Valrus, Thank you for your comments. When you say “Perl's probably not the appropriate tool for this task.” I guess that it’s because Perl is more of a language to “hold things together” is that correct?

It depends whether you were planning on programming the game itself in Perl, or doing some of the game logic in Perl (that is, the game logic that you want to put out there for easy modding). A game will often have various levels of languages/formats -- Civilization IV, if I remember correctly, has a C++ engine, but the game logic is expressed in Python, and the game data (maps, parameters, etc.) are in XML. So people can change the game logic without having to mess with the game engine, and people can make maps and change game variables without going into code at all.

(Side note, and apologies if this is too obvious: all structured data -- like, say, definitions of molecules and their properties -- should be in XML rather than in code; it's extremely standard and knowledge of it is widespread. For doing things like adding new molecules, modders shouldn't need to go into the game logic; they should just plop a new XML file into whatever directory the molecule files live in, and the game will read that in whenever it starts.)

Back to Perl: I don't think there are modern game engines in Perl, and I wouldn't recommend starting from scratch and trying to write one. (Perl shines in simple I/O tasks like text processing -- hence its usefulness in bioinformatics -- but hasn't traditionally been utilized in heavily multi-threaded applications like game engines.) But you *could* potentially do the game logic in it. You could, for example, call methods in a C++ engine from Perl, or conversely have your C++ engine interpret the Perl game logic. Both of these are technically possible. (Finding someone to do it might be a hurdle, though. Outside of bioinformatics, interest in learning Perl has rather declined in the last 15 years.)

This goes back to the audience question. If you intend this for student biochemists, modding via Perl is a potentially good idea. If they don't already know it, learning it would be a valuable job skill. If you intend this for a wider audience (and perhaps younger audience), I don't think Perl knowledge would be sufficiently common anymore.