| 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. |
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|
| Example |
| ------- |
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|
| Text file (``michaelis_menten.txt``): |
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|
| .. 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: |
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|
| .. 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 |
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| 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>`_. |
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|
| 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>`_. |
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| Any contributions to BioMASS are more than welcome! |
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|
| .. _Issues: https://github.com/biomass-dev/biomass/issues |
| .. _Discussions: https://github.com/biomass-dev/biomass/discussions |
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|
