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.

James Long

International Arctic Research Center

University of Alaska Fairbanks

PO Box 757340

Fairbanks, AK 99775-7340

USA

Voice: (907) 474-2440

```
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.