The alien text shows up in many places in Infinifactory. Most 'letters' seem to be represented as a 5x5 group of pixels. Zach confirms  that there is no direct 1:1 encoding of english-letters-to-alien-letters but there is thought put into the construction of the language.
UPDATE: Zach has a full writeup of the process of creating the alien writing here: http://www.zachtronics.com/alien-writing/
It seems to consist of two types of text:
- Blocky letters where words are all connected along the bottom edge. (often written vertically.)
- Vertical symbols which are (mostly?) grouped in 3s, with symbols like | : i ! etc.
See Alien-to-english substitution for some more details.