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=====
*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``):
.. code-block::
:linenos:
E + S ⇄ ES | kf=0.003, kr=0.001 | E=100, S=50
ES → E + P | kf=0.002
@obs Substrate: u[S]
@obs E_free: u[E]
@obs E_total: u[E] + u[ES]
@obs Product: u[P]
@obs Complex: u[ES]
@sim tspan: [0, 100]
Text-to-model conversion:
.. code-block:: python
>>> 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:
.. image:: 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 <https://biomass-core.readthedocs.io/en/latest/tutorial/cfos.html>`_.
License
-------
The software is released under the `Apache License 2.0 <https://opensource.org/licenses/Apache-2.0>`_.
For details, see the `LICENSE <https://github.com/biomass-dev/biomass/blob/master/LICENSE>`_ file in the biomass repository.
Author
------
`Hiroaki Imoto <https://github.com/himoto>`_
Contact
-------
Please contact me with any questions or comments via `Issues`_ | `Discussions`_ on GitHub.
You can also always send me an `email <mailto:hiroaki.imoto@ucd.ie>`_.
Any contributions to BioMASS are more than welcome!
.. _Issues: https://github.com/biomass-dev/biomass/issues
.. _Discussions: https://github.com/biomass-dev/biomass/discussions
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