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>I wonder what functionality you are
>thinking you will be able to offer in Little b that you simply
>could not code in C++ or Java. Are you thinking of macros that
>speak the language of MCA or flux balance analysis?

C++ and Java are turing-complete, and just as expressive as LISP from that mathematical perspective, but so is Assembly language. What LISP enabled me to do was define a terse syntax for describing objects, logical rules and symbolic mathematical expressions. LISP enabled me to do this in a way that was readable, writable. Without the syntactic & semantic capabilities, I wouldn't have been able to manage the complexity of the project.

To get a sense of what's going on, take a look at a recent presentation (http://www.littleb.org/presentation.ppt). It's hard to imagine retrofitting C++ or Java with logic-programming, symbolic math and new syntax to support these without rewriting the compilers. In LISP, this achieved by extending the language with macros (a faq on the little b site discusses macros briefly).

(Depending on the requirements, macros for FBA & MCA might be useful, though I imagine ordinary functions would fit the bill. Macros should be used sparingly.)

>Also, are you planning a native Little b file format that other
>tools could read/write, or are you planning to uses SBML with
>annotations?

On the output side, we're planning to write SBML with annotations. To get things up and running, we've written a quick-and-dirty MatLab converter.

For input (into b), other tools could write little b code directly - but XML might be a better format for interchange between programs: SBML with annotations (or extended tags) might fit the bill.

Aneil