Example models
==============

Circadian clock
---------------

.. raw:: html

    <p align="left">
        <img src="https://raw.githubusercontent.com/biomass-dev/biomass/master/biomass/models/circadian_clock/circadian_clock.png"
            width="400px" alt="Circadian clock">
    </p>

* **Code:** `circadian_clock`_
* **Paper:** :cite:p:`Leloup7051`

G1/S transition
---------------

.. raw:: html

    <p align="left">
        <img src="https://raw.githubusercontent.com/biomass-dev/biomass/master/biomass/models/g1s_transition/g1s_transition.png"
            width="400px" alt="G1/S transition">
    </p>

* **Code:** `g1s_transition`_
* **Paper:** :cite:p:`barr2016dynamical`

Immediate-early gene response
-----------------------------

.. raw:: html

    <p align="left">
        <img src="_static/img/simulation_average.png"
            width="400px" alt="Immediate-early gene response">
    </p>

* **Code:** `Nakakuki_Cell_2010`_
* **Paper:** :cite:p:`NAKAKUKI2010884`

Insulin signaling
-----------------

.. raw:: html

    <p align="left">
        <img src="https://raw.githubusercontent.com/biomass-dev/biomass/master/biomass/models/insulin_signaling/insulin_signaling.png"
            width="400px" alt="Insulin signaling">
    </p>

* **Code:** `insulin_signaling`_
* **Paper:** :cite:p:`KUBOTA2012820`

MAPK cascade
------------

.. raw:: html

    <p align="left">
        <img src="https://raw.githubusercontent.com/biomass-dev/biomass/master/biomass/models/mapk_cascade/mapk_cascade.png"
            width="400px" alt="MAPK cascade">
    </p>

* **Code:** `mapk_cascade`_
* **Paper:** :cite:p:`https://doi.org/10.1046/j.1432-1327.2000.01197.x`

NF-κB pathway
--------------

.. raw:: html

    <p align="left">
        <img src="https://raw.githubusercontent.com/biomass-dev/biomass/master/biomass/models/nfkb_pathway/nfkb_pathway.png"
            width="400px" alt="NF-κB pathway">
    </p>

* **Code:** `nfkb_pathway`_
* **Paper:** :cite:p:`oppelt2018model`

pan-RTK
-------

.. raw:: html

    <p align="left">
        <img src="https://raw.githubusercontent.com/biomass-dev/biomass/master/biomass/models/pan_rtk/pan_rtk.png"
            width="400px" alt="pan-RTK">
    </p>

* **Code:** `pan_rtk`_
* **Paper:** :cite:p:`hass2017predicting`

Proliferation-quiescence decision
---------------------------------

.. raw:: html

    <p align="left">
        <img src="https://raw.githubusercontent.com/biomass-dev/biomass/master/biomass/models/prolif_quies/prolif_quies.png"
            width="400px" alt="Proliferation-quiescence decision">
    </p>

* **Code:** `prolif_quies`_
* **Paper:** :cite:p:`heldt2018comprehensive`


TGF-β/SMAD pathway
-------------------

.. raw:: html

    <p align="left">
        <img src="https://raw.githubusercontent.com/biomass-dev/biomass/master/biomass/models/tgfb_smad/tgfb_smad.png"
            width="400px" alt="TGF-β/SMAD pathway">
    </p>

* **Code:** `tgfb_smad`_
* **Paper:** :cite:p:`LUCARELLI201875`


JAK-STAT pathway
-------------------

.. raw:: html

    <p align="left">
        <img src="https://raw.githubusercontent.com/biomass-dev/biomass/master/biomass/models/jak_stat_pathway/jak_stat_pathway.png"
            width="400px" alt="JAK-STAT pathway">
    </p>

* **Code:** `jak_stat_pathway`_
* **Paper:** :cite:p:`raia2011Dynamic`

.. _circadian_clock: https://github.com/biomass-dev/biomass/tree/master/biomass/models/circadian_clock
.. _g1s_transition: https://github.com/biomass-dev/biomass/tree/master/biomass/models/g1s_transition
.. _Nakakuki_Cell_2010: https://github.com/biomass-dev/biomass/tree/master/biomass/models/Nakakuki_Cell_2010
.. _insulin_signaling: https://github.com/biomass-dev/biomass/tree/master/biomass/models/insulin_signaling
.. _mapk_cascade: https://github.com/biomass-dev/biomass/tree/master/biomass/models/mapk_cascade
.. _nfkb_pathway: https://github.com/biomass-dev/biomass/tree/master/biomass/models/nfkb_pathway
.. _pan_rtk: https://github.com/biomass-dev/biomass/tree/master/biomass/models/pan_rtk
.. _prolif_quies: https://github.com/biomass-dev/biomass/tree/master/biomass/models/prolif_quies
.. _tgfb_smad: https://github.com/biomass-dev/biomass/tree/master/biomass/models/tgfb_smad
.. _jak_stat_pathway: https://github.com/biomass-dev/biomass/tree/master/biomass/models/jak_stat_pathway