01Syntax and semantics
The language, precisely
What each construct means, what it compiles to, and what it assumes. The reference, rather than the tour.
02At a glance
The two forms you will write most
reaction NAME(A + B -> C, k = <forward>, kr = <reverse>)
protein NAME(sub -> prod, k = <kcat>, km = <michaelis>)
A = <concentration>, B = <concentration>03Reference
01
Species and concentrations
Declaring the things that exist, and giving them a starting amount.
02
reaction
Elementary steps: reactants, products, forward and reverse constants, and what mass-action means here.
03
protein
The enzyme abstraction — one declaration standing for a binding-and-catalysis pair, parameterised by k and km.
04
Environment
The conditions a model runs under, and what the simulator does with them.
05
Output
What a run produces, at what resolution, and how to capture it.
06
Modules
Splitting a model across files and reusing parts of one model in the next.