# Example model for testing import code

# Note that blank lines and lines beginning with "#" are ignored

# A Kronecker model is divided into six sections:
# Units, Compartments, Species, Outputs, Parameters, and Reactions

# Units is not yet implemented in Kronecker so don't worry about. Talk to
# David about how to volunteer to write the code for this section if you
# need it.

# For the rest of the sections, it does not matter what order they are in. 
# In fact, you are allowed to have multiple sections by the same name. Each
# section is started by a line starting with a "%". The next word tells
# what kind of section you are starting (Compartments, etc). The section
# identifier is not case sensitive (compartments or cOmParTmEnts works 
# fine too). For some section headers, more words can follow the identifier
# that provide important parameters for that section.

# As a general rule, fields are seperated by arbitrary amounts of
# whitespace. Commas group multiple words into a single field.

# The next line declares that I am going to define the compartments for my
# system. The whitespace between "%" and "Compartments" is optional. The
# next word following Compartments provides the name of the model. It is 
# like saying that the compartments are members of this model.
% Compartments Testing

# Lines of the compartment section follow this format:
#Name  Dim  Volume
v1     3    1e-6
v2     2    1.2e-4
v3     1    1e-3

# As it stands right now, you can have anything in the Name of a
# compartment except a "." or a ",". You should avoid starting the name with
# a "%", a "#", or other operator for reasons that should be obvious. The
# Dimension of a comparment is whether the compartment is a point, a line,
# an area, or a space. The volume is the size of the compartment.

# The Species header (starting with a "%") declares that we are no longer 
# defining compartments, but species now. The important word is "Species"
# here, not case sensitive. The word following Species defines the default
# comparment. Every species must be placed in a compartment. If the
# compartment is not defined for a species, it will be placed in the 
# default compartment. This makes it really easy to add species to 
# multiple compartments, since you can make a list of species, copy it, and
# simply change the default compartment on the header.

% States v1

# The format is:
#Name  InitialAmount
v1.x1  1e4

# The full name of species is compartment.species. Here, the species is 
# being place in comparment v1. Compartment v1 does not need to be defined
# yet, but it will have to be defined somewhere before you finalize the 
# model. Because v1 is the default compartment, I could have easily written
# this, and it would be the same:
x1  1e4

# The value is the initial amount of the species, not the concentration.
# The default amount is 0, so a species can be defined with just a name.
x2 0
x2

# The initial amount can also be a seed parameter allowing to be fit as
# part of the model or the experimental conditions
x3  s1
x4  s2

# Amount for species in other compartments can also be defined here
# though most people make a seperate section for each compartment
v2.x6 
v3.x7 1

# The Inputs header (starting with a "%") is the same as the Species header
# because inputs are assigned to compartments just like states

% Inputs v1

# The input control parameters (mathematically known as q) provide a means
# of controling the value of an input species. Below shows an example of
# this. q(1) and q(2) refer to 2 and 1e4 here, but those numbers could be 
# changed after the model has already been built.
# Name Function   Parameters
x4     q(1)*q(2)  2,1e4

# An input can also be a function of time t.
x5 t^2+q(1)*q(2) 2,1e4


# Output headers do not take any additional parameters
% Outputs

# Format:
#Name Value
y1    x=1

# Value is a set of regular expressions combined with equal signs and 
# numbers, seperated by commas. The default number is 1, so the following 
# is identical to the previous line.
y1 x

# Remember that the regular expressions match the full name of the species,
# so including compartment names can match a subset of the species in a 
# compartment. Do forget that "." means any character in a regular 
# expression; use "\." to match the period after a compartment.
y2 v1\.=1

# Multiple expressions can contribute to the same output. If a species is
# matched multiple times, the last expression prevails.
y3 v2\.x4 x5

# Values do not have to be integers
y4 x3=1.2

# The Parameters section is the simplest section. There are no additional
# parameters in the header.
% Parameters
#Name Value
k1    1
k2 1.3e-4

# The Seeds section is just as simpel as the Parameters. There are no additional
# parameters in the header.
% Seeds
#Name Value
s1    1e6
s2    20

# The Reactions section takes a set of compartments that these reactions
# take place in. If there is no compartment after "Reactions", it is
# assumed that the reactions occur in any compartment that has the
# necessary reactants. These compartments only apply to reactants and 
# products of the reaction that do not have the compartment specified.
% Reactions v1
#Reac1 Reac2 Prod1 Prod2 ParaFwd ParaRev Names
x1     x2    x3    x4    k1      k2      r1 r2

# Up to two names can be given for a reaction here, if two are given, the 
# first applies to the forward and the second applies to the reverse.
# Unlike other components of a Kronecker model, reactions do not have to 
# have unique names, or even names at all. They exist only for ease of use
# and modifying the model after it has been constructed.

# Unimolecular reactions can be defined by putting a 0 in the non-existant
# reactions or products
x1     0      x2   0     k2       k1

# It is non necessary to provide both a reverse and forward parameter. 
# Irreversible reactions are defined like this.
x3    x5     0     0     0         k1    r34

# Species of a specific compartment can be defined. The various compartments
# will be tried on the other species.
x3 v3.x7 x2 x2 k1 k1 r5 r6

# The rate parameters can also be modified with * for a specific reaction.
# There are complicated reasons for this, but it isn't used much.
x1 x2 x3 x4 k1=2 k2=1/2