About

BioMASS is a computational framework for modeling and analysis of biological signaling systems in Python. It provides useful tools for model construction, numerical simulation, parameter estimation, network analysis, and result visualization.

Example

Text file (michaelis_menten.txt):

 1E + S ⇄ ES | kf=0.003, kr=0.001 | E=100, S=50
 2ES → E + P | kf=0.002
 3
 4@obs Substrate: u[S]
 5@obs E_free: u[E]
 6@obs E_total: u[E] + u[ES]
 7@obs Product: u[P]
 8@obs Complex: u[ES]
 9
10@sim tspan: [0, 100]

Text-to-model conversion:

>>> from biomass import Text2Model, create_model, run_simulation
>>> description = Text2Model("michaelis_menten.txt")
>>> description.convert()
Model information
-----------------
2 reactions
4 species
4 parameters

>>> model = create_model("michaelis_menten")
>>> run_simulation(model)

Output:

https://raw.githubusercontent.com/pasmopy/pasmopy/master/docs/_static/img/michaelis_menten_sim.png

For an advanced model, see a mechanistic model of the c-Fos expression network dynamics.

License

The software is released under the Apache License 2.0. For details, see the LICENSE file in the biomass repository.

Author

Hiroaki Imoto

Contact

Please contact me with any questions or comments via Issues | Discussions on GitHub. You can also always send me an email.

Any contributions to BioMASS are more than welcome!