NEMO: User defined input functions

NEMO language examples:

Any gene described within a DOR or GLIST construct, i.e. G0(P1+,P2+,P3-), may
append an input function to the protein list with an :F() construct, i.e.
G0(P1+,P2+,P3-:F(expr)), where "expr" is defined below. Other examples:

Feed Forward Loop (FFL)
=======================
P0(+G1-G2+) may have functions in the following positions:
P0(F(expr):+G1-G2+)
P0(+G1-G2+:F(expr))
P0(F(expr):+G1-G2+:F(expr))

Multi Feed Forward Loop
=======================
Almost the same as an FFL, but in a multi FFL, the G2 in the above example is
replace by a list of genes in parentheses. Hence the trailing :F() construct is
moved into the parentheses, and is specified for each desired gene, i.e.
P0(F(expr):+G1-(G2:F(expr), G3, G4:F(expr))+)

Single Input Module
===================
P0(+G1,G2,G3) may add a function after any combination of the genes, i.e.
P0(+G1:F(expr),G2,G3)
P0(+G1,G2:F(expr),G3)
P0(+G1,G2,G3:F(expr))
P0(+G1:F(expr),G2,G3:F(expr))
P0(+G1:F(expr),G2:F(expr),G3:F(expr))
etc.

An "expr" is any math expression involving +, -, *, and / on constants and/or 
proteins, along with functions recognized by MathML:

abs(expr)
arccos(expr)
arcsin(expr)
arctan(expr)
ceiling(expr)
cos(expr)
exp(expr)
floor(expr)
ln(expr)
log(digits, expr)
power(expr, expr)
root(digits, expr)
sin(expr)
tan(expr)

Caution: your function must use all the transcription factors for the gene
being described. The compiler checks to make sure that all (and only) the
transcription factors in a construct are used in the :F(expr).

Whatever "expr" is used, it is internally turned into a "difference" 
equation, by subtracting the current value of the expression level, 
and dividing everything by "tau", a time interval. "tau" may be set
at the command line with a '-t <tau value>' option to nemo2sbml,
otherwise 1.0 is the default. It is usually desirable to set this 
to the step interval used in a biochemical simulator.

jlong@alaska.edu

RANGE/NEMO was developed while employed at the Biotechnology Computing Research Group, supported in part by Grant Number 5P20RR016466 from the National Center for Research Resources (NCRR), a component of the National Institutes of Health (NIH), with prior support from 2P20RR016466-040005 and 2P20RR016466-049001, PI Thomas Marr.