In an earlier post I alluded to some thoughts that I had on proprietary vs free open source systems for dealing with scientific data. Somewhat out of time constraints and somewhat out of laziness, I had decided to pretty much just stick with the proprietary status quo system that I had in place, rather than commit to the time in learning something new. The double shot of my activation woes with Matlab with my recent realization of how much I had been reinventing the wheel by not using Ferret has given me a new perspective, and after a recent comment inviting me to try out Sage open source mathematical software, I figure that it was time to give it a try.

As Sage is “a free mathematics software system which combines the power of many existing open-source packages into a common Python-based interface”, that means that there are many libraries bundled together. These include ipython, numpy, scipy, R, RPy, and more. While I already had many of these installed on my Macbook, rather than look for a solution to cobble things together to save space, I just took the easy route and downloaded the .dmg file to keep everything together in one environment. I’m not sure if it’s possible (or even wise) to use existing components (probably not) but I figured that it would be more hassle than it was worth.

The .dmg file is fairly large (~256 MB), but smaller than the last Matlab release, which can put things in perspective. Download also only took about 6 minutes over wireless (>500 KB/sec). Installation was as simple as dragging the sage folder from the mounted .dmg file into my Applications folder. Expanded the folder was pretty hefty (~780 MB), which was larger than the last Matlab release (~680 MB), but not by much.

The next step in the installation instructed me to double click the sage icon (inside the Sage folder), and then change some preferences. When I double clicked it however a terminal fired up and I sage started to work

[user@localbox ~]$ /Applications/sage/sage ; exit;
| SAGE Version 3.0.2, Release Date: 2008-05-24 |
| Type notebook() for the GUI, and license() for information. |
The SAGE install tree may have moved.
Regenerating Python.pyo and .pyc files that hardcode the install PATH (please wait at most a few minutes)…
Please do not interrupt this.

Setting permissions of DOT_SAGE directory so only you can read and write it.

After this step I was presented with the sage prompt. Typing in

sage: notebook()

prompted me to create an admin password, and then opened the sage notebook GUI in my default web browser. I closed this down and then went back to the command prompt to start to play with the Tutorial.

I’m going to stop here for now, because it’s late, but I’ll post more after playing around with sage a bit. I’ve been through the tutorial a bit, and plotting works, yet on the surface there seems to be an inability to view plots “on the fly” with matplotlib, instead having to save and view with an external viewer. Just an extra step, but I as a it used to having graphics on the fly with ipython -pylab. As I said though, I just wanted to talk about installation. Once I give it a fair shake I’ll post up what I think so far.

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