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Yes - there are formulae for computing forces. But no, they don't bear much relation to reality Any simulation running anywhere near realtime is likely to be a purely classical simulation - balls and springs.

I sit next to the guy who wrote Fred and he will gladly admit one of the best predictive scoring function is the order of the entry of the compound in the pharma companies database. I.e. old compounds are not active - at all.

If you care to check you'll find very few cases of a drug discovery, say, resulting from a theoretical prediction about receptor binding.

I disagree with this, but it does depend on your starting point. If you have a known molecule bound to a protein, we are very good at finding new binders, even from different chemical classes. That being said, de-novo design leaves a bad taste in my mouth.

Finally, looking at the Scripps' website, they seem to be looking at very macro-structures like viruses. These were most likely imaged in solution using an nmr to generate the computer models. There is some pretty good software for doing these large scale fits (the homepage appears to be down). Essentially they are not doing drug-protein interactions but larger scale models. The question they are asking is if these molecules interact, how do they fit? They aren't predicting interaction, they already know that.

This might be a cart-before the horse because if they generate a computer model that packs the structures together, it isn't surprising if the 3d printed ones do. I have more faith in this than predicting drug-receptor bindings.

Not just visual cortex, but also lateral geniculate nucleus and probably a half a dozen other visual areas in brain.

Recently, though, there was some functionality I wanted added to ClamAV, an open-source virus scanner. Basically, I wanted to make sure the milter was running. So, I wrote clmilter_watch, a tool to monitor the functionality of clamav-milter. Of course, I don't trust my own programming skills enough to know if it's stable for production use. So, it gets released to the world. A few downloads later, I get a couple of suggested patches, and the thing is pretty solid. Everyone wins.

What sort of molecular structures are you thinking of? Klaus Schulten's people, (http://www.ks.uiuc.edu), are doing 100K - 1M atom simulations on workstation clusters, and people I know are modeling polymerization catalysts using quantum methods on clusters or fast desktops.

Of course, if you're thinking of simulating a ribosome in action, then, yes, you're right. We'll need (estimated) exoflop machines for that.

But I wonder what people are doing with their exotic Linux installations... What are these used for besides showing off? Is there some real-life application to having Linux on these things?

I don't know myself, but obviously some people smarter than me seem to think that it is useful:
PlayStation turns supercomputer
Scientific Computing on the Sony PlayStation 2
Playstation 2 Linux Cluster at NCSA

'The smallest mass ever measured would have to go to the electron.'

Give yourself a quick reality check ask yourself these two questions.

What's the mass of Light?
is is smaller than the mass of and electron?

The mass of an electron or light it proportional to the energy contained in the light or electron.
But they are both equally proportional, i.e. they are both leptons.

The energy of Light is Planck's constant times its frequency. E = hv, I assume this is the same for an electron. (google doesn't turn up anything).

Typically the wavelengths of light are equivalent to an electron with a potential of just a few volts, so sometimes light is heavier than an electron, but more frequently electrons are heavier than light.

I suppose for an atom you should count the ironzation levels for the potential of electrons, they they are between 500 and 2500 kj/mol, which works out as roughly between 5 and 25 electron volts. again showing electrons to be heavier than photons.

Other groups working on optical interconnects: (incomplete list)

Heriot Watt

Cornell University

IBM Zurich

Delft

UIUC

Intel

Stanford

A short word about this. The right way to do this in a distributed environment IMHO is to use something like LLVM to ship binaries in a CPU architecture independent format. This has several advantages:

• LLVM images tend to be smaller than ELF images as the bytecode format is more compact than x86 code is
• The VM can produce native code without any virtual machine overhead at install time, whilst still optimising based on the CPU features available at runtime. This gives such binaries the same advantages that Gentoo users tout as being an advantage of compiling everything as all binaries are fully optimised for your CPU, but without the massive speed hit that C/C++ parsing implies.
• As new architectures are introduced there's no need to recompile packages, you can use the pre-existing ones after writing an LLVM backend
• The LLVM image format is quite good, and more easily extended than ELF. So things like relaytool become no longer necessary because we can fix it in the binary format rather than having to hack around it.

Nobody is working on integrating LLVM and autopackage right now though.

Trailblazer

The Machine Stops by E.M. Forster

At the GCC conference in Ottawa in the summer of 2003, there were two very interesting features presented that they said might make it into GCC 4.0.

- LLVM. Low Level Virtual Machine. This is a low level and generic pseudo code generator and virtual machine.
http://llvm.cs.uiuc.edu/
This sounded fabulous, and the project appears to be progressing well (it's at v1.4 now). If I understand correctly it is only politics that has kept it out of GCC 4. Can anyone shed more light on this?

- Compiler Server. Rather than invoking GCC for each TU you would run the GCC-Server once for the whole app and then feed it the TU's. This would make the compile process much faster and allow for whole program optimization.
This would have been nice but perhaps they found better ways to achieve the same thing.

My personal Knuth story: in 1979, when I was just starting graduate school at the University of Illinois, Knuth came on campus to give three lectures as that year's Gillies Lecture.

At the time, the second edition of Volume I had just come out, and everybody was eagerly awaiting volumes 4 through 7. The lectures were all packed, and the great man, inventor of LR parsing and author of the definitive tome on computer science, spoke on...

typesetting and fonts.

Don't get me wrong, the lectures were interesting, but it didn't seem all that fundamental to computer science, if you get my meaning. 25 years later, we're still waiting for volume 4 to be completed, but at least the new editions of 1-3 had nice fonts.

The following year, Douglas Hofstadter came to campus to speak. This was fairly soon after Godel, Escher, Bach came out, so we were all excited to see what cool and interesting CS things he would lecture on. His lecture turned to be on...

typesetting and fonts.

I guess it was just the thing to do at that time; little did I suspect that much of the productivity of US offices in the 90's would be spent selecting fonts for documents. I guess great thinkers are just ahead of their time.

> Every state has collection procedures. If they didn't, the civil justice system would serve no purpose at all.

And how much of the $33million dollar damages has OJ paid?

http://www.news.uiuc.edu/biztips/01/04bankrupt.htm l

Call me ignorant, but isn't that a bit slow? Why not fly faster? Educate me on this, anyone?

I was happy to discover that they still have the original hostname hoohoo.ncsa.uiuc.edu available! I remember getting this to compile on an old NeXT box, which hosted our math department's web page before most colleges at our uni had a web page.

Use this tool to determine if the ID number of your /. comment is prime!

Also see University of Illinois' brand-spanking-new Turing Cluster, 640 dual-processor XServe G5s running X.3 Server.

Taskbar, start menu, integrated filesystem/net browser, .NET, etc.

What do all those things have in common with Linux? Oh, that's right, they're Windows features that are ripped-off in all Linux distros.

Hilarious.

• Arthur/RiscOS2 (1987/1989) and NextSTEP (1989) both included a taskbar. ( History of the GUI )
• The start menu is very similar to the apple application menu.
• NSCA Mosaic supported local files since version 0.2a, publically available was version 0.5a in 1993 ( NCSA Mosaic History ). Microsoft bought a Spyglass Mosaic Browser version and renamed it to "Internet Explorer" in 1995.
• .NET is hardly innovative. It rather blatantly copies Java which copied features from Smalltalk, Pascal and LISP.

Sure. Some people even built a computing cluster out of them. But actually getting that performance in practice is really difficult. I saw a presentation online once that indicated real games seldom if ever get more than a fraction of that.

Whether it is a positive or negative feedback is based upon the result.

Hey you - down there in the hole - shall I drop you a new shovel?

Looks like the landings were faked after all. The evidence here is quite convincing:
http://www.ews.uiuc.edu/~akapadia/moon.html

This was my senior design project in college. Or similar to it. We had grandios ideas, but got it working (hackingly I must admit). Motorola does not freely release code for interfacing digitally with their data port. Thank god for old analog phones: https://courses.ece.uiuc.edu/ece445/cgi-bin/view_p roject.pl?spring2001_25

A Google search turned up this paper on nanoscale circuits that appears to be related. It mentions HP's crossbar latch patent in particular. Interesting stuff.

Similar things have been done for OSX before:
3D-OSX

It even got Slashdotted Before

I would love this built into OS X but it is just for Windows right now.

I can recall seeing some kind of 3D finder for OS X before, so I did a google and found it. It's called 3DOSX. However, I also found another one called 3D-Space VFS as well. They aren't the same thing as the UI the Slashdot post is talking about, but still are some kind of 3D interface.

So essentially Microsoft is back to taking the approach that if they close their eyes tight enough, everything will be OK?

'Super-Linux' Cluster Declared Third-Fastest Computer On Earth

fastest computer system in the US

NCSA Linux Cluster Among Fastest Computers in the World

Two Linux clusters on Top 10 list of fastest computers

http://cm.math.uiuc.edu/~staffin/1984macintro.mov

also,

http://www.acm.uiuc.edu/~staffin/1984macintro.mov

http://cm.math.uiuc.edu/~staffin/1984macintro.mov

also,

http://www.acm.uiuc.edu/~staffin/1984macintro.mov

Whoops, add a "/partiview" to the end of that url. Like this.

Have you tried Partiview? It's pretty good with those kinds of datasets - I use it for 3d scatterplots a lot. And you can change the colors of points by whatever attribute you want, and spin the data around smoothly in realtime - I can do that with a quarter of a million points on my laptop with a GeForce Go5200, and probably more if I tried.

Also check out Partiview , a fast open source viewer from the NCSA. It has its limitations, but can handle large animated multidimensional data. The AMNH uses it as the viewer for its nifty planetarium-on-your-laptop Digital Universe, and we've used it to visualize cosmic ray showers, dark matter simulations, global computer networks, clustering patterns, and as a general infovis tool. It also works in stereo, which is really nice when you have two projectors and polarizing filters. The linux binaries supplied sometimes have shared library problems... but /.ers are used to compiling from source anyway...

I wouldn't eat that just yet...Let's see here. We have a timeline: right here. Kennedy was the new liberal on the scene, which would be the start of your "pendulum swing." What's that under 1965? First American combat troops arrive? Granted we were there training South Vietnamese troops, but we weren't in a war yet.

Now in another timeline outlining the early 60's and another policy of Kennedy (here), take a look at 1961. The Bay of Pigs. Another military action, one that we all know went terribly wrong.

My point: conservatives are not the only ones who have policies that actually involve military action. A government will do what is necessary (as did Kennedy and Johnson, as well as Eisenhower) to achieve their agenda. Clinton attempted to do this in Somalia, Bush went to Kuwait, and W. Bush is in Afghanistan and Iraq. If you look at history, both sides of politics have gone to war and/or had military actions, some terribly gruesome (Somalia, Vietnam, Iraq), but one side has not been the instigator and the other the saint.

The problem that I have with it is that it's based on scholarly work. Since he's the president of a college, that probably means that he is studying grades, homework, or teacher reports on male vs. female students. This does not take into account factors that effect the outcome before the students even reach his school.

Some studies have shown that teachers tend to call on girls less and expect them to get lower grades in math and science classes, and that parents also can have a negative effect on girls' attitude toward math. Other studies have shown that girls simply don't like math. here are some examples.

So, there are dissenting opinions on the subject. This is something that I don't think we can get a really good control case for. Without a control case, how do we know that we aren't starting out with girls that have not been negatively influenced by parents, teachers, or other peers?

I am female, and have always had a natural ability to do math. I don't particularly like it, but I am good at it. (We are talking about a level below calculus, I did not have any kind of natural ability with that!) I used to tutor people that were in the same class as me.

While I only remember having a couple of teachers pick me out or completely ignore me, I'm not sure if that was because of me as a person, or because of gender. I tend to think that it didn't have anything to do with gender. I may not be getting a general idea of what is going on with this, though, because I went to a small college where a decent percentage (about 1/4) of the math and science graduates were female. I also went to elementary/middle/high school in an extremely small town, there were only about 20 people in my graduating class.

That said about teachers specifically, I think that a lot of what happens has to do with what girls pick up from society and school. Parents are sometimes sexist, they have an idea of what their children should be like and treat them as if they were that way. My dad refused to teach me chess after teaching my younger brother, and my mom is always saying how she can't do this or that because she's a girl. This may be unusual with parents specifically, but this is the kind of influence that girls get from the people around them all the time. I went against parental influence on this particular point, but it would appear that I am unusual in this.

You graph complex numbers in the complex plane, silly =) One axis is the real axis and the other is the imaginary axis. Here's a brief intro from the math forum (a written intro, without graphics), and here's some more examples from a graphic intensive site that shows how you can perform operations on complex numbers like vectors. You can also do neat stuff like find the complex roots of numbers by manuiplating the graph, which is also mentioned in the 2nd site.

[A graphical history record]

That, combined with a history TREE instead of a linear, self-overwriting history (go back 3 pages and click another link -- those 3 pages will drop out of the history). That's what I wish for.

Something like this?. Unfortunately, it's mac-only, a browser unto its own, not an addon to safari, and not a terribly good browser at that. Would be nice if someone ported it to some other browser.

Sounds like enough is enough (which just locks down IE's security settings) which I installed on all the PC's in my company. Most of the users have no problem with the idea that they must say sites are "trusted", and EiE adds a couple of menu items that make it easy. Well worth a look for those of you to who find themselves supporting PC's for IE addicts.

http://www.news.uiuc.edu/news/04/0809firewall.html

Don't take a vacation in Cuba, that's communist and evil. But feel free to sell advanced computer and networking systems to China. That's cool.

Check out Who Eats the Energy? study. A HDD eats about 2-3 Watts when in use and 0.5 Watts when idle. A wireless card eats 1 Watt in base idle mode (less than in power saving mode) and 2-3 when transmittin/receiving. With a network computer it would be working 100% of the time, while a HDD would be mostly idle. So your assumption is not true. Also note that notebook power consumption in that study was 11-16 Watts in total, so switching to network computing mode can decrease battery life as much as 10-25%.

To get a rough idea of trends, I've been plotting stats on a mailserver I manage. In general, we see spam and viruses are increasing, while ham is decreasing. Spam is about 67% of incoming mail.

I also plot my personal spam stats but obviously an individual account is hardly representative.

To get a rough idea of trends, I've been plotting stats on a mailserver I manage. In general, we see spam and viruses are increasing, while ham is decreasing. Spam is about 67% of incoming mail.

I also plot my personal spam stats but obviously an individual account is hardly representative.

there is a serious error in TFA.

For Pentium M compiling benchmarks, look carefully HERE

IANAM (I am not a mathematician), although I did pass Calc 3, Linear Algebra and AP Statistics, but a tesseract projection shouldn't be infinitely large. You can think about the projection into 3D by analogy: let's say you start with a square, and want to make a cube. All you have to extrude the square upwards. If you look from the top down, however, it looks almost like a square still. Then, if you look at it isometrically, it looks like you dragged a copy of the square at a 45 degree angle from the original and connected it point for point with the original. The 3D projection of a hypercube similarly looks like two cubes, seperated orthoginally depending on the hypercube's rotation in 4D, but connected point for point. At the correct orientation in 4D, it'll actually be a cube. Here's some sites that explain it better and include pretty pictures:
http://www.geom.uiuc.edu/docs/outreach/4-cube/
http://casa.colorado.edu/~ajsh/sr/hypercube.html
http://mathworld.wolfram.com/Hypercube.html

I remember using Mosaic when I was in school!
</old man voice>

Well, it's technically possible: http://www.ece.uiuc.edu/pubs/plasma/plasma1.html

Seeing how Firefox is an offshoot of Mozilla, which is an offshoot of Netscape, which has been around longer than IE

Microsoft Internet Explorer is an offshoot of Spyglass Mosaic, which is an offshoot of NCSA Mosaic, first released in 1993.

Then it's flat top, dirty bob, coppin' a feel
Grubbin' on the livin' room floor (so sore)
Yeah, they send you off to college, try to gain a little knowledge,
But all you want to do is learn how to score

Some things never change. The rest of that is here

"The University Library is the largest academic library at a public university in the United States. It ranks behind Harvard and Yale as the third largest academic library in the United States. Today, with holdings of more than ten million volumes, the library has strengths in many areas ranging from hard sciences to the humanities." from http://www.library.uiuc.edu/mortenson/aboutus.htm

Octave - Matlab minus the GUI and extra toolboxes
Macaulay 2 - advanced algebra
GAP - general algebra

C'mon hax0r people - no-one needs another web server / window manager. I'm missing an OS replacement for Mathemetica. One would think this would be of high priority to the OS community...

I have personally tried a 3D Operating System implementation, and my opinions are mixed. If you have OS X you can try 3DOSX for yourself with a free download http://www.acm.uiuc.edu/macwarriors/from the University of Illinois Mac SIG.

By contrast, NCSA's surprise entry in November 2003's list, Tungsten, achieved 9.82 Tflops for $12M asset cost.

When I looked here, I found this: ``Tungsten entered production mode in Novermber 2003 and has a peak performance of 15.36 teraflops (15.36 trillion calculations per second).''

To me, that looks faster than System X, not slower.

Let's see: NCSA stands for ``National Center for Supercomputing Applications''. ``NCSA is a key partner in the National Science Foundation's TeraGrid project, a $100-million effort to offer researchers remote access ...''

Looks as if the NCSA has a huge budget. I'd guess that ``gold-plated everything'' and ``leave no dollars unspent'' are basic specs for everythig they buy.

What can we learn about Virginia Tech? How about this:

System X was conceived in February 2003 by a team of Virginia Tech faculty and administrators and represents what can happen when the academic and IT organizations collaborate.

Working closely with vendor partners, the Terascale Core Team went from drawing board to reality in little more than 90 days! Building renovations, custom racks, and a lot of volunteer labor had to be organized and managed in a very tight timeline.

Yes, System X and the Apple hardware is pretty neat, but don't use the price/performance ratio of these two systems as a metric for the relative worth of Linux and OSX clusters.

It's unfair and meaningless to compare volunteer labor and academic pricing and scrounging on a limited budget to bureaucratic design, bureaucratic procurement and an unlimited budget.