Linux and Windows systems can all help us fold to make a difference!
Anybody here using the ATI streaming processor software for folding yet? WHen the new DAAMIT video cards come out I am switching to them seeing as nVidia drivers suck and I havent dared to fold yet on Vista but I do want to get back into the ‘fold’.
Awesome video!
36120 bump!
And it is even more ‘of a clue’ than that.
There is not one of those processes that can be duplicated by any means (imperfect replication) outside of the cell.
Life itself is both an enigma, and a tribute to his glory.
My eyes didn't glaze over but my ears did hurt a bit. :=)
The narration reminded me of a very old Rockwell spoof commercial. It was for their brand-new, highly cross-planarized, oscillating, self-resonant framistat or some such outlandish thing.
IBM supposedly has an entire floor devoted to abusing the new processors, but they are not folding, just stress testing.
There is an active alpha program at Stanford testing the R600 series chips, and soon the integrated video chips will be tested.
Streaming teraflop-in-a-box DAMMIT chips are still several quarters away from reaching us, but the geeks that I talk to really think that they will leapfrog both NVidia and Intel.
As good as the video is, it is even better to start folding on one of your systems.
Its not hard, and we WILL be here to help you get started.
Using a 1950 Pro to fold on one machine. It tends to do quite well (not quite the level of SMP, but not bad either). It seems the results from the ATI card almost match the point level of the PS3, and they can work on different proteins.
No matter what you fold on, it will do some good. A simple PC can fold virtually any protein type. SMP machines can also fold virtually any type and do so very quickly. Mac’s match the PC (single and smp) in their flexiblity (don’t have any of them though). ATI (GPU) and PS3 clients do specialized folding which is a bit more limited, but they do it very fast.
So it doesn’t really matter what you have, it will contribute and make the world a better place.
One important note: make sure you put 36120 as the team name (FR gets credit) and josephw as the username (I get credit - or use your own and take credit for yourself).
Remember everyone can help and we have consistently blown away the DU as we believe in charity and they are waiting for the govt to send them a cheque for a new system and monthly (welfare) payments to show their good will.
Reminds me of TI.
Great engineering, lousy marketing.
Never put an engineer in charge of commercials. Dry hardly begins to describe it.
Somewhere I have a Byte magazine ad spoof from the early 80s for a nuclear powered battery backup. Sounds much like the Rockwell ad.
BTW, folding is adicting - not that I would know anything about that (watch your six texas booster, I’m less than two months from passing you)
Yeah, I check it out every three hours, and there is not much I can do about it. Congrats.
For a day or so, your 1950 Pro and PS3 were making you the number 1 folder on the team.
Of course, now that Klutz is back from spring break things are back to normal.
yeah, but mine are all home systems (and all in my home). My heating bill is small in the winter, but my summer electric will scare me :)
Well GPU’s are pure math crunching machines, and the R600 supposably is rumored to have it’s own physics engine on die so that will only add to its mathematical crunching power. Anyways thanks for the heads up.
Great movie and explanation; makes you realise just how ignorant we are and what else we have to discover.
I also went to their main site — http://multimedia.mcb.harvard.edu/ — and there are several other lectures on DNA and Gene Sequencing. Very informative. Thank you.
BTTT
Thanks for the overnight bump!
It is a great animation of how our cells work - but there is still much more to be discovered.
Good morning Texas booster and the other FR folder.
Nice video link btw.
Apologies for the off-topic hijack of this thread but didn’t feel that I should start a new thread on a non-folding specific forum.
Before anyone flames me I’d like to say I’ve been supporting DC projects for many years now most recently the BBC climate change (two complete models - they take many months) and Folding@home (lemonman - team 10 ~400K)
However I am in a different team (OcUK) and therefore appeal to group ethos of the folding community for my request. For those of you that use Fahmonitor on vulcan.pve-inc.com you many have noticed that Team 10 (OcUK) have appeared on the stats – that’s me.
Apologies if I’m treading on anyone’s toes - as I didn’t realise it was a single team resource (with the team variable I presumed it was open) Anyway I’ve not set-up the schedule manager yet; just did a test upload (as per guide) and that’s when I realised.
I really like this web based tool (10 gold stars to the programmer) as I’ve Pc’s crunching WU’s all over London. And FahMon 2.2 just can’t do what your site does.
I’d like to carry on using Fahmoniter but as I see it I’m now left with three options.
1) I leave Fahmonitor alone - after 7 days my stats will be deleted (as per guide) and you’ll never here from me again. (a shame but I’ve no right you use your teams resources)
2) I’m allowed to keep my stats live on your server. I’ll thankfully load 20ish pc’s and use it gratefully without fuss. I’ve no problem of you team comparing their results against mine - and will help with folding related topics posted here.
3) I’m allowed to have a copy of the stats site code (full credit to the author) and I’ll host it on my server for my team. (my preferred option as I’d doesn’t use your resources, but know I’m asking a lot)
Bit of an epic post but felt I needed to ask now I realise my mistake.
I look forward to your replies.
S
Egon is the creator of fahmonitor. He alone decides what you will be allowed to do with it. We are just glad that he lets us use it,
Its kinda like democracy here at Free Republic. If Jim and John say its OK, then its OK.
Since you are a FReeper in good standing, not having been banned yet for today, FReepmail Egon and beg to be allowed to continue. He may even have time to set up another team. ;’)
That was highly cool. I’m finishing up a microbiology class now.
Hilarious part in the middle for those of you who can’t stick the whole thing: the vesicle being hauled up the microtubule by the walking motor protein.
Mrs VS
If you're interested in tracking your folding machine(s) over the web, please Freepmail me.
Available features include:
Our posts are heavily geared towards supporting F@H and getting FReepers to join the research. The idea is to get as many people involved into research as possible.
I know that there are many FReepers that BOINC and support other folding projects. Perfectly fine with me.
I’ll toss you onto the F@H ping list with your permission. A viewpoint from outside our little group is always welcome, and any support you can give to us only benefits everyone.
I was wondering about the walking “motor protein”.
I understand the concept and the need for passive transport in a cell, but is it possible that the animators got a little carried away at that point?
As our resident Microbiologist on the forum, how close to reality is all that stuff, going on in our cells?
What kind of timeframe are we talking about here? Milliseconds or microseconds?
Yeah, just saw team 10 show up! That's what I get for missing staff meetings!
Not a problem, shadowscotland, feel free to use the tool. Glad to have you! It looks like you were able to successfully set it up!
FAHMonitor was set up to support multiple teams-- I just never have officially opened it up-- although I'm seeing multiple pointers to it on Google now.
I just fixed a bug that was taking team 10 users to team 36120's home page.
Hey doode, that is so great to see multiple teams on the home pahe of F@Hmonitor!
Wonder how many users are out there that are using F@Hmonitor and we don’t know it?
You may have to get back over to the support forum and bring that post back to life.
I guess our next scheduled staff meeting will either be in Dallas, St Paul or London. Have your appointment secretary get back to us.
Good grief, I’m taking an introductory course.
However:
Eukaryote (that’s us) DNA replicates 50 base pairs a second, with thousands of replication forks in each chromosome.
One molecule of the enzyme carbonic anhydrase can convert around 600,000 molecules of carbon dioxide to carbonic acid in a second - they’re popping in and out of one pocket that fast.
Carbonic anhydrase is a speed demon; other enzymes work at slower rates, maybe catalyzing 20, 100, 2000 reactions a second.
I have no idea how fast microtubules synthesize, maybe about as fast as DNA? and would guess similar rates for protein synthesis from the RNA.
And I’d read that the cytoskeleton guided vesicle movement by cytoplamic streaming but I never never read about any walking motor protein tethers. I’ve got to show this site to my professor.
Mrs VS
The microtubules probably synthesize faster than DNA, because you can see cells move. I didn’t see any enzyme involved in the animation though, the molecules were shown just flying into place.
Mrs VS
You understood what “Eukaryote” is without Googling.
We bow in honor of your wisdom.
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I’m still amazed at how much more we know than when I had college biology. The deeper we look the more there is to see.
Makes Intelligent Design a very respectable theory, for those that care to consider it.
None! If you back out all the way to the 'HOME' level, you can see the teams, and drill down to their members.
...I just don't very often!
I guess our next scheduled staff meeting will either be in Dallas, St Paul or London. Have your appointment secretary get back to us.
Unfortunately, my appointment secretary is also the Budget Committee...
BTTT for a video of life, instead of the videos of death that we see from the MSM.
Trying to get a discussion going that does not include speculation on the gunman in VA.
I don’t think the shootings are out of anyone’s mind today. How can one disappointed person be so evil, and so hellishly efficient. Well, the story’s not all the way known yet.
Back to the cell video - the walking motor protein looks kind of like the myosin filaments in muscle, that grab and release the actin chains.
Here is a video of that - and you get to speed it up and see it zoom.
http://www.sci.sdsu.edu/movies/actin_myosin.html
Mrs VS
I got out my Anatomy and Physiology text - it does mention the walking proteins after all - guess I need a cartoon to make it stick in my mind.
Anyway, there are two of them, and because the microtubule is polarized, dynein walks one direction and kinesin the other.
Mrs VS
‘Now that’s entertainment’ placemarker for later.
I hate it when that happens.
Howdy to JLATINY for joining the FReeper Folders Team 36120.
Please drop by and say Hi.
Thanks people - you’ve save me a few man-hours a month tracking down problem PC’s that hang durring uploads.
@TB - good to see you awake and active ;o) I did mail the forum generally without success last week so thought I’d sign up and go direct to the F@H user - and as with my own teams community you responded quickly and graciously.
@Egon - thanks for the use of your server :o) Nice bit of programming, especially the time offset (usually ignored) - the guide was easy to follow too.
A few questions - does it work with smp units? and can you mix and match linux and Windows pc stats. (I’m guessing is yes to both)
And yes I’m quite happy for you to add me to the ping list.
@All - Background on my folding farm and me ;o)
‘the office’
duel xeon server (that crunches 2 or 3 stand alone WU’s - not web enabled but networked - long story but ask if you want too)
1x E6300@2.0 running winSMP,
1x E6300@2.0 running two standard clients
4x P4’s HT running two standard clients
4x P4’s running single clients,
1x E6400@3.0 running linuxSMP via VMware/ubuntu (home)
5x P4’s running single client (office above work ;o)
1x P4 single client (dad’s)
afew others dotted about.
Use Fahmon 2.2 with the SMP patch
Architect by profession, married and have a little boy
Current issue that we’ve been talking about.
windowsSMP hanging after completing a WU. - did use the oneunit flag now have a simple batch file that runs consecutive -oneunit clients. (below change path to suit)
@echo off
echo Starting FAH for the first time
echo -———————————————
echo.
“C:\Program Files (x86)\Folding@Home Windows SMP Client V1.01\fah.exe” -oneunit -verbosity 9 -local
:restart
echo.
echo Restarting FAH
echo -———————————————
echo.
“C:\Program Files (x86)\Folding@Home Windows SMP Client V1.01\fah.exe” -oneunit -verbosity 9 -local
goto restart
standard clients getting better WU’s again - C2D getting 1k ppd with two standard clients.
more people useing 64bit ubuntu - I get 2k ppd on my home machine
many turning off P3/celeron/low P4’s due to high electric bill vs ppd.
Thanks! It's been fun to put together.
A few questions - does it work with smp units? and can you mix and match linux and Windows pc stats. (I’m guessing is yes to both) list.
I was fortunate enough to briefly have two SMP Macs folding a couple of months back, and was able to track them just fine.
Basically, my system relies on the contents of the unitinfo.txt file which, theoretically, is outside of the scope of differences between SMP and non-SMP versions of the F&H app. In essence, it shouldn't matter.
There is a PHP version of the monitor script for Linux OS's. There are a few extra hoops to jump through to get a Linux box reporting, but it is certainly do-able. All but two of my machines, for example, are Linux boxes.
On the help page, there are links at the front of the setup sections for the Linux version.
Incidentally, while there is no specific monitor script version available for Mac, the Linux version works quite nicely for it.
Thank for the answers - I’m trying out the scheduled task update (60min - should I set this higher?) on three machines all duel threaded to see how it works - FM is tracking 4 of 5 currently (don’t know why one standard client is missing...)
smp unit - progress is tracking fine but no details on type/pts etc.
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