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Read this with an open mind: consider a dialect of Lisp. There is the saying “Lisp is not the language that will solve your problem, but rather, Lisp is the language that will allow you to create the language that will solve your problem.” Perhaps what you need is a biology DSL. Lisp is excellent for creating DSLs.

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This seems to roughly be what this Schafmeister fellow is doing with clasp, no?

This is a really interesting perspective, another HNer said something similar. I’ll spend some time noodling on this.

There is already a complete lisp tool being implemented, aiming to take advantage of C++ libraries called Clasp. You can also take a look to some major Clisp/scheme libraries like biolisp (i think it's the name). I'd never make a group project in common lisp if this project do not involve either a finite-state machine or a DSL (rewriting a prolog interpretor in lisp is a breeze), and in this case, the language fits perfectly imho.

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