Category Archives: Linux

Linux

Cellular Automata and Tissue Engineering

I’m taking a tissue engineering course right now, (see previous post), and this has rekindled my interest in cellular automata. I was first introduced to them by Stephen Wolfram’s book, A New Kind of Science (freely available online). This is one of the books that helped me to understand how complex life can develop from relatively simple rules.

It’s led me to wonder how much tissue engineering experimentation could be done using 3D cellular automata. Tissue engineering requires all kinds of cell lines and biochemicals, incubation times, and so on, making it somewhat expensive and time consuming. The ability to model, say, mesenchymal stem cells with cellular automata could be used to ‘get a feel’ for tissue development with less time and expense.

I went looking for 3D cellular automata to play with, and came across this one:

Cellumat3D

Cellumat3D is a tool for simulating and exploring cellular automata in 3D space. The application uses OpenGL and is fast enough to give a good impression why cellular automata are regarded as part of artificial life research.

It’s a little obscure, and there’s not really any documentation that I’ve seen for setting up rules. I need to double-check the CVS code for documentation. The author also links to a bountiful resource page on 3D cellular automata. It looks like it hasn’t been updated in a while. At least some of the links work, including one to a java-based 3D simulator of the Game of Life. It’s pretty slick — you can grab and rotate it with the mouse and so on. Here’s another one that’s a little less intuitive but allows editing. Life3D looks interesting, but it’s only available for Windows.

If you know of any other 3D cellular automata for Linux/Unix/OS X please do pass them along in the comments or by email.

ADDENDUM: 2006-02-15 @ 21:04 CST – MathWorld has a page on cellular automata in Mathematica.

New WTUL recording script

Last year I posted about a script I wrote for recording WTUL (Tulane University’s radio station). Since Katrina, they’ve been running a different stream, rebroadcast by Stanford. It’s in the open-source OGG format, and it only took a small modification of the script to adapt to it. I’ve posted the new script. All of the directions are otherwise the same (and are on the script page). You still need mplayer and so on.

My New Home Network

In the last week or so I’ve finished setting up my home network. It includes

  • A Linksys WRT54GL
  • A Linksys NSLU2
  • A LaCie 500GB external disk
  • A Motorola SurfBoard cable modem

The WRT54GL is running a custom Linux firmware (DD-WRT), which allows me to tweak all kinds of settings (including radio power), log in with SSH, and if I solder an SD card onto the motherboard, load all sorts of additional software. The management software is much nicer than what it comes with.

The NSLU2 is also running a custom linux firmware (OpenSlug). It’s somewhat Debian-like. I added a 1GB memory stick to one of its USB ports, and hooked up the LaCie 500GB external disk to the other. The operating system resides on the 1GB memory stick, while I serve files, run backups, and serve iTunes music (with mt-daapd) from the 500GB drive. The iTunes music shows up as a shared library on the macs, available for streaming. The custom firmware also allows the use of a usb hub. Once I get one, I’m probably going to hook the printer up to it, and use it for print serving as well.

The cable modem doesn’t do much. It just hooks us up to the ‘net. Here’s a picture of the set-up. Notice the penguin in a slug suit on the NSLU2 (because the devices are referred to as slugs).

Home network

Adobe Acrobat Stupidity

I’m filling out a fellowship application that requires the use of Adobe Acrobat, and the free reader won’t cut it. I had been using a computer in Dr.Rudy’s lab, running Win XP, that had Adobe Acrobat Pro installed. Unfortunately, I’m not done filling it out yet, and I am leaving for NOLA tomorrow bright and early.

Therefore, I had to go buy Adobe Acrobat for Mac. I opted not to get the professional version. It cost $100 at the educational pricing level. It’s bad enough that I should have to fork out cash for this when a simple web form would have been just fine, but it gets worse.

It wouldn’t run. Nothing. Not run and quit. Double-click-then-nothing. I was pretty sure that I knew what the problem was right away: they assumed that my filesystem wasn’t case sensitive, and were accordingly careless in writing the program. When installing OS X v. 10.4 (Tiger), it’s possible to choose a case-sensitive HFS+ filesystem, rather than the standard non-case-sensitive HFS+. I chose case-sensitive, because I normally work with case-sensitive filesystems in Linux, and there have been times in the past where I had collisions — files that were named the same thing except where case differed, and transferring those files to Mac OS X had been a mess.

Luckily, I was able to figure out what the problem was. I ran the program from the command line, and discovered from the error message that the program was looking for AdobeBIBUtils.framework. The file that existed was AdobeBibUtils.framework. The difference is just the case in IB vs ib. I renamed the directory. The program then launched, but crashed moments later looking for AdobeBibUtils.framework. They had used two differently-cased names in the same program.

I just symlinked one name to the other, and now the program runs without a problem. Adobe has something about this problem on their support site. Their solution? Install it on a non-case-sensitive HFS+ filesystem. For many people this means reformatting their hard drive and reinstalling everything. That’s a great solution to Adobe’s shitty coding. There may be a few more of these spelling land-mines in the software. I guess I’ll have to find and fix them as I go along. How absurd.

Guess what, Adobe? It took 30 seconds to fix the problem. I suggest you take care of it on your end. I can’t believe I paid money for this.

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New Treo with Linux?

As I mentioned in my previous post, my Treo 600 sustained some damage to the screen. While it’s okay now, it may spread. Anyway, it looks like if I need to replace it, I should perhaps get a Treo 650 after all. Soon, I should be able to run linux on it and with a working phone!

Combined with my external keyboard, this would be fantastic.

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