wormsim 0.0.1__py3-none-any.whl

wormsim/abstract_circuit.py

@@ -0,0 +1,172 @@
+"""
+Modules containing class that
+    1. the most abstract circuit connection information
+"""
+
+
+class AbsSegment:
+    """class for abstract segment
+
+    Attributes:
+        cell: AbsCell class, the cell that contains the segment
+        index: int, segment index in the cell, starts from 0
+        name: str, segment name generated by Neuron
+        pre_connections, post_connections: list of AbsConnections, the segment acts as postsynaptic segment or presynaptic segment
+    """
+    def __init__(self, index, cell, name):
+        assert isinstance(cell, AbsCell)
+
+        self.cell, self.index, self.name = cell, int(index), name
+        self.pre_connections, self.post_connections = [], []
+
+    def add_pre_connection(self, new_connection):
+        """the new connection points to self segment"""
+        assert isinstance(new_connection, AbsConnection)
+
+        if self.index == new_connection.post_segment.index:
+            self.pre_connections.append(new_connection)
+        else:
+            raise ValueError("AbsSegment Index Incompatible!")
+
+    def add_post_connection(self, new_connection):
+        """the new connection points from self segment"""
+        assert isinstance(new_connection, AbsConnection)
+
+        if self.index == new_connection.pre_segment.index:
+            self.post_connections.append(new_connection)
+        else:
+            raise ValueError("AbsSegment Index Incompatible!")
+
+
+class AbsConnection:
+    """class for abstract connection
+    either be synapse (positive weight for excitatory and negative for inhibitory) or gap-junction
+
+    Attributes:
+        pre_segment, post_segment: AbsSegment class, pre-synaptic segment or post-synaptic segment
+        pre_cell, post_cell: AbsCell class, pre-synaptic cell or post-synaptic cell
+        category: str, either 'syn' or 'gj'
+        weight: float
+        pair_key: int or None, two gj belongs to one pair has the same unique key in the circuit, syn's key is None
+    """
+    def __init__(self, pre_segment, post_segment, category, weight, pair_key=None):
+        assert category in ('syn', 'gj')
+        assert isinstance(pre_segment, (AbsSegment, type(None))) and isinstance(post_segment, (AbsSegment, type(None)))
+
+        self.pre_segment, self.post_segment = pre_segment, post_segment
+        self.pre_cell = pre_segment.cell if pre_segment is not None else None
+        self.post_cell = post_segment.cell if post_segment is not None else None
+        self.category, self.weight, self.pair_key = category, weight, pair_key
+
+    def update_info(self, new_weight=None):
+        """change the weight or category of the connection"""
+        assert new_weight is not None
+        self.weight = new_weight
+
+
+class AbsCell:
+    """class for abstract cell
+
+    Attributes:
+        index: int, cell index
+        name: str, cell name
+        segments: list of AbsSegment object
+        pre_connections, post_connections: list of connection, the Cell acts as post-synaptic cell or pre-synaptic cell respectively
+    """
+    def __init__(self, index, name):
+        self.index, self.name = int(index), name
+        self.segments = []
+        self.pre_connections, self.post_connections = [], []
+
+    def add_segment(self, new_segment):
+        """adding AbsSegment into self.segments"""
+        assert isinstance(new_segment, AbsSegment)
+        assert new_segment.cell.index == self.index
+
+        for segment in self.segments:
+            if segment.index == new_segment.index:
+                raise ValueError("Segment already inserted!")
+        self.segments.append(new_segment)
+
+    def add_pre_connection(self, new_connection):
+        """the new connection points to the cell"""
+        assert isinstance(new_connection, AbsConnection)
+
+        if new_connection.post_cell.index == self.index:
+            self.pre_connections.append(new_connection)
+        else:
+            raise ValueError("Connection post-synaptic cell incompatible!")
+
+    def add_post_connection(self, new_connection):
+        """the new connection points out of the cell"""
+        assert isinstance(new_connection, AbsConnection)
+
+        if new_connection.pre_cell.index == self.index:
+            self.post_connections.append(new_connection)
+        else:
+            raise ValueError("Connection pre-synaptic cell incompatible!")
+
+    def segment(self, segment_index=None, segment_name=None):
+        """obtain the segment object according to its index or name"""
+        assert (segment_index is not None) or (segment_name is not None)
+        for segment in self.segments:
+            if ((segment.index == segment_index) or (segment_index is None)) and \
+                    ((segment.name == segment_name) or (segment_name is None)):
+                return segment
+        raise ValueError("Segment not found!")
+
+    def update_connections(self, new_weights):
+        """updating pre_connections weight"""
+        assert len(self.pre_connections) == len(new_weights)
+        for connection, new_weight in zip(self.pre_connections, new_weights):
+            connection.update_info(new_weight)
+
+
+class AbstractCircuit:
+    """class for abstract circuit
+
+    Attributes:
+        cells: list of all AbsCell object in the circuit
+        connections: list of AbsConnection, all connections include input and output connections
+        input_connections: list of AbsConnection, input connections
+        output_connections: list of AbsConnection, output connections
+    """
+    def __init__(self):
+        self.cells, self.connections = [], []
+        self.input_connections, self.output_connections = [], []
+
+    def add_cell(self, new_cell):
+        """cell append interface"""
+        assert isinstance(new_cell, AbsCell)
+        self.cells.append(new_cell)
+
+    def add_connection(self, new_connection):
+        """connection append interface"""
+        assert isinstance(new_connection, AbsConnection)
+        self.connections.append(new_connection)
+        if new_connection.pre_segment is None:
+            self.input_connections.append(new_connection)
+        else:
+            new_connection.pre_segment.add_post_connection(new_connection)
+            new_connection.pre_cell.add_post_connection(new_connection)
+
+        if new_connection.post_segment is None:
+            self.output_connections.append(new_connection)
+        else:
+            new_connection.post_segment.add_pre_connection(new_connection)
+            new_connection.post_cell.add_pre_connection(new_connection)
+
+    def cell(self, cell_index=None, cell_name=None):
+        """obtain the cell object according to its index or name"""
+        assert (cell_index is not None) or (cell_name is not None)
+        for cell in self.cells:
+            if ((cell.index == cell_index) or (cell_index is None)) and \
+                    ((cell.name == cell_name) or (cell_name is None)):
+                return cell
+        raise ValueError("Cell not found!")
+
+    def update_connections(self, new_weights):
+        """updating connects weight"""
+        assert len(self.connections) == len(new_weights)
+        for connection, new_weight in zip(self.connections, new_weights):
+            connection.update_info(new_weight)

wormsim/components/mechanism/modfile/cainternm.mod

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+TITLE the microscale internal calcium concentration
+
+COMMENT
+Internal calcium concentration calculated in response to a calcium current.
+
+model and parameters from:
+Nicoletti, M., et al. (2019). "Biophysical modeling of C. elegans neurons: Single ion currents and whole-cell dynamics of AWCon and RMD." PLoS One 14(7): e0218738.
+ENDCOMMENT
+
+
+UNITS {
+	(molar) = (1/liter)			: moles do not appear in units
+    (uM)    = (micromolar)
+	(um)	= (micron)
+	(mA)	= (milliamp)
+    (pS)    = (picosiemens)
+}
+
+
+NEURON {
+	SUFFIX cainternm
+	USEION ca READ ica, cai WRITE cai
+	RANGE vcell
+}
+
+
+CONSTANT {
+	FARADAY = 96485		(coul)		: moles do not appear in units
+}
+
+
+PARAMETER {
+	vcell = 31.16 (um3)
+	f = 0.001         : free intracellular calcium fraction
+	tca = 50 (ms)     : calcium removal time constant
+	caeq = 0.05 (uM/um2)  : the baseline calcium concentration
+}
+
+
+ASSIGNED {
+	v  (mV)
+	ica (pA/um2)
+	alpha
+}
+
+
+STATE {
+    cai  (uM/um2)
+}
+
+
+INITIAL {
+    setparames(v)
+}
+
+
+BREAKPOINT {
+	SOLVE states METHOD derivimplicit
+}
+
+
+DERIVATIVE states {
+    setparames(v)
+    cai' = alpha
+}
+
+
+PROCEDURE setparames(v (mV)) {
+	if (v <= 60.) { : eca=60 mV
+		alpha = (-f * ica * 10^6 / (2 * FARADAY * vcell)) - ((cai - caeq) / tca)
+	}
+	else {
+		alpha = -(cai - caeq) / tca
+	}
+}

wormsim/components/mechanism/modfile/cca1.mod

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+TITLE cca1 current for C. elegans neuron model
+
+
+COMMENT
+channel type: voltage-gated calcium channel
+
+model and parameters from:
+Nicoletti, M., et al. (2019). "Biophysical modeling of C. elegans neurons: Single ion currents and whole-cell dynamics of AWCon and RMD." PLoS One 14(7): e0218738.
+ENDCOMMENT
+
+
+UNITS {
+    (nS) = (nanosiemens)
+    (mV) = (millivolt)
+    (pA) = (picoamp)
+    (um) = (micron)
+}
+
+
+NEURON {
+    SUFFIX cca1
+    USEION ca READ eca WRITE ica
+    RANGE gbcca1, minf, hinf, tm, th, m, h
+}
+
+
+PARAMETER {
+    gbcca1 = 1 (nS/um2)
+    vhm = -43.32 (mV)
+    ka = 7.6 (mV)
+    vhh = -58.0 (mV)
+    ki = 7.0 (mV)
+    atm = 40.0 (ms)
+    btm = -62.5 (mV)
+    ctm = -12.6 (mV)
+    dtm = 0.7 (ms)
+    ath = 280 (ms)
+    bth = -60.7 (mV)
+    cth = 8.5 (mV)
+    dth = 19.8 (ms)
+}
+
+
+ASSIGNED {
+    v (mV)
+    eca (mV)
+    ica (pA/um2)
+    minf
+    hinf
+    tm (ms)
+    th (ms)
+}
+
+
+STATE {
+    m
+    h
+}
+
+
+BREAKPOINT {
+    SOLVE states METHOD cnexp
+    :ica = gbcca1 * m * m * h * (v - eca)
+    ica = gbcca1 * m * m * h * (v - 60) : eca=60 mV
+}
+
+
+INITIAL {
+    setparames(v)
+    m = minf
+    h = hinf
+}
+
+
+DERIVATIVE states {
+    setparames(v)
+    m' = (minf - m) / tm
+    h' = (hinf - h) / th
+}
+
+
+PROCEDURE setparames(v (mV)) {
+    minf = 1 / (1 + exp(-(v - vhm) / ka))
+    hinf = 1 / (1 + exp((v - vhh) / ki))
+    tm = atm / (1 + exp(-(v - btm) / ctm)) + dtm
+    th = ath / (1 + exp((v - bth) / cth)) + dth
+} 

wormsim/components/mechanism/modfile/egl19.mod

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+TITLE egl19 current for C. elegans neuron model
+
+
+COMMENT
+voltage-gated calcium channel
+
+model and parameters from:
+Nicoletti, M., et al. (2019). "Biophysical modeling of C. elegans neurons: Single ion currents and whole-cell dynamics of AWCon and RMD." PLoS One 14(7): e0218738.
+ENDCOMMENT
+
+
+UNITS {
+    (nS) = (nanosiemens)
+    (mV) = (millivolt)
+    (pA) = (picoamp)
+    (um) = (micron)
+}
+
+
+NEURON {
+    SUFFIX egl19
+    USEION ca READ eca WRITE ica
+    RANGE gbegl19, minf, hinf, tm, th, m, h
+}
+
+
+PARAMETER {
+    gbegl19 = 1 (nS/um2)
+    vhm = 5.6 (mV)
+    ka = 7.5 (mV)
+    vhh = 24.9 (mV)
+    ki = 12.0 (mV)
+    vhhb = -20.5 (mV)
+    kib = 8.1 (mV)
+    ahinf = 1.43
+    bhinf = 0.14
+    chinf = 5.96
+    dhinf = 0.60
+    atm = 2.9 (ms)
+    btm = 5.2 (mV)
+    ctm = 6.0 (mV)
+    dtm = 1.9 (ms)
+    etm = 1.4 (mV)
+    ftm = 30.0 (mV)
+    gtm = 2.3 (ms)
+    ath = 0.4
+    bth = 44.6 (ms)
+    cth = -23.0 (mV)
+    dth = 5.0 (mV)
+    eth = 36.4 (ms)
+    fth = 28.7 (mV)
+    gth = 3.7 (mV)
+    hth = 43.1 (ms)
+}
+
+
+ASSIGNED {
+    v (mV)
+    eca (mV)
+    ica (pA/um2)
+    minf
+    hinf
+    tm (ms)
+    th (ms)
+}
+
+
+STATE {
+    m
+    h
+}
+
+
+BREAKPOINT {
+    SOLVE states METHOD cnexp
+    :ica = gbegl19 * m * h * (v - eca)
+    ica = gbegl19 * m * h * (v - 60)  : eca=60 mV
+}
+
+
+INITIAL {
+    setparames(v)
+    m = minf
+    h = hinf
+}
+
+
+DERIVATIVE states {
+    setparames(v)
+    m' = (minf - m) / tm
+    h' = (hinf - h) / th
+}
+
+
+PROCEDURE setparames(v (mV)) {
+    minf = 1 / (1 + exp(-(v - vhm) / ka))
+    hinf = (ahinf / (1 + exp(-(v - vhh) / ki)) + bhinf) * (chinf / (1 + exp((v - vhhb) / kib)) + dhinf)
+    tm = atm * exp(-((v - btm) / ctm) ^ 2) + dtm * exp(-((v - etm) / ftm) ^ 2) + gtm
+    th = ath * ((bth / (1 + exp((v - cth) / dth))) + (eth / (1 + exp((v - fth) / gth))) + hth)
+}

wormsim/components/mechanism/modfile/egl2.mod

@@ -0,0 +1,76 @@
+TITLE egl2 current for C. elegans neuron model
+
+
+COMMENT
+channel type: voltage-gated potassium channel
+
+patch clamp data from:
+Weinshenker, D. , et al. "Block of an ether-a-go-go-like K(+) channel by imipramine rescues egl-2 excitation defects in Caenorhabditis elegans. " Journal of Neuroscience the Official Journal of the Society for Neuroscience 19.22(1999):9831.
+Figure 3a upper left
+
+ENDCOMMENT
+
+
+UNITS {
+    (nS) = (nanosiemens)
+    (mV) = (millivolt)
+    (pA) = (picoamp)
+    (um) = (micron)
+}
+
+
+NEURON {
+    SUFFIX egl2
+    USEION k READ ek WRITE ik
+    RANGE gbegl2, minf, tm, m
+}
+
+
+PARAMETER {
+    gbegl2 = 1 (nS/um2)
+    vhm = -6.9 (mV)
+    ka = 14.9 (mV)
+    atm = 1845.8 (ms)
+    btm = -122.6 (mV)
+    ctm = 13.8 (mV)
+    dtm = 1517.74 (ms)
+}
+
+
+ASSIGNED {
+    v (mV)
+    ek (mV)
+    ik (pA/um2)
+    minf
+    tm (ms)
+}
+
+
+STATE {
+    m
+}
+
+
+BREAKPOINT {
+    SOLVE states METHOD cnexp
+    :ik = gbegl2 * m * (v - ek)
+    ik = gbegl2 * m * (v + 80) : ek = -80
+}
+
+
+INITIAL {
+    setparames(v)
+    m = minf
+}
+
+
+DERIVATIVE states {
+    setparames(v)
+    m' = (minf - m) / tm
+}
+
+
+PROCEDURE setparames(v (mV)) {
+    minf = 1 / (1 + exp(-(v - vhm) / ka))
+    tm = atm / (1 + exp((v - btm) / ctm)) + dtm
+}

wormsim/components/mechanism/modfile/egl36.mod

@@ -0,0 +1,92 @@
+TITLE egl36 current for C. elegans neuron model
+
+
+COMMENT
+Channel type: voltage-gated potassium channel.
+
+Model, parameters and patch clamp data from:
+Johnstone, D. B. , et al. "Behavioral Defects in C. elegans egl-36 Mutants Result from Potassium Channels Shifted in Voltage-Dependence of Activation." Neuron 19.1(1997):151-64.
+
+patch clamp data in Figure 2A left upper
+https://www.cell.com/action/showPdf?pii=S0896-6273%2800%2980355-4
+
+
+ENDCOMMENT
+
+
+UNITS {
+    (nS) = (nanosiemens)
+    (mV) = (millivolt)
+    (pA) = (picoamp)
+    (um) = (micron)
+}
+
+
+NEURON {
+    SUFFIX egl36
+    USEION k READ ek WRITE ik
+    RANGE gbegl36, mfinf, mminf, msinf, tmf, tmm, tms, mf, mm, ms
+}
+
+
+PARAMETER {
+    gbegl36 = 1 (nS/um2)
+    vhm = 63.0 (mV)
+    ka = 28.5 (mV)
+    atms = 355.0 (ms)
+    atmm = 63.0 (ms)
+    atmf = 13.0 (ms)
+}
+
+
+ASSIGNED {
+    v (mV)
+    ek (mV)
+    ik (pA/um2)
+    mfinf
+    mminf
+    msinf
+    tmf (ms)
+    tmm (ms)
+    tms (ms)
+}
+
+
+STATE {
+    mf
+    mm
+    ms
+}
+
+
+BREAKPOINT {
+    SOLVE states METHOD cnexp
+    :ik = gbegl36 * (0.33 * mf + 0.36 * mm + 0.39 * ms) * (v - ek)
+    ik = gbegl36 * (0.33 * mf + 0.36 * mm + 0.39 * ms) * (v + 80) : ek = -80
+}
+
+
+INITIAL {
+    setparames(v)
+    mf = mfinf
+    mm = mminf
+    ms = msinf
+}
+
+
+DERIVATIVE states {
+    setparames(v)
+    mf' = (mfinf - mf) / tmf
+    mm' = (mminf - mm) / tmm
+    ms' = (msinf - ms) / tms
+}
+
+
+PROCEDURE setparames(v (mV)) {
+    mfinf = 1 / (1 + exp(-(v - vhm) / ka))
+    mminf = 1 / (1 + exp(-(v - vhm) / ka))
+    msinf = 1 / (1 + exp(-(v - vhm) / ka))
+    tmf = atmf
+    tmm = atmm
+    tms = atms
+} 

wormsim/components/mechanism/modfile/exc_syn_advance.mod

@@ -0,0 +1,91 @@
+COMMENT
+Based on NMODL code for neuron_to_neuron_exc_syn
+
+Code and comments have been normalized--that is,
+they are now of the usual form employed in 
+NMODL-specified synaptic mechanisms.
+
+Oddities that save neither storage nor time, 
+or preclude use with adaptive integration, 
+or deliberately introduce errors in an attempt
+to save a few CPU cycles, have been removed.
+
+Unused variables and parameters have also been removed.
+
+vpre is now a POINTER.
+
+In the INITIAL block, the completely unnecessary repeat
+execution of procedure rates() has been removed, 
+and the state variable s is now set to the correct 
+initial value.
+
+The value of the current i is now calculated in the
+BREAKPOINT block, instead of being calculated as a 
+side-effect of calling rates().
+ENDCOMMENT
+
+TITLE excitatory to excitatory synapse
+
+NEURON {
+    POINT_PROCESS exc_syn_advance
+    NONSPECIFIC_CURRENT i
+    RANGE weight, conductance, i, vpre
+    RANGE delta, k, Vth, erev
+}
+
+UNITS {
+    (nA) = (nanoamp)
+    (uA) = (microamp)
+    (mA) = (milliamp)
+    (A) = (amp)
+    (mV) = (millivolt)
+    (mS) = (millisiemens)
+    (uS) = (microsiemens)
+    (molar) = (1/liter)
+    (kHz) = (kilohertz)
+    (mM) = (millimolar)
+    (um) = (micrometer)
+    (umol) = (micromole)
+    (S) = (siemens)
+}
+
+PARAMETER {
+    weight = 1
+    conductance = 4.9E-4 (uS)
+    delta = 5 (mV)
+    k = 0.5 (kHz)
+    Vth = 0 (mV)
+    erev = 30 (mV) : -10
+}
+
+ASSIGNED {
+    v (mV)
+    vpre (mV)
+    inf
+    tau (ms)
+    i (nA)
+}
+
+STATE {
+    s  
+}
+
+INITIAL {
+    rates()
+    s = inf : NTC original code did not properly initialize s
+}
+
+BREAKPOINT {
+    SOLVE states METHOD cnexp
+    i = weight * conductance * s * (v - erev)
+}
+
+DERIVATIVE states {
+    rates()
+    s' = (inf - s)/tau
+}
+
+PROCEDURE rates() {
+    inf = 1/( 1 + exp((Vth - vpre)/delta) )
+    tau = (1 - inf)/k
+}