Category Archives: Tech

Tech

If they outlaw evolution, only outlaws will evolve…

My friend Alex from Back In The Day™wrote an interesting post about his hope for the future of Humanity based on the democratizing effects of technology and the Internet. Except that he put it a lot more poetically. Here’s a snippet:

earthbound01: the internet is wide

broadly, there’s some kind of metaphorical Library of Alexandria here, it’s depth of knowledge wide and deep. Virtually all human learning is available here if you have the right passwords and authorization. I’m able to read scholarly journals now from a little terminal. All of our culture is slowly being uploaded, explained, digested. Perhaps one day all cultures will be there. Just think for a minute how sweet the future is going to be now that information is available broadly. Think of it though- all knowledge, all art, all human creation and technology available, or at least explicable. And communication! Instantaneous text, sound, or video transmission. Amazing!

…

There’s some kind of air-strike going on in Iraq, and I’m worried about “collateral damage”, and our soldiers, and really everyone involved. Wars are great for stopping nazis, but I am starting to think they aren’t very good for stopping concepts like or terrorism. Still, these things are temporary, and I think people aren’t stupid and are learning.
Life goes on.
and adapts.
Maybe we can tell the creationistas that if they outlaw evolution only outlaws will evolve.

Electronic Journals and Cost

Post-Katrina we are definitely having journal access issues at Tulane. The sheer cost and lack of thought toward online access from Elsevier (as mentioned in the linked article) and its peers are a continual aggravation when looking for papers to read.

Over on Kalimna there’s an interesting look at what I hope is a new wave in academic publishing — purely electronic publication. Honestly, when you can print a PDF of any article you want, and customize search feeds to aggregate articles you’re interested in as they’re released, why do you want paper journals that you often have to go to the library for and that cost a fortune?

Kalimna

Let’s get some perspective on publication costs. As BEP point out there is a cost crisis in most university libraries stemming from the monopoly pricing power, based on reputation and prestige, of large ‘for-profit’ publishing houses. For-profit publishers in economics charge around 83 cents per page of a journal article whereas not-for-profit publishers associated with universities charge around 17 cents per page: See here for data. BEP costs 36 cents.

Implementing and Studying the Conjugate Gradient Method

When I start up a simulation on our cluster, I’m used to seeing this after some information scrolls by:

Solver = Conjugate gradient
preconditioner=block Jacobi with ILU(5) on each block

I knew before that this was some way of solving a big matrix representing the problem at hand, but never knew how it was done. (Un)luckily, my midterm project in one of my classes this semester is to implement and play around with the conjugate gradient method. We were given a little introduction to the method of steepest descent, then sent on our merry ways to the Mardi Gras and subsequent break.

I was terrified.

I started reading the course notes that we’re using for the class, but they used a bunch of terminology I’ve never heard of before. They were extremely concise. Attempts at understanding the information on MathWorld and other sites ended in confusion. And then, I came upon this title on google:

An Introduction to the Conjugate Gradient Method Without the Agonizing Pain

With the agonizing pain still acutely in my mind, I clicked on the link and gave it a try. It’s excellent! The author, Jonathan Richard Shewchuk, writes with clarity, knowledge that I’m probably not a numerical analysis professor, and a little dry humor here and there. After searching for him on google, I discovered why the name looked so familiar — I used his Triangle software to generate my 2D cross-section of our model of the rabbit ventricles! The CJ paper has pretty much saved me, and perhaps more importantly has shown me just how cool and clever numerical analysis can be.

If you want to learn about the CJ method, you really must read his paper.

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.

Online Biomedical Articles, Reviewed

The author of HubMed (an alternative and nicer interface to PubMed‘s database) recently posted an online journal review on his blog. While he prefers PDFs (as do I, for now), there are various aspects of articles-in-HTML that make them more or less useful and easy to read. All of the major publishers of online biomedical texts are scored. From the post:

HubLog: The state of online biomedical full text articles

I carried out a survey of HTML fulltext pages from the major publishers with the aim of identifying a) problems with usability and b) recurring themes in semantic markup of article elements (which will hopefully lend itself to a microformat recommendation for scientific, or at least biomedical, articles).

This is an issue on which the publishers are way behind. There’s little competition, and therefore little impetus for them to improve.