Location: 12 L Platform 1 model codes @ a8a92308e217 / USMC / Patch_clamp_protocol.cellml

Author:
aram148 <42922407+aram148@users.noreply.github.com>
Date:
2022-07-22 15:47:05+12:00
Desc:
Added documentation for VSM model
Permanent Source URI:
https://models.physiomeproject.org/workspace/6b0/rawfile/a8a92308e217ac5626809237dd90a31240b22834/USMC/Patch_clamp_protocol.cellml

<?xml version='1.0' encoding='UTF-8'?>
<model name="Patch_clamp_protocol" xmlns="http://www.cellml.org/cellml/1.1#" xmlns:cellml="http://www.cellml.org/cellml/1.1#" xmlns:cmeta="http://www.cellml.org/metadata/1.0#" xmlns:xlink="http://www.w3.org/1999/xlink">
    <!-- clamp the voltage for the activation behaviour-->
    <import xlink:href="../Components/units.cellml">
        <units name="ms" units_ref="ms"/>
        <units name="mV" units_ref="mV"/>
    </import>
    <component name="sPulse_protocol_ms">
        <variable name="time" public_interface="in" units="ms"/>
        <variable cmeta:id="steady_state_time" name="t_ss" public_interface="in" units="ms"/>
        <variable cmeta:id="activation_holding_potential" name="V_actHolding" public_interface="in" units="mV"/>
        <variable cmeta:id="activation_duration" name="t_act" public_interface="in" units="ms"/>
        <variable cmeta:id="activation_test_potential" name="V_actTest" public_interface="in" units="mV"/>
        <variable name="V" public_interface="out" units="mV"/>
        <!--get the model to steady state at the holding potential.-->
        <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply id="activation_protocol_clamping">
                <eq/>
                <ci>V</ci>
                <piecewise>
                    <piece>
                        <ci>V_actHolding</ci>
                        <apply>
                            <lt/>
                            <ci>time</ci>
                            <ci>t_ss</ci>
                        </apply>
                    </piece>
                    <piece>
                        <ci>V_actTest</ci>
                        <apply>
                            <and/>
                            <apply>
                                <geq/>
                                <ci>time</ci>
                                <ci>t_ss</ci>
                            </apply>
                            <apply>
                                <lt/>
                                <ci>time</ci>
                                <apply>
                                    <plus/>
                                    <ci>t_act</ci>
                                    <ci>t_ss</ci>
                                </apply>
                            </apply>
                        </apply>
                    </piece>
                    <otherwise>
                        <ci>V_actHolding</ci>
                    </otherwise>
                </piecewise>
            </apply>
        </math>
    </component>
    <component name="sPulse_protocol_s">
        <variable name="time" public_interface="in" units="second"/>
        <variable cmeta:id="steady_state_time" name="t_ss" public_interface="in" units="second"/>
        <variable cmeta:id="activation_holding_potential" name="V_actHolding" public_interface="in" units="mV"/>
        <variable cmeta:id="activation_duration" name="t_act" public_interface="in" units="second"/>
        <variable cmeta:id="activation_test_potential" name="V_actTest" public_interface="in" units="mV"/>
        <variable name="V" public_interface="out" units="mV"/>
        <!--get the model to steady state at the holding potential.-->
        <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply id="activation_protocol_clamping">
                <eq/>
                <ci>V</ci>
                <piecewise>
                    <piece>
                        <ci>V_actHolding</ci>
                        <apply>
                            <lt/>
                            <ci>time</ci>
                            <ci>t_ss</ci>
                        </apply>
                    </piece>
                    <piece>
                        <ci>V_actTest</ci>
                        <apply>
                            <and/>
                            <apply>
                                <geq/>
                                <ci>time</ci>
                                <ci>t_ss</ci>
                            </apply>
                            <apply>
                                <lt/>
                                <ci>time</ci>
                                <apply>
                                    <plus/>
                                    <ci>t_act</ci>
                                    <ci>t_ss</ci>
                                </apply>
                            </apply>
                        </apply>
                    </piece>
                    <otherwise>
                        <ci>V_actHolding</ci>
                    </otherwise>
                </piecewise>
            </apply>
        </math>
    </component>
    <component name="mPulse_protocol_ms">
        <variable name="time" public_interface="in" units="ms"/>
        <variable cmeta:id="steady_state_time" name="t_ss" public_interface="in" units="ms"/>
        <variable cmeta:id="activation_holding_potential" name="V_actHolding" public_interface="in" units="mV"/>
        <variable cmeta:id="activation_duration" name="t_act" public_interface="in" units="ms"/>
        <variable cmeta:id="activation_test_potential" name="V_actTest" public_interface="in" units="mV"/>
        <variable cmeta:id="interpulse" name="t_intp" public_interface="in" units="ms"/>
        <variable cmeta:id="period" name="stimPeriod" units="ms"/>
        <variable cmeta:id="localTimer" name="t" units="ms"/>
        <variable cmeta:id="pulse_number" name="np" public_interface="in" units="dimensionless"/>
        <variable name="V" public_interface="out" units="mV"/>
        <!--get the model to steady state at the holding potential.-->
        <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
                <eq/>
                <ci>stimPeriod</ci>
                <apply>
                    <plus/>
                    <ci>t_act</ci>
                    <ci>t_intp</ci>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>t</ci>
                <apply>
                    <minus/>
                    <apply>
                        <minus/>
                        <ci>time</ci>
                        <ci>t_ss</ci>
                    </apply>
                    <apply>
                        <times/>
                        <ci>stimPeriod</ci>
                        <apply>
                            <floor/>
                            <apply>
                                <divide/>
                                <apply>
                                    <minus/>
                                    <ci>time</ci>
                                    <ci>t_ss</ci>
                                </apply>
                                <ci>stimPeriod</ci>
                            </apply>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply id="activation_protocol_clamping">
                <eq/>
                <ci>V</ci>
                <piecewise>
                    <piece>
                        <ci>V_actHolding</ci>
                        <apply>
                            <lt/>
                            <ci>time</ci>
                            <ci>t_ss</ci>
                        </apply>
                    </piece>
                    <piece>
                        <ci>V_actTest</ci>
                        <apply>
                            <and/>
                            <apply>
                                <geq/>
                                <ci>time</ci>
                                <ci>t_ss</ci>
                            </apply>
                            <apply>
                                <leq/>
                                <ci>t</ci>
                                <ci>t_act</ci>
                            </apply>
                            <apply>
                                <leq/>
                                <ci>time</ci>
                                <apply>
                                    <plus/>
                                    <ci>t_ss</ci>
                                    <apply>
                                        <times/>
                                        <ci>stimPeriod</ci>
                                        <ci>np</ci>
                                    </apply>
                                </apply>
                            </apply>
                        </apply>
                    </piece>
                    <otherwise>
                        <ci>V_actHolding</ci>
                    </otherwise>
                </piecewise>
            </apply>
        </math>
    </component>
    <component name="mPulse_protocol_s">
        <variable name="time" public_interface="in" units="second"/>
        <variable cmeta:id="steady_state_time" name="t_ss" public_interface="in" units="second"/>
        <variable cmeta:id="activation_holding_potential" name="V_actHolding" public_interface="in" units="mV"/>
        <variable cmeta:id="activation_duration" name="t_act" public_interface="in" units="second"/>
        <variable cmeta:id="activation_test_potential" name="V_actTest" public_interface="in" units="mV"/>
        <variable cmeta:id="interpulse" name="t_intp" public_interface="in" units="second"/>
        <variable cmeta:id="period" name="stimPeriod" units="second"/>
        <variable cmeta:id="localTimer" name="t" units="second"/>
        <variable cmeta:id="pulse_number" name="np" public_interface="in" units="dimensionless"/>
        <variable name="V" public_interface="out" units="mV"/>
        <!--get the model to steady state at the holding potential.-->
        <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
                <eq/>
                <ci>stimPeriod</ci>
                <apply>
                    <plus/>
                    <ci>t_act</ci>
                    <ci>t_intp</ci>
                </apply>
            </apply>
            <apply>
                <eq/>
                <ci>t</ci>
                <apply>
                    <minus/>
                    <apply>
                        <minus/>
                        <ci>time</ci>
                        <ci>t_ss</ci>
                    </apply>
                    <apply>
                        <times/>
                        <ci>stimPeriod</ci>
                        <apply>
                            <floor/>
                            <apply>
                                <divide/>
                                <apply>
                                    <minus/>
                                    <ci>time</ci>
                                    <ci>t_ss</ci>
                                </apply>
                                <ci>stimPeriod</ci>
                            </apply>
                        </apply>
                    </apply>
                </apply>
            </apply>
            <apply id="activation_protocol_clamping">
                <eq/>
                <ci>V</ci>
                <piecewise>
                    <piece>
                        <ci>V_actHolding</ci>
                        <apply>
                            <leq/>
                            <ci>time</ci>
                            <ci>t_ss</ci>
                        </apply>
                    </piece>
                    <piece>
                        <ci>V_actTest</ci>
                        <apply>
                            <and/>
                            <apply>
                                <gt/>
                                <ci>time</ci>
                                <ci>t_ss</ci>
                            </apply>
                            <apply>
                                <leq/>
                                <ci>t</ci>
                                <ci>t_act</ci>
                            </apply>
                            <apply>
                                <leq/>
                                <ci>time</ci>
                                <apply>
                                    <plus/>
                                    <ci>t_ss</ci>
                                    <apply>
                                        <times/>
                                        <ci>stimPeriod</ci>
                                        <ci>np</ci>
                                    </apply>
                                </apply>
                            </apply>
                        </apply>
                    </piece>
                    <otherwise>
                        <ci>V_actHolding</ci>
                    </otherwise>
                </piecewise>
            </apply>
        </math>
    </component>
</model>