Custom Rate Law Classifications

ratesb_python allows the use of custom rate law classifications. To utilize this, you must create a JSON file defining your rate laws. Each rate law object in the JSON file should include:

1. name: A string that specifies the name of the rate law.

2. expression: A valid mathematical equation using specific symbols (compartment, parameter, reactant1, reactant2, reactant3, product1, product2, product3, and enzyme). “species” is NOT allowed, instead you should specify whether a species is reactant, product or enzyme. Any other symbols should not be used in the expression. Mathematical operators such as +, -, , /, *, and parentheses should be used to construct the equation.

3. optional_symbols: An array of symbols not necessarily required in the model’s rate law.

4. power_limited_species: An array of species where the power (exponent) matters in the analysis. If a species is listed here, it should be raised to a specific power in the rate law (specified in the expression).

Here’s an example of how to define your rate laws in the JSON file:

[
    {
        "name": "Unidirectional Mass Action with two reactants",
        "expression": "compartment * parameter * reactant1 * reactant2**2",
        "optional_symbols": ["compartment", "parameter"],
        "power_limited_species": ["reactant1,reactant2"]
    },
    {
        "name": "Michaelis Menten",
        "expression": "compartment * parameter * reactant1 / (reactant1 + parameter)",
        "optional_symbols": ["compartment"],
        "power_limited_species": ["reactant1"]
    },
    {
        "name": "Your own rate law",
        "expression": "use: compartment, parameter, reactant1, reactant2, reactant3, product1, product2, product3, enzyme. Do NOT use: species",
        "optional_symbols": ["symbols that do not have to include in a rate law"],
        "power_limited_species": ["RateSB will pay attention to the power of these species (power matters in this case) symbols that have to be set to a certain power in a rate law (please specify power in the expression)"]
    }
]