SimBio 0.4.0

Simulation of Biological Systems

SimBio

simbio is a Python-based package for simulation of Chemical Reaction Networks (CRNs). It extends poincare, a package for modelling dynamical systems, to add functionality for CRNs.

Usage

To create a system with two species $A$ and $B$ and a reaction converting $2A \rightarrow B$ with rate 1:

>>> from simbio import Compartment, Species, RateLaw, initial
>>> class Model(Compartment):
...    A: Species = initial(default=1)
...    B: Species = initial(default=0)
...    r = RateLaw(
...        reactants=[2 * A],
...        products=[B],
...        rate_law=1,
...    )

This corresponds to the following system of equations

$$ \begin{cases} \frac{dA}{dt} = -2 \ \frac{dB}{dt} = +1 \end{cases} $$

with initial conditions

$$ \begin{cases} A(0) = 1 \ B(0) = 0 \end{cases} $$

In CRNs, we usually deal with mass-action reactions. Using MassAction instead of Reaction automatically adds the reactants to the rate law:

>>> from simbio import MassAction
>>> class MassActionModel(Compartment):
...    A: Species = initial(default=1)
...    B: Species = initial(default=0)
...    r = MassAction(
...        reactants=[2 * A],
...        products=[B],
...        rate=1,
...    )

generating the following equations:

$$ \begin{cases} \frac{dA}{dt} = -2 A^2 \ \frac{dB}{dt} = +1 A^2 \end{cases} $$

To simulate the system, use the Simulator.solve which outputs a pandas.DataFrame:

>>> from simbio import Simulator
>>> Simulator(MassActionModel).solve(save_at=range(5))
             A         B
time
0     1.000000  0.000000
1     0.333266  0.333367
2     0.199937  0.400032
3     0.142798  0.428601
4     0.111061  0.444470

For more details into SimBio's capabilities, we recommend reading poincaré's README.

SBML

SimBio can import models from Systems Biology Markup Language (SBML) files:

>>> from simbio.io import sbml
>>> sbml.load("repressilator.sbml")
Elowitz2000 - Repressilator
-----------------------------------------------------------------------------------
type          total  names
----------  -------  --------------------------------------------------------------
variables         6  PX, PY, PZ, X, Y, Z
parameters       17  cell, beta, alpha0, alpha, eff, n, KM, tau_mRNA, tau_prot, ...
equations        12  Reaction1, Reaction2, Reaction3, Reaction4, Reaction5, ...

or download them from the BioModels repository:

>>> from simbio.io import biomodels
>>> biomodels.load("BIOMD12")
Elowitz2000 - Repressilator
-----------------------------------------------------------------------------------
type          total  names
----------  -------  --------------------------------------------------------------
variables         6  PX, PY, PZ, X, Y, Z
parameters       17  cell, beta, alpha0, alpha, eff, n, KM, tau_mRNA, tau_prot, ...
equations        12  Reaction1, Reaction2, Reaction3, Reaction4, Reaction5, ...

Installation

It can be installed from PyPI with pip:

pip install simbio

Or, to additionally install the SBML importer:

pip install simbio[io]

While poincaré is installed automatically as a dependency, if you are using conda/mamba, you might prefer to install it from conda-forge:

conda install --channel conda-forge poincare