Model Construction

pasmopy.Text2Model allows you to build a BioMASS model from text. You simply describe biochemical reactions and the molecular mechanisms extracted from text are converted into an executable model.

Example

This example shows you how to build a simple Michaelis-Menten two-step enzyme catalysis model with Pasmopy.

E + S ⇄ ES → E + P

An enzyme, E, binding to a substrate, S, to form a complex, ES, which in turn releases a product, P, regenerating the original enzyme.

  1. Prepare a text file describing biochemical reactions (e.g., michaelis_menten.txt)

    ``` E binds S <–> ES | kf=0.003, kr=0.001 | E=100, S=50 ES dissociates to E and P | kf=0.002, kr=0

    @obs Substrate: u[S] @obs Efree: u[E] @obs Etotal: u[E] + u[ES] @obs Product: u[P] @obs Complex: u[ES]

    @sim tspan: [0, 100] ```

  2. Convert the text into an executable model

    shell $ python ```python

    from pasmopy import Text2Model description = Text2Model("michaelismenten.txt", lang="julia") description.convert() # generate 'michaelismenten_jl/'

    Model information

    2 reactions 4 species 4 parameters ```

  3. Run simulation

    shell $ julia ```julia using BioMASS

    model = Model("./michaelismentenjl"); run_simulation(model) ```

    michaelis_menten