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BioSCRAPE XML
As a rule, names should not contain any strange characters. Basically, only use alpha numeric characters and underscores in the names of parameters and species and do not start names with numbers. Do not use whitespace, colons, semicolons, ^, |, etc. as part of your species and parameter names. Additionally, simple functions like abs, log, exp, and heaviside are reserved keywords for functions, so do not use them as variable names. Also, the variable t is reserved for time and should not be used as a variable name. The word volume is reserved for cell volume and also should not be used as a variable name.
The XML spec gives a way to specify the reaction related pieces of the model, i.e. the species, reactions, and rates/propensities and delays associated with each reaction. The other aspects of the model such a cell growth and division and type of simulation used (deterministic/stochastic/etc) all must be specified in your Python code.
An example XML reaction looks like this.
<reaction text="DNA+RNAP--DNA_RNAP" after="DNA_RNAP--DNA+RNAP+mRNA" >
<propensity type="massaction" k="k_tx" species="DNA*RNAP" />
<delay type="fixed" delay="tx_delay" />
</reaction>
The first part of the reaction tag specifies what happens in the reaction. The text field specifies what reactants go to what products immediately. The reactants are split by + signs and the -- separates the reactants from the products. The ideal delimiter would of course be an arrow --> but the ">" character is not allowed in XML :-)
The after part of the reaction tag has the same syntax as the text field, but it contains the stoichiometry that should be executed after some delay. In this case, when this reaction fires, we will immediately subtract one DNA and one RNAP and make one DNA_RNAP. After some delay, we will get rid of that DNA_RNAP and make one mRNA, one RNAP, and one mRNA. This represents a transcription with delay that models binding of a single polymerase to each copy of DNA at a time.
The propensity field specifies the reaction rate/propensity. The type field tells you the type of rate and based on the type of propensity, there are different additional parameters required. To see all the possible propensities, please see below. In this case, the propensity is a mass action propensity, so we have to specify what species are involved as well as the parameter involved. In this case, the propensity will have the form k_tx * DNA * RNA_P.
The delay field specifies the delay. The type field again tells you the type of delay. In this case, we have a fixed delay, and the delay="tx_delay" tells us that parameter tx_delay contains the value of that fixed delay.
Details on different kinds of propensities and delays can be found in the propensity functions and delay functions wiki pages, respectively.
RULE Specification: TODO
SPECIE and PARAMETER DECLARATION AND INITIALIZATION: TODO
General propensities and assignment rules make use of general algebraic equations. The kinds of expressions and functions supported are detailed below.
The following gives time.
t
The following gives cell volume.
volume
Variables beginning in a "_" (such as _k) refer to parameters in the XML model.
Variables which are beginning with a letter (and may contain "", and numerals but cannot start with "" or numerals) refer to species in the XML model.
In addition to the usual parentheses, exponents, mutiplication/division, addition/subtraction, the following functions are possible.
The following computes the natural logarithm.
log(x)
The following computes the exponential.
exp(x)
The following computes the absolute value. Note the case!! Must be uppercase A.
Abs(x)
The following computes the maximum or minimum of a bunch of values. Note the case!! Must be uppercase M.
Max(x,y,z)
Min(x,y,z)
The two following statements both compute the Heaviside step function. This is 1 if x is positive and 0 otherwise. Case does not matter here.
heaviside(x)
Heaviside(x)