[](https://github.com/hgrecco/simbio/actions/workflows/ci.yml)
# SimBio
`simbio` is a Python-based package for simulation of Chemical Reaction Networks (CRNs).
It extends [`poincare`](https://github.com/maurosilber/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:
```python
>>> 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](https://en.wikipedia.org/wiki/Law_of_mass_action) reactions.
Using `MassAction` instead of `Reaction` automatically adds the reactants to the rate law:
```python
>>> 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`:
```python
>>> 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](https://github.com/maurosilber/poincare).
## SBML
SimBio can import models from Systems Biology Markup Language (SBML) files:
```python
>>> 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](https://www.ebi.ac.uk/biomodels/) repository:
```python
>>> 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](https://pypi.org/p/simbio) 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
```
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"description": "\n\n\n\n[](https://github.com/hgrecco/simbio/actions/workflows/ci.yml)\n\n# SimBio\n\n`simbio` is a Python-based package for simulation of Chemical Reaction Networks (CRNs).\nIt extends [`poincare`](https://github.com/maurosilber/poincare),\na package for modelling dynamical systems,\nto add functionality for CRNs.\n\n## Usage\n\nTo create a system with two species $A$ and $B$\nand a reaction converting $2A \\\\rightarrow B$ with rate 1:\n\n```python\n>>> from simbio import Compartment, Species, RateLaw, initial\n>>> class Model(Compartment):\n... A: Species = initial(default=1)\n... B: Species = initial(default=0)\n... r = RateLaw(\n... reactants=[2 * A],\n... products=[B],\n... rate_law=1,\n... )\n```\n\nThis corresponds to the following system of equations\n\n$$\n\\\\begin{cases}\n\\\\frac{dA}{dt} = -2 \\\\\n\\\\frac{dB}{dt} = +1\n\\\\end{cases}\n$$\n\nwith initial conditions\n\n$$\n\\\\begin{cases}\nA(0) = 1 \\\\\nB(0) = 0\n\\\\end{cases}\n$$\n\nIn CRNs,\nwe usually deal with [mass-action](https://en.wikipedia.org/wiki/Law_of_mass_action) reactions.\nUsing `MassAction` instead of `Reaction` automatically adds the reactants to the rate law:\n\n```python\n>>> from simbio import MassAction\n>>> class MassActionModel(Compartment):\n... A: Species = initial(default=1)\n... B: Species = initial(default=0)\n... r = MassAction(\n... reactants=[2 * A],\n... products=[B],\n... rate=1,\n... )\n```\n\ngenerating the following equations:\n\n$$\n\\\\begin{cases}\n\\\\frac{dA}{dt} = -2 A^2 \\\\\n\\\\frac{dB}{dt} = +1 A^2\n\\\\end{cases}\n$$\n\nTo simulate the system,\nuse the `Simulator.solve` which outputs a `pandas.DataFrame`:\n\n```python\n>>> from simbio import Simulator\n>>> Simulator(MassActionModel).solve(save_at=range(5))\n A B\ntime\n0 1.000000 0.000000\n1 0.333266 0.333367\n2 0.199937 0.400032\n3 0.142798 0.428601\n4 0.111061 0.444470\n```\n\nFor more details into SimBio's capabilities,\nwe recommend reading [poincar\u00e9's README](https://github.com/maurosilber/poincare).\n\n## SBML\n\nSimBio can import models from Systems Biology Markup Language (SBML) files:\n\n```python\n>>> from simbio.io import sbml\n>>> sbml.load(\"repressilator.sbml\")\nElowitz2000 - Repressilator\n-----------------------------------------------------------------------------------\ntype total names\n---------- ------- --------------------------------------------------------------\nvariables 6 PX, PY, PZ, X, Y, Z\nparameters 17 cell, beta, alpha0, alpha, eff, n, KM, tau_mRNA, tau_prot, ...\nequations 12 Reaction1, Reaction2, Reaction3, Reaction4, Reaction5, ...\n```\n\nor download them from the [BioModels](https://www.ebi.ac.uk/biomodels/) repository:\n\n```python\n>>> from simbio.io import biomodels\n>>> biomodels.load(\"BIOMD12\")\nElowitz2000 - Repressilator\n-----------------------------------------------------------------------------------\ntype total names\n---------- ------- --------------------------------------------------------------\nvariables 6 PX, PY, PZ, X, Y, Z\nparameters 17 cell, beta, alpha0, alpha, eff, n, KM, tau_mRNA, tau_prot, ...\nequations 12 Reaction1, Reaction2, Reaction3, Reaction4, Reaction5, ...\n```\n\n## Installation\n\nIt can be installed from [PyPI](https://pypi.org/p/simbio) with `pip`:\n\n```\npip install simbio\n```\n\nOr, to additionally install the SBML importer:\n\n```\npip install simbio[io]\n```\n\nWhile `poincar\u00e9` is installed automatically as a dependency,\nif you are using conda/mamba,\nyou might prefer to install it from conda-forge:\n\n```\nconda install --channel conda-forge poincare\n```\n",
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