diff --git a/.gitignore b/.gitignore index 3e6c6c27..8298fba1 100644 --- a/.gitignore +++ b/.gitignore @@ -91,3 +91,7 @@ arm64 /c302/.ipynb_checkpoints .ipynb_checkpoints /c302/data/~$*.xlsx +/examples/test/images/cell_C.xml +/examples/test/images/c302_C1_Oscillator.net.nml +/examples/test/images/LEMS_c302_C1_Oscillator.xml +/c302/VarshneyDataReader2.py diff --git a/c302/ConnectomeReader.py b/c302/ConnectomeReader.py new file mode 100644 index 00000000..44663112 --- /dev/null +++ b/c302/ConnectomeReader.py @@ -0,0 +1,180 @@ +# -*- coding: utf-8 -*- + +############################################################ + +# Utilities for reading/writing/parsing NeuroML 2 files + +############################################################ + +from c302 import print_ + +PREFERRED_NEURON_NAMES = ['ADAL', 'ADAR', 'ADEL', 'ADER', 'ADFL', 'ADFR', 'ADLL', 'ADLR', 'AFDL', 'AFDR', 'AIAL', 'AIAR', 'AIBL', 'AIBR', 'AIML', 'AIMR', 'AINL', 'AINR', 'AIYL', 'AIYR', 'AIZL', 'AIZR', 'ALA', 'ALML', 'ALMR', 'ALNL', 'ALNR', 'AQR', 'AS1', 'AS10', 'AS11', 'AS2', 'AS3', 'AS4', 'AS5', 'AS6', 'AS7', 'AS8', 'AS9', 'ASEL', 'ASER', 'ASGL', 'ASGR', 'ASHL', 'ASHR', 'ASIL', 'ASIR', 'ASJL', 'ASJR', 'ASKL', 'ASKR', 'AUAL', 'AUAR', 'AVAL', 'AVAR', 'AVBL', 'AVBR', 'AVDL', 'AVDR', 'AVEL', 'AVER', 'AVFL', 'AVFR', 'AVG', 'AVHL', 'AVHR', 'AVJL', 'AVJR', 'AVKL', 'AVKR', 'AVL', 'AVM', 'AWAL', 'AWAR', 'AWBL', 'AWBR', 'AWCL', 'AWCR', 'BAGL', 'BAGR', 'BDUL', 'BDUR', 'CANL', 'CANR', 'CEPDL', 'CEPDR', 'CEPVL', 'CEPVR', 'DA1', 'DA2', 'DA3', 'DA4', 'DA5', 'DA6', 'DA7', 'DA8', 'DA9', 'DB1', 'DB2', 'DB3', 'DB4', 'DB5', 'DB6', 'DB7', 'DD1', 'DD2', 'DD3', 'DD4', 'DD5', 'DD6', 'DVA', 'DVB', 'DVC', 'FLPL', 'FLPR', 'HSNL', 'HSNR', 'I1L', 'I1R', 'I2L', 'I2R', 'I3', 'I4', 'I5', 'I6', 'IL1DL', 'IL1DR', 'IL1L', 'IL1R', 'IL1VL', 'IL1VR', 'IL2DL', 'IL2DR', 'IL2L', 'IL2R', 'IL2VL', 'IL2VR', 'LUAL', 'LUAR', 'M1', 'M2L', 'M2R', 'M3L', 'M3R', 'M4', 'M5', 'MCL', 'MCR', 'MI', 'NSML', 'NSMR', 'OLLL', 'OLLR', 'OLQDL', 'OLQDR', 'OLQVL', 'OLQVR', 'PDA', 'PDB', 'PDEL', 'PDER', 'PHAL', 'PHAR', 'PHBL', 'PHBR', 'PHCL', 'PHCR', 'PLML', 'PLMR', 'PLNL', 'PLNR', 'PQR', 'PVCL', 'PVCR', 'PVDL', 'PVDR', 'PVM', 'PVNL', 'PVNR', 'PVPL', 'PVPR', 'PVQL', 'PVQR', 'PVR', 'PVT', 'PVWL', 'PVWR', 'RIAL', 'RIAR', 'RIBL', 'RIBR', 'RICL', 'RICR', 'RID', 'RIFL', 'RIFR', 'RIGL', 'RIGR', 'RIH', 'RIML', 'RIMR', 'RIPL', 'RIPR', 'RIR', 'RIS', 'RIVL', 'RIVR', 'RMDDL', 'RMDDR', 'RMDL', 'RMDR', 'RMDVL', 'RMDVR', 'RMED', 'RMEL', 'RMER', 'RMEV', 'RMFL', 'RMFR', 'RMGL', 'RMGR', 'RMHL', 'RMHR', 'SAADL', 'SAADR', 'SAAVL', 'SAAVR', 'SABD', 'SABVL', 'SABVR', 'SDQL', 'SDQR', 'SIADL', 'SIADR', 'SIAVL', 'SIAVR', 'SIBDL', 'SIBDR', 'SIBVL', 'SIBVR', 'SMBDL', 'SMBDR', 'SMBVL', 'SMBVR', 'SMDDL', 'SMDDR', 'SMDVL', 'SMDVR', 'URADL', 'URADR', 'URAVL', 'URAVR', 'URBL', 'URBR', 'URXL', 'URXR', 'URYDL', 'URYDR', 'URYVL', 'URYVR', 'VA1', 'VA10', 'VA11', 'VA12', 'VA2', 'VA3', 'VA4', 'VA5', 'VA6', 'VA7', 'VA8', 'VA9', 'VB1', 'VB10', 'VB11', 'VB2', 'VB3', 'VB4', 'VB5', 'VB6', 'VB7', 'VB8', 'VB9', 'VC1', 'VC2', 'VC3', 'VC4', 'VC5', 'VC6', 'VD1', 'VD10', 'VD11', 'VD12', 'VD13', 'VD2', 'VD3', 'VD4', 'VD5', 'VD6', 'VD7', 'VD8', 'VD9'] +PREFERRED_MUSCLE_NAMES = ['MANAL', 'MDL01', 'MDL02', 'MDL03', 'MDL04', 'MDL05', 'MDL06', 'MDL07', 'MDL08', 'MDL09', 'MDL10', 'MDL11', 'MDL12', 'MDL13', 'MDL14', 'MDL15', 'MDL16', 'MDL17', 'MDL18', 'MDL19', 'MDL20', 'MDL21', 'MDL22', 'MDL23', 'MDL24', 'MDR01', 'MDR02', 'MDR03', 'MDR04', 'MDR05', 'MDR06', 'MDR07', 'MDR08', 'MDR09', 'MDR10', 'MDR11', 'MDR12', 'MDR13', 'MDR14', 'MDR15', 'MDR16', 'MDR17', 'MDR18', 'MDR19', 'MDR20', 'MDR21', 'MDR22', 'MDR23', 'MDR24', 'MVL01', 'MVL02', 'MVL03', 'MVL04', 'MVL05', 'MVL06', 'MVL07', 'MVL08', 'MVL09', 'MVL10', 'MVL11', 'MVL12', 'MVL13', 'MVL14', 'MVL15', 'MVL16', 'MVL17', 'MVL18', 'MVL19', 'MVL20', 'MVL21', 'MVL22', 'MVL23', 'MVR01', 'MVR02', 'MVR03', 'MVR04', 'MVR05', 'MVR06', 'MVR07', 'MVR08', 'MVR09', 'MVR10', 'MVR11', 'MVR12', 'MVR13', 'MVR14', 'MVR15', 'MVR16', 'MVR17', 'MVR18', 'MVR19', 'MVR20', 'MVR21', 'MVR22', 'MVR23', 'MVR24', 'MVULVA'] + + +def convert_to_preferred_muscle_name(muscle): + + if muscle.startswith("BWM-VL"): + return "MVL%s" %muscle[6:] + elif muscle.startswith("BWM-VR"): + return "MVR%s" %muscle[6:] + elif muscle.startswith("BWM-DL"): + return "MDL%s" %muscle[6:] + elif muscle.startswith("BWM-DR"): + return "MDR%s" %muscle[6:] + elif muscle=='LegacyBodyWallMuscles': + return 'BWM' + else: + return muscle + "???" + +def get_all_muscle_prefixes(): + return ["pm", "vm", "um", "BWM-D", "BWM-V", "LegacyBodyWallMuscles"] + + +def get_body_wall_muscle_prefixes(): + return ["BWM-D", "BWM-V", "LegacyBodyWallMuscles"] + + +def is_muscle(cell): + known_muscle_prefixes = get_all_muscle_prefixes() + return cell.startswith(tuple(known_muscle_prefixes)) + + +def is_body_wall_muscle(cell): + known_muscle_prefixes = get_body_wall_muscle_prefixes() + return cell.startswith(tuple(known_muscle_prefixes)) + + +def is_neuron(cell): + return not is_body_wall_muscle(cell) + +class ConnectionInfo: + + def __init__(self, + pre_cell, + post_cell, + number, + syntype, + synclass): + + self.pre_cell = pre_cell + self.post_cell = post_cell + self.number = number + self.syntype = syntype + self.synclass = synclass + + + def __str__(self): + return "Connection from %s to %s (%i times, type: %s, neurotransmitter: %s)"%(self.pre_cell, self.post_cell, self.number, self.syntype, self.synclass) + + def short(self): + return "Connection from %s to %s (%s)"%(self.pre_cell, self.post_cell, self.syntype) + + def __eq__(self, other): + return other.pre_cell == self.pre_cell and other.post_cell == self.post_cell and other.number == self.number and other.syntype == self.syntype and other.synclass == self.synclass + + def __lt__(self, other): + if other.pre_cell+other.post_cell > self.pre_cell+self.post_cell: + return True + else: + return False + + def __repr__(self): + return self.__str__() + + +def check_neurons(cells): + + preferred = [] + not_in_preferred = [] + missing_preferred = [n for n in PREFERRED_NEURON_NAMES] + for c in cells: + if not c in PREFERRED_NEURON_NAMES: + not_in_preferred.append(c) + else: + preferred.append(c) + if c in missing_preferred: + missing_preferred.remove(c) + + return preferred, not_in_preferred, missing_preferred + +def analyse_connections(cells, neuron_conns, neurons2muscles, muscles, muscle_conns): + + print_("Found %s cells: %s\n"%(len(cells),sorted(cells))) + #assert(len(cells) == 302) + #print_("Expected number of cells correct if include_nonconnected_cells=True") + + preferred, not_in_preferred, missing_preferred = check_neurons(cells) + + print_("Found %s non-neuron(s) here: %s\n"%(len(not_in_preferred),sorted(not_in_preferred))) + print_("Known neurons not present: %s\n"%(sorted(missing_preferred))) + + print_("Found %s connections..."%(len(neuron_conns))) + for c in neuron_conns[:5]: print_(" %s"%c) + + print_(" ...\n") + nts = {} + nts_tot = {} + for c in neuron_conns: + nt = c.synclass + if not nt in nts: + nts[nt] = 0 + nts_tot[nt] = 0 + nts[nt]+=1 + nts_tot[nt]+=c.number + + for nt in sorted(nts.keys()): + print_(" %s present in %s connections, %s synapses total (avg %.3f syns per conn)"%(nt, nts[nt], nts_tot[nt], nts_tot[nt]/nts[nt])) + + print_("") + print_(" --- Muscles ---") + print_("") + + print_("Found %s muscles: %s\n"%(len(muscles),sorted(muscles))) + not_in_preferred = [] + for m in muscles: + if not m in PREFERRED_MUSCLE_NAMES: + not_in_preferred.append(m) + + print_("Found %s unidentified muscles: %s\n"%(len(not_in_preferred),sorted(not_in_preferred))) + + print_("Found %i neurons connected to muscles: %s\n"%(len(neurons2muscles), sorted(neurons2muscles))) + print_("Found %i muscles connected to neurons: %s\n"%(len(muscles), sorted(muscles))) + + print_("Found %i connections between neurons and muscles%s\n"%(len(muscle_conns), (', e.g. %s'%muscle_conns[0]) if len(muscle_conns)>0 else '')) + + nts = {} + nts_tot = {} + for c in muscle_conns: + nt = c.synclass + if not nt in nts: + nts[nt] = 0 + nts_tot[nt] = 0 + nts[nt]+=1 + nts_tot[nt]+=c.number + + for nt in nts: + print_(" %s present in %s connections, %s synapses total (avg %.3f syns per conn)"%(nt, nts[nt], nts_tot[nt], nts_tot[nt]/nts[nt])) + + + core_set = ['AVBL','PVCL','VA6', 'VB6', 'VD6', 'DB4', 'DD4'] + #core_set = ['VA6', 'VD6'] + print_("\n\nConnections between cells in the subset %s:\n"%(core_set)) + + + for c in neuron_conns: + if c.pre_cell in core_set and c.post_cell in core_set: + print_(str(c)) + + + print_("") + + +if __name__ == "__main__": + + from SpreadsheetDataReader import read_data, read_muscle_data + + cells, neuron_conns = read_data(include_nonconnected_cells=True) + neurons2muscles, muscles, muscle_conns = read_muscle_data() + + analyse_connections(cells, neuron_conns, neurons2muscles, muscles, muscle_conns) \ No newline at end of file diff --git a/c302/NeuroMLUtilities.py b/c302/NeuroMLUtilities.py index 790e5d36..9c5d9eee 100644 --- a/c302/NeuroMLUtilities.py +++ b/c302/NeuroMLUtilities.py @@ -8,44 +8,11 @@ from c302 import print_ -PREFERRED_NEURON_NAMES = ['ADAL', 'ADAR', 'ADEL', 'ADER', 'ADFL', 'ADFR', 'ADLL', 'ADLR', 'AFDL', 'AFDR', 'AIAL', 'AIAR', 'AIBL', 'AIBR', 'AIML', 'AIMR', 'AINL', 'AINR', 'AIYL', 'AIYR', 'AIZL', 'AIZR', 'ALA', 'ALML', 'ALMR', 'ALNL', 'ALNR', 'AQR', 'AS1', 'AS10', 'AS11', 'AS2', 'AS3', 'AS4', 'AS5', 'AS6', 'AS7', 'AS8', 'AS9', 'ASEL', 'ASER', 'ASGL', 'ASGR', 'ASHL', 'ASHR', 'ASIL', 'ASIR', 'ASJL', 'ASJR', 'ASKL', 'ASKR', 'AUAL', 'AUAR', 'AVAL', 'AVAR', 'AVBL', 'AVBR', 'AVDL', 'AVDR', 'AVEL', 'AVER', 'AVFL', 'AVFR', 'AVG', 'AVHL', 'AVHR', 'AVJL', 'AVJR', 'AVKL', 'AVKR', 'AVL', 'AVM', 'AWAL', 'AWAR', 'AWBL', 'AWBR', 'AWCL', 'AWCR', 'BAGL', 'BAGR', 'BDUL', 'BDUR', 'CANL', 'CANR', 'CEPDL', 'CEPDR', 'CEPVL', 'CEPVR', 'DA1', 'DA2', 'DA3', 'DA4', 'DA5', 'DA6', 'DA7', 'DA8', 'DA9', 'DB1', 'DB2', 'DB3', 'DB4', 'DB5', 'DB6', 'DB7', 'DD1', 'DD2', 'DD3', 'DD4', 'DD5', 'DD6', 'DVA', 'DVB', 'DVC', 'FLPL', 'FLPR', 'HSNL', 'HSNR', 'I1L', 'I1R', 'I2L', 'I2R', 'I3', 'I4', 'I5', 'I6', 'IL1DL', 'IL1DR', 'IL1L', 'IL1R', 'IL1VL', 'IL1VR', 'IL2DL', 'IL2DR', 'IL2L', 'IL2R', 'IL2VL', 'IL2VR', 'LUAL', 'LUAR', 'M1', 'M2L', 'M2R', 'M3L', 'M3R', 'M4', 'M5', 'MCL', 'MCR', 'MI', 'NSML', 'NSMR', 'OLLL', 'OLLR', 'OLQDL', 'OLQDR', 'OLQVL', 'OLQVR', 'PDA', 'PDB', 'PDEL', 'PDER', 'PHAL', 'PHAR', 'PHBL', 'PHBR', 'PHCL', 'PHCR', 'PLML', 'PLMR', 'PLNL', 'PLNR', 'PQR', 'PVCL', 'PVCR', 'PVDL', 'PVDR', 'PVM', 'PVNL', 'PVNR', 'PVPL', 'PVPR', 'PVQL', 'PVQR', 'PVR', 'PVT', 'PVWL', 'PVWR', 'RIAL', 'RIAR', 'RIBL', 'RIBR', 'RICL', 'RICR', 'RID', 'RIFL', 'RIFR', 'RIGL', 'RIGR', 'RIH', 'RIML', 'RIMR', 'RIPL', 'RIPR', 'RIR', 'RIS', 'RIVL', 'RIVR', 'RMDDL', 'RMDDR', 'RMDL', 'RMDR', 'RMDVL', 'RMDVR', 'RMED', 'RMEL', 'RMER', 'RMEV', 'RMFL', 'RMFR', 'RMGL', 'RMGR', 'RMHL', 'RMHR', 'SAADL', 'SAADR', 'SAAVL', 'SAAVR', 'SABD', 'SABVL', 'SABVR', 'SDQL', 'SDQR', 'SIADL', 'SIADR', 'SIAVL', 'SIAVR', 'SIBDL', 'SIBDR', 'SIBVL', 'SIBVR', 'SMBDL', 'SMBDR', 'SMBVL', 'SMBVR', 'SMDDL', 'SMDDR', 'SMDVL', 'SMDVR', 'URADL', 'URADR', 'URAVL', 'URAVR', 'URBL', 'URBR', 'URXL', 'URXR', 'URYDL', 'URYDR', 'URYVL', 'URYVR', 'VA1', 'VA10', 'VA11', 'VA12', 'VA2', 'VA3', 'VA4', 'VA5', 'VA6', 'VA7', 'VA8', 'VA9', 'VB1', 'VB10', 'VB11', 'VB2', 'VB3', 'VB4', 'VB5', 'VB6', 'VB7', 'VB8', 'VB9', 'VC1', 'VC2', 'VC3', 'VC4', 'VC5', 'VC6', 'VD1', 'VD10', 'VD11', 'VD12', 'VD13', 'VD2', 'VD3', 'VD4', 'VD5', 'VD6', 'VD7', 'VD8', 'VD9'] -PREFERRED_MUSCLE_NAMES = ['MANAL', 'MDL01', 'MDL02', 'MDL03', 'MDL04', 'MDL05', 'MDL06', 'MDL07', 'MDL08', 'MDL09', 'MDL10', 'MDL11', 'MDL12', 'MDL13', 'MDL14', 'MDL15', 'MDL16', 'MDL17', 'MDL18', 'MDL19', 'MDL20', 'MDL21', 'MDL22', 'MDL23', 'MDL24', 'MDR01', 'MDR02', 'MDR03', 'MDR04', 'MDR05', 'MDR06', 'MDR07', 'MDR08', 'MDR09', 'MDR10', 'MDR11', 'MDR12', 'MDR13', 'MDR14', 'MDR15', 'MDR16', 'MDR17', 'MDR18', 'MDR19', 'MDR20', 'MDR21', 'MDR22', 'MDR23', 'MDR24', 'MVL01', 'MVL02', 'MVL03', 'MVL04', 'MVL05', 'MVL06', 'MVL07', 'MVL08', 'MVL09', 'MVL10', 'MVL11', 'MVL12', 'MVL13', 'MVL14', 'MVL15', 'MVL16', 'MVL17', 'MVL18', 'MVL19', 'MVL20', 'MVL21', 'MVL22', 'MVL23', 'MVR01', 'MVR02', 'MVR03', 'MVR04', 'MVR05', 'MVR06', 'MVR07', 'MVR08', 'MVR09', 'MVR10', 'MVR11', 'MVR12', 'MVR13', 'MVR14', 'MVR15', 'MVR16', 'MVR17', 'MVR18', 'MVR19', 'MVR20', 'MVR21', 'MVR22', 'MVR23', 'MVR24', 'MVULVA'] - - -class ConnectionInfo: - - def __init__(self, - pre_cell, - post_cell, - number, - syntype, - synclass): - - self.pre_cell = pre_cell - self.post_cell = post_cell - self.number = number - self.syntype = syntype - self.synclass = synclass - - - def __str__(self): - return "Connection from %s to %s (%i times, type: %s, neurotransmitter: %s)"%(self.pre_cell, self.post_cell, self.number, self.syntype, self.synclass) - - def short(self): - return "Connection from %s to %s (%s)"%(self.pre_cell, self.post_cell, self.syntype) - - def __eq__(self, other): - return other.pre_cell == self.pre_cell and other.post_cell == self.post_cell and other.number == self.number and other.syntype == self.syntype and other.synclass == self.synclass - - def __lt__(self, other): - if other.pre_cell+other.post_cell > self.pre_cell+self.post_cell: - return True - else: - return False - - def __repr__(self): - return self.__str__() +from c302.ConnectomeReader import PREFERRED_NEURON_NAMES +from c302.ConnectomeReader import PREFERRED_MUSCLE_NAMES +from c302.ConnectomeReader import ConnectionInfo +from c302.ConnectomeReader import analyse_connections def getSegmentIds(cell): @@ -78,63 +45,12 @@ def fract(a, b, f): return a+(b-a)*f -def analyse_connections(cells, neuron_conns, neurons2muscles, muscles, muscle_conns): - - print_("Found %s cells: %s\n"%(len(cells),sorted(cells))) - #assert(len(cells) == 302) - #print_("Expected number of cells correct if include_nonconnected_cells=True") - not_in_preferred = [] - for c in cells: - if not c in PREFERRED_NEURON_NAMES: - not_in_preferred.append(c) +if __name__ == "__main__": - print_("Found %s non-neuron(s): %s\n"%(len(not_in_preferred),sorted(not_in_preferred))) - - print_("Found %s connections..."%(len(neuron_conns))) - for c in neuron_conns[:5]: print_(" %s"%c) - - print_(" ...\n") - nts = {} - nts_tot = {} - for c in neuron_conns: - nt = c.synclass - if not nt in nts: - nts[nt] = 0 - nts_tot[nt] = 0 - nts[nt]+=1 - nts_tot[nt]+=c.number - - for nt in sorted(nts.keys()): - print_(" %s present in %s connections, %s synapses total (avg %.3f syns per conn)"%(nt, nts[nt], nts_tot[nt], nts_tot[nt]/nts[nt])) - - print_("") - print_(" --- Muscles ---") - print_("") - - print_("Found %s muscles: %s\n"%(len(muscles),sorted(muscles))) - not_in_preferred = [] - for m in muscles: - if not m in PREFERRED_MUSCLE_NAMES: - not_in_preferred.append(m) - - print_("Found %s unidentified muscles: %s\n"%(len(not_in_preferred),sorted(not_in_preferred))) - - print_("Found %i neurons connected to muscles: %s\n"%(len(neurons2muscles), sorted(neurons2muscles))) - print_("Found %i muscles connected to neurons: %s\n"%(len(muscles), sorted(muscles))) - - print_("Found %i connections between neurons and muscles%s\n"%(len(muscle_conns), (', e.g. %s'%muscle_conns[0]) if len(muscle_conns)>0 else '')) - - nts = {} - nts_tot = {} - for c in muscle_conns: - nt = c.synclass - if not nt in nts: - nts[nt] = 0 - nts_tot[nt] = 0 - nts[nt]+=1 - nts_tot[nt]+=c.number + from SpreadsheetDataReader import read_data, read_muscle_data + from WormNeuroAtlasReader import read_data, read_muscle_data - for nt in nts: - print_(" %s present in %s connections, %s synapses total (avg %.3f syns per conn)"%(nt, nts[nt], nts_tot[nt], nts_tot[nt]/nts[nt])) + cells, neuron_conns = read_data(include_nonconnected_cells=True) + neurons2muscles, muscles, muscle_conns = read_muscle_data() - print_("") \ No newline at end of file + analyse_connections(cells, neuron_conns, neurons2muscles, muscles, muscle_conns) \ No newline at end of file diff --git a/c302/VarshneyDataReader.py b/c302/VarshneyDataReader.py index 2ee2ef9d..69ce15df 100644 --- a/c302/VarshneyDataReader.py +++ b/c302/VarshneyDataReader.py @@ -30,7 +30,7 @@ def read_data(include_nonconnected_cells=False, neuron_connect=True): if not post==NMJ_ENDPOINT: syntype = str(row[2]) num = int(row[3]) - synclass = 'Generic_GJ' if 'EJ' in syntype else 'Chemical_Synapse' + synclass = 'Generic_GJ' if 'EJ' in syntype else 'Generic_CS' conns.append(ConnectionInfo(pre, post, num, syntype, synclass)) if pre not in cells: @@ -60,7 +60,7 @@ def read_muscle_data(): if post==NMJ_ENDPOINT: syntype = str(row[2]) num = int(row[3]) - synclass = 'Generic_GJ' if 'EJ' in syntype else 'Chemical_Synapse' + synclass = 'Generic_GJ' if 'EJ' in syntype else 'Generic_CS' conns.append(ConnectionInfo(pre, post, num, syntype, synclass)) if pre not in neurons: diff --git a/c302/W_SpreadsheetDataReader.py b/c302/W_SpreadsheetDataReader.py index 4db6ffae..c152aa91 100644 --- a/c302/W_SpreadsheetDataReader.py +++ b/c302/W_SpreadsheetDataReader.py @@ -1,5 +1,8 @@ -from c302.NeuroMLUtilities import ConnectionInfo -from c302.NeuroMLUtilities import analyse_connections +from c302.ConnectomeReader import ConnectionInfo +from c302.ConnectomeReader import analyse_connections +from c302.ConnectomeReader import convert_to_preferred_muscle_name +from c302.ConnectomeReader import is_neuron +from c302.ConnectomeReader import is_body_wall_muscle from openpyxl import load_workbook import os @@ -8,214 +11,95 @@ spreadsheet_location = os.path.dirname(os.path.abspath(__file__))+"/data/" -def get_old_muscle_name(name): - if name.startswith("BWM-VL"): - return "MVL%s" %name[6:] - elif name.startswith("BWM-VR"): - return "MVR%s" %name[6:] - elif name.startswith("BWM-DL"): - return "MDL%s" %name[6:] - elif name.startswith("BWM-DR"): - return "MDR%s" %name[6:] - -class WitvlietDataReader1: - - def read_data(include_nonconnected_cells=False, neuron_connect=False): - - if neuron_connect: - conns = [] - cells = [] - filename = "%switvliet_2020_7.xlsx"%spreadsheet_location - wb = load_workbook(filename) - sheet = wb.worksheets[0] - print_("Opened the Excel file: " + filename) - - - for row in sheet.iter_rows(min_row=2, values_only=True): # Assuming data starts from the second row - pre = str(row[0]) - post = str(row[1]) - syntype = str(row[2]) - num = int(row[3]) - synclass = 'Generic_GJ' if 'electrical' in syntype else 'Chemical_Synapse' - - - conns.append(ConnectionInfo(pre, post, num, syntype, synclass)) - if pre not in cells: - cells.append(pre) - if post not in cells: - cells.append(post) - return cells, conns +class WitvlietDataReader: - else: - conns = [] - cells = [] - filename = "%switvliet_2020_7.xlsx"%spreadsheet_location - wb = load_workbook(filename) - sheet = wb.worksheets[0] + def __init__(self, spreadsheet): - print_("Opened Excel file..: " + filename) + self.filename = "%s%s"%(spreadsheet_location,spreadsheet) - known_nonconnected_cells = ['CANL', 'CANR', 'VC6'] - - - for row in sheet.iter_rows(min_row=2, values_only=True): - pre = str(row[0]) - post = str(row[1]) - syntype = str(row[2]) - num = int(row[3]) - synclass = 'Generic_GJ' if 'electrical' in syntype else 'Chemical_Synapse' + def read_data(self,include_nonconnected_cells=True): + if not include_nonconnected_cells: + raise Exception('Option include_nonconnected_cells=False not supported') + + conns = [] + cells = [] - conns.append(ConnectionInfo(pre, post, num, syntype, synclass)) - if pre not in cells: - cells.append(pre) - if post not in cells: - cells.append(post) + wb = load_workbook(self.filename) + sheet = wb.worksheets[0] + print_("Opened the Excel file: " + self.filename) + + for row in sheet.iter_rows(min_row=2, values_only=True): # Assuming data starts from the second row + #print(row) + pre = str(row[0]) + post = str(row[1]) + + if not is_neuron(pre) or not is_neuron(post): + continue # pre or post is not a neuron + + syntype = str(row[2]) + num = int(row[3]) + synclass = 'Generic_GJ' if 'electrical' in syntype else 'Generic_CS' + + conns.append(ConnectionInfo(pre, post, num, syntype, synclass)) - if include_nonconnected_cells: - for c in known_nonconnected_cells: cells.append(c) + if pre not in cells: + cells.append(pre) + if post not in cells: + cells.append(post) - return cells, conns + return cells, conns - - - def read_muscle_data(): + def read_muscle_data(self): conns = [] neurons = [] muscles = [] - filename = "%switvliet_2020_7.xlsx"%spreadsheet_location - wb = load_workbook(filename) + wb = load_workbook(self.filename) sheet = wb.worksheets[0] - print_("Opened Excel file: "+ filename) + print_("Opened Excel file: "+ self.filename) for row in sheet.iter_rows(min_row=2, values_only=True): - pre = str(row[0]) - post = str(row[1]) - syntype = str(row[2]) - num = int(row[3]) - synclass = 'Generic_GJ' if 'EJ' in syntype else 'Chemical_Synapse' - if post.startswith("BWM-"): - post = get_old_muscle_name(post) - else: - continue - - conns.append(ConnectionInfo(pre, post, num, syntype, synclass)) - if pre not in neurons: - neurons.append(pre) - if post not in muscles: - muscles.append(post) + pre = str(row[0]) + post = str(row[1]) + syntype = str(row[2]) + num = int(row[3]) + synclass = 'Generic_GJ' if 'EJ' in syntype else 'Generic_CS' + + if post.startswith("BWM-"): + post = convert_to_preferred_muscle_name(post) + else: + continue + + conns.append(ConnectionInfo(pre, post, num, syntype, synclass)) + if pre not in neurons: + neurons.append(pre) + if post not in muscles: + muscles.append(post) return neurons, muscles, conns def main1(): - cells, neuron_conns = WitvlietDataReader1.read_data(include_nonconnected_cells=True) - neurons2muscles, muscles, muscle_conns = WitvlietDataReader1.read_muscle_data() - - analyse_connections(cells, neuron_conns, neurons2muscles, muscles, muscle_conns) - - -class WitvlietDataReader2: - def read_data(include_nonconnected_cells=False, neuron_connect=False): - - if neuron_connect: - conns = [] - cells = [] - filename = "%switvliet_2020_8.xlsx"%spreadsheet_location - wb = load_workbook(filename) - sheet = wb.worksheets[0] - print_("Opened the Excel file: " + filename) - - - for row in sheet.iter_rows(min_row=2, values_only=True): # Assuming data starts from the second row - pre = str(row[0]) - post = str(row[1]) - syntype = str(row[2]) - num = int(row[3]) - synclass = 'Generic_GJ' if 'electrical' in syntype else 'Chemical_Synapse' - - conns.append(ConnectionInfo(pre, post, num, syntype, synclass)) - if pre not in cells: - cells.append(pre) - if post not in cells: - cells.append(post) - - return cells, conns - - else: - conns = [] - cells = [] - filename = "%switvliet_2020_8.xlsx"%spreadsheet_location - wb = load_workbook(filename) - sheet = wb.worksheets[0] + wdr = WitvlietDataReader('witvliet_2020_7.xlsx') - print_("Opened Excel file..: " + filename) + cells, neuron_conns = wdr.read_data() + neurons2muscles, muscles, muscle_conns = wdr.read_muscle_data() - known_nonconnected_cells = ['CANL', 'CANR', 'VC6'] - - - for row in sheet.iter_rows(min_row=2, values_only=True): - pre = str(row[0]) - post = str(row[1]) - syntype = str(row[2]) - num = int(row[3]) - synclass = 'Generic_GJ' if 'electrical' in syntype else 'Chemical_Synapse' - - - conns.append(ConnectionInfo(pre, post, num, syntype, synclass)) - if pre not in cells: - cells.append(pre) - if post not in cells: - cells.append(post) - - if include_nonconnected_cells: - for c in known_nonconnected_cells: cells.append(c) - - return cells, conns - - - def read_muscle_data(): - - conns = [] - neurons = [] - muscles = [] - - filename = "%switvliet_2020_8.xlsx"%spreadsheet_location - wb = load_workbook(filename) - sheet = wb.worksheets[0] - - print_("Opened Excel file: "+ filename) - - for row in sheet.iter_rows(min_row=2, values_only=True): - pre = str(row[0]) - post = str(row[1]) - syntype = str(row[2]) - num = int(row[3]) - synclass = 'Generic_GJ' if 'electrical' in syntype else 'Chemical_Synapse' - if post.startswith("BWM-"): - post = get_old_muscle_name(post) - else: - continue - - conns.append(ConnectionInfo(pre, post, num, syntype, synclass)) - if pre not in neurons: - neurons.append(pre) - if post not in muscles: - muscles.append(post) + analyse_connections(cells, neuron_conns, neurons2muscles, muscles, muscle_conns) - return neurons, muscles, conns - def main2(): - cells, neuron_conns = WitvlietDataReader2.read_data(include_nonconnected_cells=True) - neurons2muscles, muscles, muscle_conns = WitvlietDataReader2.read_muscle_data() + wdr = WitvlietDataReader('witvliet_2020_8.xlsx') + + cells, neuron_conns = wdr.read_data() + neurons2muscles, muscles, muscle_conns = wdr.read_muscle_data() analyse_connections(cells, neuron_conns, neurons2muscles, muscles, muscle_conns) diff --git a/c302/WhiteDataReader.py b/c302/WhiteDataReader.py index 12c3341e..b84931b1 100644 --- a/c302/WhiteDataReader.py +++ b/c302/WhiteDataReader.py @@ -11,32 +11,16 @@ import csv -from c302.NeuroMLUtilities import ConnectionInfo -from c302.NeuroMLUtilities import analyse_connections -import os - -from c302 import print_ - -def get_all_muscle_prefixes(): - return ["pm", "vm", "um", "BWM-D", "BWM-V", "LegacyBodyWallMuscles"] - - -def get_body_wall_muscle_prefixes(): - return ["BWM-D", "BWM-V", "LegacyBodyWallMuscles"] +from c302.ConnectomeReader import ConnectionInfo +from c302.ConnectomeReader import analyse_connections +from c302.ConnectomeReader import convert_to_preferred_muscle_name +from c302.ConnectomeReader import is_neuron +from c302.ConnectomeReader import is_body_wall_muscle -def is_muscle(cell): - known_muscle_prefixes = get_all_muscle_prefixes() - return cell.startswith(tuple(known_muscle_prefixes)) - - -def is_body_wall_muscle(cell): - known_muscle_prefixes = get_body_wall_muscle_prefixes() - return cell.startswith(tuple(known_muscle_prefixes)) - +import os -def is_neuron(cell): - return not is_body_wall_muscle(cell) +from c302 import print_ def remove_leading_index_zero(cell): @@ -47,17 +31,6 @@ def remove_leading_index_zero(cell): return "%s%s" % (cell[:-2], cell[-1:]) return cell -def get_old_muscle_name(muscle): - if muscle.startswith("BWM-VL"): - return "MVL%s" %muscle[6:] - elif muscle.startswith("BWM-VR"): - return "MVR%s" %muscle[6:] - elif muscle.startswith("BWM-DL"): - return "MDL%s" %muscle[6:] - elif muscle.startswith("BWM-DR"): - return "MDR%s" %muscle[6:] - else: - return muscle + "???" def get_syntype(syntype): if syntype == "electrical": @@ -142,7 +115,7 @@ def read_muscle_data(): if is_neuron(pre): pre = remove_leading_index_zero(pre) - post = get_old_muscle_name(post) + post = convert_to_preferred_muscle_name(post) conns.append(ConnectionInfo(pre, post, num, syntype, synclass)) @@ -213,7 +186,7 @@ def read_muscle_data(): if is_neuron(pre): pre = remove_leading_index_zero(pre) - post = get_old_muscle_name(post) + post = convert_to_preferred_muscle_name(post) conns.append(ConnectionInfo(pre, post, num, syntype, synclass)) @@ -289,7 +262,7 @@ def read_muscle_data(): if is_neuron(pre): pre = remove_leading_index_zero(pre) - post = get_old_muscle_name(post) + post = convert_to_preferred_muscle_name(post) conns.append(ConnectionInfo(pre, post, num, syntype, synclass)) diff --git a/c302/White_A.py b/c302/White_A.py new file mode 100644 index 00000000..cdc1f389 --- /dev/null +++ b/c302/White_A.py @@ -0,0 +1,18 @@ +# Temporary class to allow this to be used in comparison notebook. +# Should be tidied up. + +from c302.WhiteDataReader import White_A + +from c302.NeuroMLUtilities import analyse_connections + +read_data = White_A.read_data +read_muscle_data = White_A.read_muscle_data + +def main1(): + cells, neuron_conns = read_data(include_nonconnected_cells=True) + neurons2muscles, muscles, muscle_conns = read_muscle_data() + analyse_connections(cells, neuron_conns, neurons2muscles, muscles, muscle_conns) + + +if __name__ == '__main__': + main1() \ No newline at end of file diff --git a/c302/White_L4.py b/c302/White_L4.py new file mode 100644 index 00000000..8728af97 --- /dev/null +++ b/c302/White_L4.py @@ -0,0 +1,19 @@ +# Temporary class to allow this to be used in comparison notebook. +# Should be tidied up. + +from c302.WhiteDataReader import White_L4 + +from c302.NeuroMLUtilities import analyse_connections + +read_data = White_L4.read_data +read_muscle_data = White_L4.read_muscle_data + + +def main1(): + cells, neuron_conns = read_data(include_nonconnected_cells=True) + neurons2muscles, muscles, muscle_conns = read_muscle_data() + analyse_connections(cells, neuron_conns, neurons2muscles, muscles, muscle_conns) + + +if __name__ == '__main__': + main1() \ No newline at end of file diff --git a/c302/White_whole.py b/c302/White_whole.py new file mode 100644 index 00000000..f688c5fe --- /dev/null +++ b/c302/White_whole.py @@ -0,0 +1,18 @@ +# Temporary class to allow this to be used in comparison notebook. +# Should be tidied up. + +from c302.WhiteDataReader import White_whole + +from c302.NeuroMLUtilities import analyse_connections + +read_data = White_whole.read_data +read_muscle_data = White_whole.read_muscle_data + +def main1(): + cells, neuron_conns = read_data(include_nonconnected_cells=True) + neurons2muscles, muscles, muscle_conns = read_muscle_data() + analyse_connections(cells, neuron_conns, neurons2muscles, muscles, muscle_conns) + + +if __name__ == '__main__': + main1() \ No newline at end of file diff --git a/c302/WitvlietDataReader1.py b/c302/WitvlietDataReader1.py new file mode 100644 index 00000000..dd1ff29b --- /dev/null +++ b/c302/WitvlietDataReader1.py @@ -0,0 +1,21 @@ +# Temporary class to allow this to be used in comparison notebook. +# Should be tidied up. + +from c302.W_SpreadsheetDataReader import WitvlietDataReader +from c302.NeuroMLUtilities import analyse_connections + +wdr = WitvlietDataReader('witvliet_2020_7.xlsx') + +read_data = wdr.read_data +read_muscle_data = wdr.read_muscle_data + +def main1(): + + cells, neuron_conns = read_data() + neurons2muscles, muscles, muscle_conns = read_muscle_data() + + analyse_connections(cells, neuron_conns, neurons2muscles, muscles, muscle_conns) + + +if __name__ == '__main__': + main1() \ No newline at end of file diff --git a/c302/WitvlietDataReader2.py b/c302/WitvlietDataReader2.py new file mode 100644 index 00000000..fd0e70d5 --- /dev/null +++ b/c302/WitvlietDataReader2.py @@ -0,0 +1,22 @@ +# Temporary class to allow this to be used in comparison notebook. +# Should be tidied up. + +from c302.W_SpreadsheetDataReader import WitvlietDataReader +from c302.NeuroMLUtilities import analyse_connections + +wdr = WitvlietDataReader('witvliet_2020_8.xlsx') + +read_data = wdr.read_data +read_muscle_data = wdr.read_muscle_data + + +def main2(): + + cells, neuron_conns = read_data() + neurons2muscles, muscles, muscle_conns = read_muscle_data() + + analyse_connections(cells, neuron_conns, neurons2muscles, muscles, muscle_conns) + + +if __name__ == '__main__': + main2() \ No newline at end of file diff --git a/c302/WormNeuroAtlasReader.py b/c302/WormNeuroAtlasReader.py index 7a6356a7..93005948 100644 --- a/c302/WormNeuroAtlasReader.py +++ b/c302/WormNeuroAtlasReader.py @@ -24,21 +24,58 @@ class WormNeuroAtlasReader(object): def __init__(self): self.atlas = wa.NeuroAtlas() + syn_sign = wa.SynapseSign() + + self.dom_glu = syn_sign.get_neurons_producing("Glu", mode='dominant') + self.dom_ach = syn_sign.get_neurons_producing("ACh", mode='dominant') + self.dom_gaba = syn_sign.get_neurons_producing("GABA", mode='dominant') + + self.alt_glu = syn_sign.get_neurons_producing("Glu", mode='alternative') + self.alt_ach = syn_sign.get_neurons_producing("ACh", mode='alternative') + self.alt_gaba = syn_sign.get_neurons_producing("GABA", mode='alternative') + self.all_cells = self.atlas.neuron_ids + for i in range(len(self.all_cells)): + if self.all_cells[i] == 'AWCOFF': + self.all_cells[i] = 'AWCL' + if self.all_cells[i] == 'AWCON': + self.all_cells[i] = 'AWCR' + + def determine_nt(self, neuron): + if neuron in self.dom_glu: + return 'Glutamate' + elif neuron in self.dom_ach: + return 'Acetylcholine' + elif neuron in self.dom_gaba: + return 'GABA' + else: + + nt = 'Generic_CS' + if neuron in self.alt_glu: + nt += '_Glutamate' + if neuron in self.alt_ach: + nt += '_Acetylcholine' + if neuron in self.dom_gaba: + nt += '_GABA' + return nt def read_data(self, include_nonconnected_cells=False): print_("Initialising WormNeuroAtlasReader") - cell_names = self.atlas.neuron_ids conns = [] gj = self.atlas.get_gap_junctions() + cs = self.atlas.get_chemical_synapses() + + connected_cells = [] for pre in self.all_cells: apre = self.atlas.ids_to_ai([pre]) for post in self.all_cells: apost = self.atlas.ids_to_ai([post]) + connection = False + gji = gj[apre, apost] num = gji[0] if num>0: @@ -46,11 +83,27 @@ def read_data(self, include_nonconnected_cells=False): synclass = 'Generic_GJ' syntype = "GapJunction" conns.append(ConnectionInfo(pre, post, num, syntype, synclass)) + connection = True + csi = cs[apre, apost] + num = csi[0] + if num>0: + #print("Chem syn (%s (%i) -> %s (%i): %s"%(pre, apre, post, apost, gji)) + synclass = self.determine_nt(pre) + syntype = "Chemical" + conns.append(ConnectionInfo(pre, post, num, syntype, synclass)) + connection = True + + if connection: + if not pre in connected_cells: + connected_cells.append(pre) + if not post in connected_cells: + connected_cells.append(post) + if include_nonconnected_cells: - return cell_names, conns + return self.all_cells, conns else: - return pre + post, conns + return connected_cells, conns def read_muscle_data(self): neurons = [] diff --git a/c302/backers.py b/c302/backers.py index a416c720..377b0c89 100644 --- a/c302/backers.py +++ b/c302/backers.py @@ -8,12 +8,12 @@ def get_adopted_cell_names(root=os.path.dirname(os.path.abspath(__file__))+"/data/"): - file = open(root+"adopters.txt") - ads = {} - for line in file: - cell = line.split(":")[0].strip() - name = line.split(":")[1].strip() - ads[cell] = name + with open(root+"adopters.txt") as file: + ads = {} + for line in file: + cell = line.split(":")[0].strip() + name = line.split(":")[1].strip() + ads[cell] = name return ads diff --git a/c302/c302_utils.py b/c302/c302_utils.py index d81d9fe6..784d321e 100644 --- a/c302/c302_utils.py +++ b/c302/c302_utils.py @@ -14,6 +14,7 @@ natsort = lambda s: [int(t) if t.isdigit() else t for t in re.split(r'(\d+)', s)] +default_figsize = (6.4,4.8) def plots(a_n, info, cells, dt): @@ -349,7 +350,7 @@ def plot_c302_results(lems_results, plt.close("all") -def _show_conn_matrix(data, t, all_info_pre,all_info_post, type, save_figure_to=False): +def _show_conn_matrix(data, t, all_info_pre, all_info_post, type, save_figure_to=False, verbose=True, figsize=default_figsize): if data.shape[0]>0 and data.shape[1]>0 and np.amax(data)>0: @@ -359,13 +360,13 @@ def _show_conn_matrix(data, t, all_info_pre,all_info_post, type, save_figure_to= ##norm = None maxn = 0 - c302.print_("Plotting data of size %s, max %s: %s"%(str(data.shape),maxn, t)) + c302.print_("Plotting data of size %s, max %s: %s"%(str(data.shape),maxn, t), verbose) if maxn==0: - c302.print_("No connections!!") + c302.print_("No connections!!", verbose) return - fig, ax = plt.subplots() + fig, ax = plt.subplots(figsize=figsize) title = '%s: %s'%(type,t) plt.title(title) fig.canvas.manager.set_window_title(title) @@ -406,9 +407,9 @@ def _show_conn_matrix(data, t, all_info_pre,all_info_post, type, save_figure_to= c302.print_("Saving connectivity figure to: %s"%save_figure_to) plt.savefig(save_figure_to,bbox_inches='tight') else: - c302.print_("Not saving figure") + c302.print_("Not saving figure", verbose) -def generate_conn_matrix(nml_doc, save_fig_dir=None, verbose=False): +def generate_conn_matrix(nml_doc, save_fig_dir=None, verbose=False, figsize=default_figsize): net = nml_doc.networks[0] @@ -494,15 +495,24 @@ def generate_conn_matrix(nml_doc, save_fig_dir=None, verbose=False): _show_conn_matrix(data_exc_n, 'Excitatory (non GABA) conns to neurons',all_neuron_info,all_neuron_info, - net.id, save_figure_to='%s/%s_exc_to_neurons.png'%(save_fig_dir,net.id) if save_fig_dir else None) + net.id, save_figure_to='%s/%s_exc_to_neurons.png'%(save_fig_dir,net.id) if save_fig_dir else None, + verbose=verbose, + figsize=figsize) _show_conn_matrix(data_exc_m, 'Excitatory (non GABA) conns to muscles',all_neuron_info,all_muscle_info, - net.id, save_figure_to='%s/%s_exc_to_muscles.png'%(save_fig_dir,net.id) if save_fig_dir else None) + net.id, save_figure_to='%s/%s_exc_to_muscles.png'%(save_fig_dir,net.id) if save_fig_dir else None, + verbose=verbose, + figsize=figsize) _show_conn_matrix(data_inh_n, 'Inhibitory (GABA) conns to neurons',all_neuron_info,all_neuron_info, - net.id, save_figure_to='%s/%s_inh_to_neurons.png'%(save_fig_dir,net.id) if save_fig_dir else None) + net.id, save_figure_to='%s/%s_inh_to_neurons.png'%(save_fig_dir,net.id) if save_fig_dir else None, + verbose=verbose, + figsize=figsize) + _show_conn_matrix(data_inh_m, 'Inhibitory (GABA) conns to muscles',all_neuron_info,all_muscle_info, - net.id, save_figure_to='%s/%s_inh_to_muscles.png'%(save_fig_dir,net.id) if save_fig_dir else None) + net.id, save_figure_to='%s/%s_inh_to_muscles.png'%(save_fig_dir,net.id) if save_fig_dir else None, + verbose=verbose, + figsize=figsize) data_n = np.zeros((len(all_neurons),len(all_neurons))) @@ -532,19 +542,26 @@ def generate_conn_matrix(nml_doc, save_fig_dir=None, verbose=False): _show_conn_matrix(data_n, 'Electrical (gap junction) conns to neurons',all_neuron_info,all_neuron_info, - net.id, save_figure_to='%s/%s_elec_neurons_neurons.png'%(save_fig_dir,net.id) if save_fig_dir else None) + net.id, save_figure_to='%s/%s_elec_neurons_neurons.png'%(save_fig_dir,net.id) if save_fig_dir else None, + verbose=verbose, + figsize=figsize) if neuron_muscle: _show_conn_matrix(data_n_m, 'Electrical (gap junction) conns between neurons and muscles', all_neuron_info, all_muscle_info, net.id, - save_figure_to='%s/%s_elec_neurons_muscles.png' % (save_fig_dir, net.id) if save_fig_dir else None) + save_figure_to='%s/%s_elec_neurons_muscles.png' % (save_fig_dir, net.id) if save_fig_dir else None, + verbose=verbose, + figsize=figsize) if muscle_muscle: _show_conn_matrix(data_m_m, 'Electrical (gap junction) conns between muscles', all_muscle_info, all_muscle_info, net.id, save_figure_to='%s/%s_elec_muscles_muscles.png' % ( - save_fig_dir, net.id) if save_fig_dir else None) + save_fig_dir, net.id) if save_fig_dir else None, + verbose=verbose, + figsize=figsize) + #_show_conn_matrix(data_m, 'Electrical (gap junction) conns to muscles',all_neuron_info,all_muscle_info, net.id) @@ -564,11 +581,15 @@ def generate_conn_matrix(nml_doc, save_fig_dir=None, verbose=False): configs = ['c302_C0_Pharyngeal.net.nml'] + elif '-osc' in sys.argv: + + configs = ['c302_C1_Oscillator.net.nml'] + for c in configs: nml_doc = read_neuroml2_file('examples/%s'%c) - generate_conn_matrix(nml_doc, save_fig_dir='./examples/summary/images') + generate_conn_matrix(nml_doc, save_fig_dir='./examples/summary/images', figsize=(6.4,4.8)) if not '-nogui' in sys.argv: plt.show() diff --git a/examples/LEMS_c302_A_Full.xml b/examples/LEMS_c302_A_Full.xml index 9d80eb64..4c04c408 100644 --- a/examples/LEMS_c302_A_Full.xml +++ b/examples/LEMS_c302_A_Full.xml @@ -6,7 +6,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: All cells diff --git a/examples/LEMS_c302_A_IClamp.xml b/examples/LEMS_c302_A_IClamp.xml index b08f77b9..ce089f65 100644 --- a/examples/LEMS_c302_A_IClamp.xml +++ b/examples/LEMS_c302_A_IClamp.xml @@ -6,7 +6,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['ADAL', 'PVCL'] diff --git a/examples/LEMS_c302_A_Muscles.xml b/examples/LEMS_c302_A_Muscles.xml index 57d3e647..35876b5a 100644 --- a/examples/LEMS_c302_A_Muscles.xml +++ b/examples/LEMS_c302_A_Muscles.xml @@ -6,7 +6,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['AS1', 'AS10', 'AS11', 'AS2', 'AS3', 'AS4', 'AS5', 'AS6', 'AS7', 'AS8', 'AS9', 'AVFL', 'AVFR', 'AVKR', 'AVL', 'CEPVL', 'CEPVR', 'DA1', 'DA2', 'DA3', 'DA4', 'DA5', 'DA6', 'DA7', 'DA8', 'DA9', 'DB1', 'DB2', 'DB3', 'DB4', 'DB5', 'DB6', 'DB7', 'DD1', 'DD2', 'DD3', 'DD4', 'DD5', 'DD6', 'DVB', 'HSNL', 'HSNR', 'IL1DL', 'IL1DR', 'IL1L', 'IL1R', 'IL1VL', 'IL1VR', 'PDA', 'PDB', 'PVNL', 'PVNR', 'RID', 'RIML', 'RIMR', 'RIVL', 'RIVR', 'RMDDL', 'RMDDR', 'RMDL', 'RMDR', 'RMDVL', 'RMDVR', 'RMED', 'RMEL', 'RMER', 'RMEV', 'RMFL', 'RMGL', 'RMGR', 'RMHL', 'RMHR', 'SMBDL', 'SMBDR', 'SMBVL', 'SMBVR', 'SMDDL', 'SMDDR', 'SMDVL', 'SMDVR', 'URADL', 'URADR', 'URAVL', 'URAVR', 'VA1', 'VA10', 'VA11', 'VA12', 'VA2', 'VA3', 'VA4', 'VA5', 'VA6', 'VA7', 'VA8', 'VA9', 'VB1', 'VB10', 'VB11', 'VB2', 'VB3', 'VB4', 'VB5', 'VB6', 'VB7', 'VB8', 'VB9', 'VC1', 'VC2', 'VC3', 'VC4', 'VC5', 'VC6', 'VD1', 'VD10', 'VD11', 'VD12', 'VD13', 'VD2', 'VD3', 'VD4', 'VD5', 'VD6', 'VD7', 'VD8', 'VD9', 'AVAL', 'AVAR', 'AVBL', 'AVBR', 'AVDL', 'AVDR', 'PVCL', 'PVCR'] diff --git a/examples/LEMS_c302_A_Oscillator.xml b/examples/LEMS_c302_A_Oscillator.xml index 9a9c6b67..f49d8c52 100644 --- a/examples/LEMS_c302_A_Oscillator.xml +++ b/examples/LEMS_c302_A_Oscillator.xml @@ -6,7 +6,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['DB2', 'VB2', 'DD2', 'VD2', 'DB3', 'VB3', 'DD3', 'VD3', 'DA2', 'VA2', 'DA3', 'VA3', 'AVBL', 'AVBR'] diff --git a/examples/LEMS_c302_A_Pharyngeal.xml b/examples/LEMS_c302_A_Pharyngeal.xml index bb87768f..52b4ce85 100644 --- a/examples/LEMS_c302_A_Pharyngeal.xml +++ b/examples/LEMS_c302_A_Pharyngeal.xml @@ -6,7 +6,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['M1', 'M2L', 'M2R', 'M3L', 'M3R', 'M4', 'M5', 'I1L', 'I1R', 'I2L', 'I2R', 'I3', 'I4', 'I5', 'I6', 'MI', 'NSML', 'NSMR', 'MCL', 'MCR'] diff --git a/examples/LEMS_c302_A_Social.xml b/examples/LEMS_c302_A_Social.xml index bc9bc698..b06f72fe 100644 --- a/examples/LEMS_c302_A_Social.xml +++ b/examples/LEMS_c302_A_Social.xml @@ -6,7 +6,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['RMGR', 'ASHR', 'ASKR', 'AWBR', 'IL2R', 'RMHR', 'URXR'] diff --git a/examples/LEMS_c302_A_Syns.xml b/examples/LEMS_c302_A_Syns.xml index 80e8b58c..e40da337 100644 --- a/examples/LEMS_c302_A_Syns.xml +++ b/examples/LEMS_c302_A_Syns.xml @@ -6,7 +6,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['URYDL', 'SMDDR', 'VD12', 'VB11', 'AS2'] diff --git a/examples/LEMS_c302_B_Full.xml b/examples/LEMS_c302_B_Full.xml index e3317516..3d02edc1 100644 --- a/examples/LEMS_c302_B_Full.xml +++ b/examples/LEMS_c302_B_Full.xml @@ -6,7 +6,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: All cells diff --git a/examples/LEMS_c302_B_IClamp.xml b/examples/LEMS_c302_B_IClamp.xml index a78e02cb..84112fdd 100644 --- a/examples/LEMS_c302_B_IClamp.xml +++ b/examples/LEMS_c302_B_IClamp.xml @@ -6,7 +6,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['ADAL', 'PVCL'] diff --git a/examples/LEMS_c302_B_Muscles.xml b/examples/LEMS_c302_B_Muscles.xml index 782c7bcc..bee930d5 100644 --- a/examples/LEMS_c302_B_Muscles.xml +++ b/examples/LEMS_c302_B_Muscles.xml @@ -6,7 +6,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['AS1', 'AS10', 'AS11', 'AS2', 'AS3', 'AS4', 'AS5', 'AS6', 'AS7', 'AS8', 'AS9', 'AVFL', 'AVFR', 'AVKR', 'AVL', 'CEPVL', 'CEPVR', 'DA1', 'DA2', 'DA3', 'DA4', 'DA5', 'DA6', 'DA7', 'DA8', 'DA9', 'DB1', 'DB2', 'DB3', 'DB4', 'DB5', 'DB6', 'DB7', 'DD1', 'DD2', 'DD3', 'DD4', 'DD5', 'DD6', 'DVB', 'HSNL', 'HSNR', 'IL1DL', 'IL1DR', 'IL1L', 'IL1R', 'IL1VL', 'IL1VR', 'PDA', 'PDB', 'PVNL', 'PVNR', 'RID', 'RIML', 'RIMR', 'RIVL', 'RIVR', 'RMDDL', 'RMDDR', 'RMDL', 'RMDR', 'RMDVL', 'RMDVR', 'RMED', 'RMEL', 'RMER', 'RMEV', 'RMFL', 'RMGL', 'RMGR', 'RMHL', 'RMHR', 'SMBDL', 'SMBDR', 'SMBVL', 'SMBVR', 'SMDDL', 'SMDDR', 'SMDVL', 'SMDVR', 'URADL', 'URADR', 'URAVL', 'URAVR', 'VA1', 'VA10', 'VA11', 'VA12', 'VA2', 'VA3', 'VA4', 'VA5', 'VA6', 'VA7', 'VA8', 'VA9', 'VB1', 'VB10', 'VB11', 'VB2', 'VB3', 'VB4', 'VB5', 'VB6', 'VB7', 'VB8', 'VB9', 'VC1', 'VC2', 'VC3', 'VC4', 'VC5', 'VC6', 'VD1', 'VD10', 'VD11', 'VD12', 'VD13', 'VD2', 'VD3', 'VD4', 'VD5', 'VD6', 'VD7', 'VD8', 'VD9', 'AVAL', 'AVAR', 'AVBL', 'AVBR', 'AVDL', 'AVDR', 'PVCL', 'PVCR'] diff --git a/examples/LEMS_c302_B_Oscillator.xml b/examples/LEMS_c302_B_Oscillator.xml index ff0af361..5a86a2d2 100644 --- a/examples/LEMS_c302_B_Oscillator.xml +++ b/examples/LEMS_c302_B_Oscillator.xml @@ -6,7 +6,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['DB2', 'VB2', 'DD2', 'VD2', 'DB3', 'VB3', 'DD3', 'VD3', 'DA2', 'VA2', 'DA3', 'VA3', 'AVBL', 'AVBR'] diff --git a/examples/LEMS_c302_B_Pharyngeal.xml b/examples/LEMS_c302_B_Pharyngeal.xml index 37639184..03f92387 100644 --- a/examples/LEMS_c302_B_Pharyngeal.xml +++ b/examples/LEMS_c302_B_Pharyngeal.xml @@ -6,7 +6,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['M1', 'M2L', 'M2R', 'M3L', 'M3R', 'M4', 'M5', 'I1L', 'I1R', 'I2L', 'I2R', 'I3', 'I4', 'I5', 'I6', 'MI', 'NSML', 'NSMR', 'MCL', 'MCR'] diff --git a/examples/LEMS_c302_B_Social.xml b/examples/LEMS_c302_B_Social.xml index 41cf73a4..b497c768 100644 --- a/examples/LEMS_c302_B_Social.xml +++ b/examples/LEMS_c302_B_Social.xml @@ -6,7 +6,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['RMGR', 'ASHR', 'ASKR', 'AWBR', 'IL2R', 'RMHR', 'URXR'] diff --git a/examples/LEMS_c302_B_Syns.xml b/examples/LEMS_c302_B_Syns.xml index 210266d7..a5def0d9 100644 --- a/examples/LEMS_c302_B_Syns.xml +++ b/examples/LEMS_c302_B_Syns.xml @@ -6,7 +6,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['URYDL', 'SMDDR', 'VD12', 'VB11', 'AS2', 'AIZL', 'ASHL'] diff --git a/examples/LEMS_c302_C0_Full.xml b/examples/LEMS_c302_C0_Full.xml index 39822703..2b919ffa 100644 --- a/examples/LEMS_c302_C0_Full.xml +++ b/examples/LEMS_c302_C0_Full.xml @@ -6,7 +6,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: All cells diff --git a/examples/LEMS_c302_C0_IClamp.xml b/examples/LEMS_c302_C0_IClamp.xml index 2157be9d..6fc753f9 100644 --- a/examples/LEMS_c302_C0_IClamp.xml +++ b/examples/LEMS_c302_C0_IClamp.xml @@ -6,7 +6,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['ADAL', 'PVCL'] diff --git a/examples/LEMS_c302_C0_Muscles.xml b/examples/LEMS_c302_C0_Muscles.xml index bdc28b40..b420b0fe 100644 --- a/examples/LEMS_c302_C0_Muscles.xml +++ b/examples/LEMS_c302_C0_Muscles.xml @@ -6,7 +6,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['AS1', 'AS10', 'AS11', 'AS2', 'AS3', 'AS4', 'AS5', 'AS6', 'AS7', 'AS8', 'AS9', 'AVFL', 'AVFR', 'AVKR', 'AVL', 'CEPVL', 'CEPVR', 'DA1', 'DA2', 'DA3', 'DA4', 'DA5', 'DA6', 'DA7', 'DA8', 'DA9', 'DB1', 'DB2', 'DB3', 'DB4', 'DB5', 'DB6', 'DB7', 'DD1', 'DD2', 'DD3', 'DD4', 'DD5', 'DD6', 'DVB', 'HSNL', 'HSNR', 'IL1DL', 'IL1DR', 'IL1L', 'IL1R', 'IL1VL', 'IL1VR', 'PDA', 'PDB', 'PVNL', 'PVNR', 'RID', 'RIML', 'RIMR', 'RIVL', 'RIVR', 'RMDDL', 'RMDDR', 'RMDL', 'RMDR', 'RMDVL', 'RMDVR', 'RMED', 'RMEL', 'RMER', 'RMEV', 'RMFL', 'RMGL', 'RMGR', 'RMHL', 'RMHR', 'SMBDL', 'SMBDR', 'SMBVL', 'SMBVR', 'SMDDL', 'SMDDR', 'SMDVL', 'SMDVR', 'URADL', 'URADR', 'URAVL', 'URAVR', 'VA1', 'VA10', 'VA11', 'VA12', 'VA2', 'VA3', 'VA4', 'VA5', 'VA6', 'VA7', 'VA8', 'VA9', 'VB1', 'VB10', 'VB11', 'VB2', 'VB3', 'VB4', 'VB5', 'VB6', 'VB7', 'VB8', 'VB9', 'VC1', 'VC2', 'VC3', 'VC4', 'VC5', 'VC6', 'VD1', 'VD10', 'VD11', 'VD12', 'VD13', 'VD2', 'VD3', 'VD4', 'VD5', 'VD6', 'VD7', 'VD8', 'VD9', 'AVAL', 'AVAR', 'AVBL', 'AVBR', 'AVDL', 'AVDR', 'PVCL', 'PVCR'] diff --git a/examples/LEMS_c302_C0_Oscillator.xml b/examples/LEMS_c302_C0_Oscillator.xml index 9ed8553d..937deb48 100644 --- a/examples/LEMS_c302_C0_Oscillator.xml +++ b/examples/LEMS_c302_C0_Oscillator.xml @@ -6,7 +6,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['DB2', 'VB2', 'DD2', 'VD2', 'DB3', 'VB3', 'DD3', 'VD3', 'DA2', 'VA2', 'DA3', 'VA3', 'AVBL', 'AVBR'] diff --git a/examples/LEMS_c302_C0_Pharyngeal.xml b/examples/LEMS_c302_C0_Pharyngeal.xml index 067aeb67..6c4a4f44 100644 --- a/examples/LEMS_c302_C0_Pharyngeal.xml +++ b/examples/LEMS_c302_C0_Pharyngeal.xml @@ -6,7 +6,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['M1', 'M2L', 'M2R', 'M3L', 'M3R', 'M4', 'M5', 'I1L', 'I1R', 'I2L', 'I2R', 'I3', 'I4', 'I5', 'I6', 'MI', 'NSML', 'NSMR', 'MCL', 'MCR'] diff --git a/examples/LEMS_c302_C0_Social.xml b/examples/LEMS_c302_C0_Social.xml index ec312203..a74b503d 100644 --- a/examples/LEMS_c302_C0_Social.xml +++ b/examples/LEMS_c302_C0_Social.xml @@ -6,7 +6,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['RMGR', 'ASHR', 'ASKR', 'AWBR', 'IL2R', 'RMHR', 'URXR'] diff --git a/examples/LEMS_c302_C0_Syns.xml b/examples/LEMS_c302_C0_Syns.xml index 68591c96..f32659d7 100644 --- a/examples/LEMS_c302_C0_Syns.xml +++ b/examples/LEMS_c302_C0_Syns.xml @@ -6,7 +6,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['URYDL', 'SMDDR', 'VD12', 'VB11', 'AS2', 'AIZL', 'ASHL'] diff --git a/examples/LEMS_c302_C1_Full.xml b/examples/LEMS_c302_C1_Full.xml index db1af8b7..fbfa833c 100644 --- a/examples/LEMS_c302_C1_Full.xml +++ b/examples/LEMS_c302_C1_Full.xml @@ -6,7 +6,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: All cells diff --git a/examples/LEMS_c302_C1_IClamp.xml b/examples/LEMS_c302_C1_IClamp.xml index 371306c2..ce42b434 100644 --- a/examples/LEMS_c302_C1_IClamp.xml +++ b/examples/LEMS_c302_C1_IClamp.xml @@ -6,7 +6,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['ADAL', 'PVCL'] diff --git a/examples/LEMS_c302_C1_Muscles.xml b/examples/LEMS_c302_C1_Muscles.xml index debd812a..ce9caa1b 100644 --- a/examples/LEMS_c302_C1_Muscles.xml +++ b/examples/LEMS_c302_C1_Muscles.xml @@ -6,7 +6,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['AS1', 'AS10', 'AS11', 'AS2', 'AS3', 'AS4', 'AS5', 'AS6', 'AS7', 'AS8', 'AS9', 'AVFL', 'AVFR', 'AVKR', 'AVL', 'CEPVL', 'CEPVR', 'DA1', 'DA2', 'DA3', 'DA4', 'DA5', 'DA6', 'DA7', 'DA8', 'DA9', 'DB1', 'DB2', 'DB3', 'DB4', 'DB5', 'DB6', 'DB7', 'DD1', 'DD2', 'DD3', 'DD4', 'DD5', 'DD6', 'DVB', 'HSNL', 'HSNR', 'IL1DL', 'IL1DR', 'IL1L', 'IL1R', 'IL1VL', 'IL1VR', 'PDA', 'PDB', 'PVNL', 'PVNR', 'RID', 'RIML', 'RIMR', 'RIVL', 'RIVR', 'RMDDL', 'RMDDR', 'RMDL', 'RMDR', 'RMDVL', 'RMDVR', 'RMED', 'RMEL', 'RMER', 'RMEV', 'RMFL', 'RMGL', 'RMGR', 'RMHL', 'RMHR', 'SMBDL', 'SMBDR', 'SMBVL', 'SMBVR', 'SMDDL', 'SMDDR', 'SMDVL', 'SMDVR', 'URADL', 'URADR', 'URAVL', 'URAVR', 'VA1', 'VA10', 'VA11', 'VA12', 'VA2', 'VA3', 'VA4', 'VA5', 'VA6', 'VA7', 'VA8', 'VA9', 'VB1', 'VB10', 'VB11', 'VB2', 'VB3', 'VB4', 'VB5', 'VB6', 'VB7', 'VB8', 'VB9', 'VC1', 'VC2', 'VC3', 'VC4', 'VC5', 'VC6', 'VD1', 'VD10', 'VD11', 'VD12', 'VD13', 'VD2', 'VD3', 'VD4', 'VD5', 'VD6', 'VD7', 'VD8', 'VD9', 'AVAL', 'AVAR', 'AVBL', 'AVBR', 'AVDL', 'AVDR', 'PVCL', 'PVCR'] diff --git a/examples/LEMS_c302_C1_Oscillator.xml b/examples/LEMS_c302_C1_Oscillator.xml index bd80292d..06d2e0e0 100644 --- a/examples/LEMS_c302_C1_Oscillator.xml +++ b/examples/LEMS_c302_C1_Oscillator.xml @@ -6,7 +6,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['DB2', 'VB2', 'DD2', 'VD2', 'DB3', 'VB3', 'DD3', 'VD3', 'DA2', 'VA2', 'DA3', 'VA3', 'AVBL', 'AVBR'] diff --git a/examples/LEMS_c302_C1_Pharyngeal.xml b/examples/LEMS_c302_C1_Pharyngeal.xml index 9698b74d..1011e3df 100644 --- a/examples/LEMS_c302_C1_Pharyngeal.xml +++ b/examples/LEMS_c302_C1_Pharyngeal.xml @@ -6,7 +6,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['M1', 'M2L', 'M2R', 'M3L', 'M3R', 'M4', 'M5', 'I1L', 'I1R', 'I2L', 'I2R', 'I3', 'I4', 'I5', 'I6', 'MI', 'NSML', 'NSMR', 'MCL', 'MCR'] diff --git a/examples/LEMS_c302_C1_Social.xml b/examples/LEMS_c302_C1_Social.xml index 20d5065d..925b0f5a 100644 --- a/examples/LEMS_c302_C1_Social.xml +++ b/examples/LEMS_c302_C1_Social.xml @@ -6,7 +6,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['RMGR', 'ASHR', 'ASKR', 'AWBR', 'IL2R', 'RMHR', 'URXR'] diff --git a/examples/LEMS_c302_C1_Syns.xml b/examples/LEMS_c302_C1_Syns.xml index fee35999..179f7450 100644 --- a/examples/LEMS_c302_C1_Syns.xml +++ b/examples/LEMS_c302_C1_Syns.xml @@ -6,7 +6,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['URYDL', 'SMDDR', 'VD12', 'VB11', 'AS2', 'AIZL', 'ASHL'] diff --git a/examples/LEMS_c302_C2_FW.xml b/examples/LEMS_c302_C2_FW.xml index 9e688c19..a9887f0c 100644 --- a/examples/LEMS_c302_C2_FW.xml +++ b/examples/LEMS_c302_C2_FW.xml @@ -6,7 +6,7 @@ Parameters and setting used to generate this network: Data reader: UpdatedSpreadsheetDataReader2 - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['AVBL', 'AVBR', 'DB1', 'DB2', 'DB3', 'DB4', 'DB5', 'DB6', 'DB7', 'VD1', 'VD2', 'VD3', 'VD4', 'VD5', 'VD6', 'VD7', 'VD8', 'VD9', 'VD10', 'VD11', 'VD12', 'VD13', 'VB1', 'VB2', 'VB3', 'VB4', 'VB5', 'VB6', 'VB7', 'VB8', 'VB9', 'VB10', 'VB11', 'DD1', 'DD2', 'DD3', 'DD4', 'DD5', 'DD6'] diff --git a/examples/LEMS_c302_C2_Full.xml b/examples/LEMS_c302_C2_Full.xml index 7c0365b7..d468c708 100644 --- a/examples/LEMS_c302_C2_Full.xml +++ b/examples/LEMS_c302_C2_Full.xml @@ -6,7 +6,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: All cells diff --git a/examples/LEMS_c302_C2_IClamp.xml b/examples/LEMS_c302_C2_IClamp.xml index 0c8e5964..953704d1 100644 --- a/examples/LEMS_c302_C2_IClamp.xml +++ b/examples/LEMS_c302_C2_IClamp.xml @@ -6,7 +6,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['ADAL', 'PVCL'] diff --git a/examples/LEMS_c302_C2_Muscles.xml b/examples/LEMS_c302_C2_Muscles.xml index a556dba7..aa93b134 100644 --- a/examples/LEMS_c302_C2_Muscles.xml +++ b/examples/LEMS_c302_C2_Muscles.xml @@ -6,7 +6,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['AS1', 'AS10', 'AS11', 'AS2', 'AS3', 'AS4', 'AS5', 'AS6', 'AS7', 'AS8', 'AS9', 'AVFL', 'AVFR', 'AVKR', 'AVL', 'CEPVL', 'CEPVR', 'DA1', 'DA2', 'DA3', 'DA4', 'DA5', 'DA6', 'DA7', 'DA8', 'DA9', 'DB1', 'DB2', 'DB3', 'DB4', 'DB5', 'DB6', 'DB7', 'DD1', 'DD2', 'DD3', 'DD4', 'DD5', 'DD6', 'DVB', 'HSNL', 'HSNR', 'IL1DL', 'IL1DR', 'IL1L', 'IL1R', 'IL1VL', 'IL1VR', 'PDA', 'PDB', 'PVNL', 'PVNR', 'RID', 'RIML', 'RIMR', 'RIVL', 'RIVR', 'RMDDL', 'RMDDR', 'RMDL', 'RMDR', 'RMDVL', 'RMDVR', 'RMED', 'RMEL', 'RMER', 'RMEV', 'RMFL', 'RMGL', 'RMGR', 'RMHL', 'RMHR', 'SMBDL', 'SMBDR', 'SMBVL', 'SMBVR', 'SMDDL', 'SMDDR', 'SMDVL', 'SMDVR', 'URADL', 'URADR', 'URAVL', 'URAVR', 'VA1', 'VA10', 'VA11', 'VA12', 'VA2', 'VA3', 'VA4', 'VA5', 'VA6', 'VA7', 'VA8', 'VA9', 'VB1', 'VB10', 'VB11', 'VB2', 'VB3', 'VB4', 'VB5', 'VB6', 'VB7', 'VB8', 'VB9', 'VC1', 'VC2', 'VC3', 'VC4', 'VC5', 'VC6', 'VD1', 'VD10', 'VD11', 'VD12', 'VD13', 'VD2', 'VD3', 'VD4', 'VD5', 'VD6', 'VD7', 'VD8', 'VD9', 'AVAL', 'AVAR', 'AVBL', 'AVBR', 'AVDL', 'AVDR', 'PVCL', 'PVCR'] diff --git a/examples/LEMS_c302_C2_Oscillator.xml b/examples/LEMS_c302_C2_Oscillator.xml index 9bfac534..4d0b336a 100644 --- a/examples/LEMS_c302_C2_Oscillator.xml +++ b/examples/LEMS_c302_C2_Oscillator.xml @@ -6,7 +6,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['DB2', 'VB2', 'DD2', 'VD2', 'DB3', 'VB3', 'DD3', 'VD3', 'DA2', 'VA2', 'DA3', 'VA3', 'AVBL', 'AVBR'] diff --git a/examples/LEMS_c302_C2_Pharyngeal.xml b/examples/LEMS_c302_C2_Pharyngeal.xml index 3e7f822f..03fe1915 100644 --- a/examples/LEMS_c302_C2_Pharyngeal.xml +++ b/examples/LEMS_c302_C2_Pharyngeal.xml @@ -6,7 +6,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['M1', 'M2L', 'M2R', 'M3L', 'M3R', 'M4', 'M5', 'I1L', 'I1R', 'I2L', 'I2R', 'I3', 'I4', 'I5', 'I6', 'MI', 'NSML', 'NSMR', 'MCL', 'MCR'] diff --git a/examples/LEMS_c302_C2_Social.xml b/examples/LEMS_c302_C2_Social.xml index d12b156f..5e1b62ce 100644 --- a/examples/LEMS_c302_C2_Social.xml +++ b/examples/LEMS_c302_C2_Social.xml @@ -6,7 +6,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['RMGR', 'ASHR', 'ASKR', 'AWBR', 'IL2R', 'RMHR', 'URXR'] diff --git a/examples/LEMS_c302_C2_Syns.xml b/examples/LEMS_c302_C2_Syns.xml index 60c55f40..d571ffc7 100644 --- a/examples/LEMS_c302_C2_Syns.xml +++ b/examples/LEMS_c302_C2_Syns.xml @@ -6,7 +6,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['URYDL', 'SMDDR', 'VD12', 'VB11', 'AS2', 'AIZL', 'ASHL'] diff --git a/examples/LEMS_c302_C_Full.xml b/examples/LEMS_c302_C_Full.xml index 82bc9945..5c844f02 100644 --- a/examples/LEMS_c302_C_Full.xml +++ b/examples/LEMS_c302_C_Full.xml @@ -6,7 +6,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: All cells diff --git a/examples/LEMS_c302_C_IClamp.xml b/examples/LEMS_c302_C_IClamp.xml index fd16888f..2707f2b8 100644 --- a/examples/LEMS_c302_C_IClamp.xml +++ b/examples/LEMS_c302_C_IClamp.xml @@ -6,7 +6,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['ADAL', 'PVCL'] diff --git a/examples/LEMS_c302_C_Muscles.xml b/examples/LEMS_c302_C_Muscles.xml index 01d1baaa..4da1f31f 100644 --- a/examples/LEMS_c302_C_Muscles.xml +++ b/examples/LEMS_c302_C_Muscles.xml @@ -6,7 +6,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['AS1', 'AS10', 'AS11', 'AS2', 'AS3', 'AS4', 'AS5', 'AS6', 'AS7', 'AS8', 'AS9', 'AVFL', 'AVFR', 'AVKR', 'AVL', 'CEPVL', 'CEPVR', 'DA1', 'DA2', 'DA3', 'DA4', 'DA5', 'DA6', 'DA7', 'DA8', 'DA9', 'DB1', 'DB2', 'DB3', 'DB4', 'DB5', 'DB6', 'DB7', 'DD1', 'DD2', 'DD3', 'DD4', 'DD5', 'DD6', 'DVB', 'HSNL', 'HSNR', 'IL1DL', 'IL1DR', 'IL1L', 'IL1R', 'IL1VL', 'IL1VR', 'PDA', 'PDB', 'PVNL', 'PVNR', 'RID', 'RIML', 'RIMR', 'RIVL', 'RIVR', 'RMDDL', 'RMDDR', 'RMDL', 'RMDR', 'RMDVL', 'RMDVR', 'RMED', 'RMEL', 'RMER', 'RMEV', 'RMFL', 'RMGL', 'RMGR', 'RMHL', 'RMHR', 'SMBDL', 'SMBDR', 'SMBVL', 'SMBVR', 'SMDDL', 'SMDDR', 'SMDVL', 'SMDVR', 'URADL', 'URADR', 'URAVL', 'URAVR', 'VA1', 'VA10', 'VA11', 'VA12', 'VA2', 'VA3', 'VA4', 'VA5', 'VA6', 'VA7', 'VA8', 'VA9', 'VB1', 'VB10', 'VB11', 'VB2', 'VB3', 'VB4', 'VB5', 'VB6', 'VB7', 'VB8', 'VB9', 'VC1', 'VC2', 'VC3', 'VC4', 'VC5', 'VC6', 'VD1', 'VD10', 'VD11', 'VD12', 'VD13', 'VD2', 'VD3', 'VD4', 'VD5', 'VD6', 'VD7', 'VD8', 'VD9', 'AVAL', 'AVAR', 'AVBL', 'AVBR', 'AVDL', 'AVDR', 'PVCL', 'PVCR'] diff --git a/examples/LEMS_c302_C_Oscillator.xml b/examples/LEMS_c302_C_Oscillator.xml index c9fc3b29..33b2c811 100644 --- a/examples/LEMS_c302_C_Oscillator.xml +++ b/examples/LEMS_c302_C_Oscillator.xml @@ -6,7 +6,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['DB2', 'VB2', 'DD2', 'VD2', 'DB3', 'VB3', 'DD3', 'VD3', 'DA2', 'VA2', 'DA3', 'VA3', 'AVBL', 'AVBR'] diff --git a/examples/LEMS_c302_C_Pharyngeal.xml b/examples/LEMS_c302_C_Pharyngeal.xml index 804a1c59..b1626106 100644 --- a/examples/LEMS_c302_C_Pharyngeal.xml +++ b/examples/LEMS_c302_C_Pharyngeal.xml @@ -6,7 +6,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['M1', 'M2L', 'M2R', 'M3L', 'M3R', 'M4', 'M5', 'I1L', 'I1R', 'I2L', 'I2R', 'I3', 'I4', 'I5', 'I6', 'MI', 'NSML', 'NSMR', 'MCL', 'MCR'] diff --git a/examples/LEMS_c302_C_Social.xml b/examples/LEMS_c302_C_Social.xml index f9fc8332..093d2f0a 100644 --- a/examples/LEMS_c302_C_Social.xml +++ b/examples/LEMS_c302_C_Social.xml @@ -6,7 +6,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['RMGR', 'ASHR', 'ASKR', 'AWBR', 'IL2R', 'RMHR', 'URXR'] diff --git a/examples/LEMS_c302_C_Syns.xml b/examples/LEMS_c302_C_Syns.xml index 0bfca82b..3f0bdc8c 100644 --- a/examples/LEMS_c302_C_Syns.xml +++ b/examples/LEMS_c302_C_Syns.xml @@ -6,7 +6,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['URYDL', 'SMDDR', 'VD12', 'VB11', 'AS2', 'AIZL', 'ASHL'] diff --git a/examples/LEMS_c302_D1_Full.xml b/examples/LEMS_c302_D1_Full.xml index 0841edd0..0160c9ff 100644 --- a/examples/LEMS_c302_D1_Full.xml +++ b/examples/LEMS_c302_D1_Full.xml @@ -6,7 +6,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: All cells diff --git a/examples/LEMS_c302_D1_IClamp.xml b/examples/LEMS_c302_D1_IClamp.xml index f5f42fc1..ec847c6a 100644 --- a/examples/LEMS_c302_D1_IClamp.xml +++ b/examples/LEMS_c302_D1_IClamp.xml @@ -6,7 +6,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['ADAL', 'PVCL'] diff --git a/examples/LEMS_c302_D1_Muscles.xml b/examples/LEMS_c302_D1_Muscles.xml index bc05e033..6c7b7ce3 100644 --- a/examples/LEMS_c302_D1_Muscles.xml +++ b/examples/LEMS_c302_D1_Muscles.xml @@ -6,7 +6,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['AS1', 'AS10', 'AS11', 'AS2', 'AS3', 'AS4', 'AS5', 'AS6', 'AS7', 'AS8', 'AS9', 'AVFL', 'AVFR', 'AVKR', 'AVL', 'CEPVL', 'CEPVR', 'DA1', 'DA2', 'DA3', 'DA4', 'DA5', 'DA6', 'DA7', 'DA8', 'DA9', 'DB1', 'DB2', 'DB3', 'DB4', 'DB5', 'DB6', 'DB7', 'DD1', 'DD2', 'DD3', 'DD4', 'DD5', 'DD6', 'DVB', 'HSNL', 'HSNR', 'IL1DL', 'IL1DR', 'IL1L', 'IL1R', 'IL1VL', 'IL1VR', 'PDA', 'PDB', 'PVNL', 'PVNR', 'RID', 'RIML', 'RIMR', 'RIVL', 'RIVR', 'RMDDL', 'RMDDR', 'RMDL', 'RMDR', 'RMDVL', 'RMDVR', 'RMED', 'RMEL', 'RMER', 'RMEV', 'RMFL', 'RMGL', 'RMGR', 'RMHL', 'RMHR', 'SMBDL', 'SMBDR', 'SMBVL', 'SMBVR', 'SMDDL', 'SMDDR', 'SMDVL', 'SMDVR', 'URADL', 'URADR', 'URAVL', 'URAVR', 'VA1', 'VA10', 'VA11', 'VA12', 'VA2', 'VA3', 'VA4', 'VA5', 'VA6', 'VA7', 'VA8', 'VA9', 'VB1', 'VB10', 'VB11', 'VB2', 'VB3', 'VB4', 'VB5', 'VB6', 'VB7', 'VB8', 'VB9', 'VC1', 'VC2', 'VC3', 'VC4', 'VC5', 'VC6', 'VD1', 'VD10', 'VD11', 'VD12', 'VD13', 'VD2', 'VD3', 'VD4', 'VD5', 'VD6', 'VD7', 'VD8', 'VD9', 'AVAL', 'AVAR', 'AVBL', 'AVBR', 'AVDL', 'AVDR', 'PVCL', 'PVCR'] diff --git a/examples/LEMS_c302_D1_Oscillator.xml b/examples/LEMS_c302_D1_Oscillator.xml index e2a3a56f..25b3d5e0 100644 --- a/examples/LEMS_c302_D1_Oscillator.xml +++ b/examples/LEMS_c302_D1_Oscillator.xml @@ -6,7 +6,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['DB2', 'VB2', 'DD2', 'VD2', 'DB3', 'VB3', 'DD3', 'VD3', 'DA2', 'VA2', 'DA3', 'VA3', 'AVBL', 'AVBR'] diff --git a/examples/LEMS_c302_D1_Pharyngeal.xml b/examples/LEMS_c302_D1_Pharyngeal.xml index ee104157..32473d40 100644 --- a/examples/LEMS_c302_D1_Pharyngeal.xml +++ b/examples/LEMS_c302_D1_Pharyngeal.xml @@ -6,7 +6,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['M1', 'M2L', 'M2R', 'M3L', 'M3R', 'M4', 'M5', 'I1L', 'I1R', 'I2L', 'I2R', 'I3', 'I4', 'I5', 'I6', 'MI', 'NSML', 'NSMR', 'MCL', 'MCR'] diff --git a/examples/LEMS_c302_D1_Social.xml b/examples/LEMS_c302_D1_Social.xml index 05cec033..c38af0ff 100644 --- a/examples/LEMS_c302_D1_Social.xml +++ b/examples/LEMS_c302_D1_Social.xml @@ -6,7 +6,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['RMGR', 'ASHR', 'ASKR', 'AWBR', 'IL2R', 'RMHR', 'URXR'] diff --git a/examples/LEMS_c302_D1_Syns.xml b/examples/LEMS_c302_D1_Syns.xml index 5674fa9f..69ef7e56 100644 --- a/examples/LEMS_c302_D1_Syns.xml +++ b/examples/LEMS_c302_D1_Syns.xml @@ -6,7 +6,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['URYDL', 'SMDDR', 'VD12', 'VB11', 'AS2', 'AIZL', 'ASHL'] diff --git a/examples/LEMS_c302_D_Full.xml b/examples/LEMS_c302_D_Full.xml index 7ada2f15..67956719 100644 --- a/examples/LEMS_c302_D_Full.xml +++ b/examples/LEMS_c302_D_Full.xml @@ -6,7 +6,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: All cells diff --git a/examples/LEMS_c302_D_IClamp.xml b/examples/LEMS_c302_D_IClamp.xml index 816771be..afbd86c8 100644 --- a/examples/LEMS_c302_D_IClamp.xml +++ b/examples/LEMS_c302_D_IClamp.xml @@ -6,7 +6,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['ADAL', 'PVCL'] diff --git a/examples/LEMS_c302_D_Muscles.xml b/examples/LEMS_c302_D_Muscles.xml index ac50e5b6..69decd74 100644 --- a/examples/LEMS_c302_D_Muscles.xml +++ b/examples/LEMS_c302_D_Muscles.xml @@ -6,7 +6,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['AS1', 'AS10', 'AS11', 'AS2', 'AS3', 'AS4', 'AS5', 'AS6', 'AS7', 'AS8', 'AS9', 'AVFL', 'AVFR', 'AVKR', 'AVL', 'CEPVL', 'CEPVR', 'DA1', 'DA2', 'DA3', 'DA4', 'DA5', 'DA6', 'DA7', 'DA8', 'DA9', 'DB1', 'DB2', 'DB3', 'DB4', 'DB5', 'DB6', 'DB7', 'DD1', 'DD2', 'DD3', 'DD4', 'DD5', 'DD6', 'DVB', 'HSNL', 'HSNR', 'IL1DL', 'IL1DR', 'IL1L', 'IL1R', 'IL1VL', 'IL1VR', 'PDA', 'PDB', 'PVNL', 'PVNR', 'RID', 'RIML', 'RIMR', 'RIVL', 'RIVR', 'RMDDL', 'RMDDR', 'RMDL', 'RMDR', 'RMDVL', 'RMDVR', 'RMED', 'RMEL', 'RMER', 'RMEV', 'RMFL', 'RMGL', 'RMGR', 'RMHL', 'RMHR', 'SMBDL', 'SMBDR', 'SMBVL', 'SMBVR', 'SMDDL', 'SMDDR', 'SMDVL', 'SMDVR', 'URADL', 'URADR', 'URAVL', 'URAVR', 'VA1', 'VA10', 'VA11', 'VA12', 'VA2', 'VA3', 'VA4', 'VA5', 'VA6', 'VA7', 'VA8', 'VA9', 'VB1', 'VB10', 'VB11', 'VB2', 'VB3', 'VB4', 'VB5', 'VB6', 'VB7', 'VB8', 'VB9', 'VC1', 'VC2', 'VC3', 'VC4', 'VC5', 'VC6', 'VD1', 'VD10', 'VD11', 'VD12', 'VD13', 'VD2', 'VD3', 'VD4', 'VD5', 'VD6', 'VD7', 'VD8', 'VD9', 'AVAL', 'AVAR', 'AVBL', 'AVBR', 'AVDL', 'AVDR', 'PVCL', 'PVCR'] diff --git a/examples/LEMS_c302_D_Oscillator.xml b/examples/LEMS_c302_D_Oscillator.xml index 8d11df70..9f2d9dcd 100644 --- a/examples/LEMS_c302_D_Oscillator.xml +++ b/examples/LEMS_c302_D_Oscillator.xml @@ -6,7 +6,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['DB2', 'VB2', 'DD2', 'VD2', 'DB3', 'VB3', 'DD3', 'VD3', 'DA2', 'VA2', 'DA3', 'VA3', 'AVBL', 'AVBR'] diff --git a/examples/LEMS_c302_D_Pharyngeal.xml b/examples/LEMS_c302_D_Pharyngeal.xml index d85e18eb..c8eaf6d6 100644 --- a/examples/LEMS_c302_D_Pharyngeal.xml +++ b/examples/LEMS_c302_D_Pharyngeal.xml @@ -6,7 +6,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['M1', 'M2L', 'M2R', 'M3L', 'M3R', 'M4', 'M5', 'I1L', 'I1R', 'I2L', 'I2R', 'I3', 'I4', 'I5', 'I6', 'MI', 'NSML', 'NSMR', 'MCL', 'MCR'] diff --git a/examples/LEMS_c302_D_Social.xml b/examples/LEMS_c302_D_Social.xml index ffeb804e..51c7c058 100644 --- a/examples/LEMS_c302_D_Social.xml +++ b/examples/LEMS_c302_D_Social.xml @@ -6,7 +6,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['RMGR', 'ASHR', 'ASKR', 'AWBR', 'IL2R', 'RMHR', 'URXR'] diff --git a/examples/LEMS_c302_D_Syns.xml b/examples/LEMS_c302_D_Syns.xml index db3445e5..15f079be 100644 --- a/examples/LEMS_c302_D_Syns.xml +++ b/examples/LEMS_c302_D_Syns.xml @@ -6,7 +6,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['URYDL', 'SMDDR', 'VD12', 'VB11', 'AS2', 'AIZL', 'ASHL'] diff --git a/examples/c302_A_Full.net.nml b/examples/c302_A_Full.net.nml index ada51c7f..08f26e4a 100644 --- a/examples/c302_A_Full.net.nml +++ b/examples/c302_A_Full.net.nml @@ -4,7 +4,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: All cells diff --git a/examples/c302_A_IClamp.net.nml b/examples/c302_A_IClamp.net.nml index 7c459cf8..c8e618a8 100644 --- a/examples/c302_A_IClamp.net.nml +++ b/examples/c302_A_IClamp.net.nml @@ -4,7 +4,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['ADAL', 'PVCL'] diff --git a/examples/c302_A_Muscles.net.nml b/examples/c302_A_Muscles.net.nml index 2cd5c959..5446bd88 100644 --- a/examples/c302_A_Muscles.net.nml +++ b/examples/c302_A_Muscles.net.nml @@ -4,7 +4,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['AS1', 'AS10', 'AS11', 'AS2', 'AS3', 'AS4', 'AS5', 'AS6', 'AS7', 'AS8', 'AS9', 'AVFL', 'AVFR', 'AVKR', 'AVL', 'CEPVL', 'CEPVR', 'DA1', 'DA2', 'DA3', 'DA4', 'DA5', 'DA6', 'DA7', 'DA8', 'DA9', 'DB1', 'DB2', 'DB3', 'DB4', 'DB5', 'DB6', 'DB7', 'DD1', 'DD2', 'DD3', 'DD4', 'DD5', 'DD6', 'DVB', 'HSNL', 'HSNR', 'IL1DL', 'IL1DR', 'IL1L', 'IL1R', 'IL1VL', 'IL1VR', 'PDA', 'PDB', 'PVNL', 'PVNR', 'RID', 'RIML', 'RIMR', 'RIVL', 'RIVR', 'RMDDL', 'RMDDR', 'RMDL', 'RMDR', 'RMDVL', 'RMDVR', 'RMED', 'RMEL', 'RMER', 'RMEV', 'RMFL', 'RMGL', 'RMGR', 'RMHL', 'RMHR', 'SMBDL', 'SMBDR', 'SMBVL', 'SMBVR', 'SMDDL', 'SMDDR', 'SMDVL', 'SMDVR', 'URADL', 'URADR', 'URAVL', 'URAVR', 'VA1', 'VA10', 'VA11', 'VA12', 'VA2', 'VA3', 'VA4', 'VA5', 'VA6', 'VA7', 'VA8', 'VA9', 'VB1', 'VB10', 'VB11', 'VB2', 'VB3', 'VB4', 'VB5', 'VB6', 'VB7', 'VB8', 'VB9', 'VC1', 'VC2', 'VC3', 'VC4', 'VC5', 'VC6', 'VD1', 'VD10', 'VD11', 'VD12', 'VD13', 'VD2', 'VD3', 'VD4', 'VD5', 'VD6', 'VD7', 'VD8', 'VD9', 'AVAL', 'AVAR', 'AVBL', 'AVBR', 'AVDL', 'AVDR', 'PVCL', 'PVCR'] diff --git a/examples/c302_A_Oscillator.net.nml b/examples/c302_A_Oscillator.net.nml index 67e9b8c9..c5fe9125 100644 --- a/examples/c302_A_Oscillator.net.nml +++ b/examples/c302_A_Oscillator.net.nml @@ -4,7 +4,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['DB2', 'VB2', 'DD2', 'VD2', 'DB3', 'VB3', 'DD3', 'VD3', 'DA2', 'VA2', 'DA3', 'VA3', 'AVBL', 'AVBR'] diff --git a/examples/c302_A_Pharyngeal.net.nml b/examples/c302_A_Pharyngeal.net.nml index 16af93c1..0b05c7a7 100644 --- a/examples/c302_A_Pharyngeal.net.nml +++ b/examples/c302_A_Pharyngeal.net.nml @@ -4,7 +4,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['M1', 'M2L', 'M2R', 'M3L', 'M3R', 'M4', 'M5', 'I1L', 'I1R', 'I2L', 'I2R', 'I3', 'I4', 'I5', 'I6', 'MI', 'NSML', 'NSMR', 'MCL', 'MCR'] diff --git a/examples/c302_A_Social.net.nml b/examples/c302_A_Social.net.nml index 6ce96f51..dce8d443 100644 --- a/examples/c302_A_Social.net.nml +++ b/examples/c302_A_Social.net.nml @@ -4,7 +4,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['RMGR', 'ASHR', 'ASKR', 'AWBR', 'IL2R', 'RMHR', 'URXR'] diff --git a/examples/c302_A_Syns.net.nml b/examples/c302_A_Syns.net.nml index 34bb6e9d..c06cf558 100644 --- a/examples/c302_A_Syns.net.nml +++ b/examples/c302_A_Syns.net.nml @@ -4,7 +4,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['URYDL', 'SMDDR', 'VD12', 'VB11', 'AS2'] diff --git a/examples/c302_B_Full.net.nml b/examples/c302_B_Full.net.nml index fa9dd20d..38dc3176 100644 --- a/examples/c302_B_Full.net.nml +++ b/examples/c302_B_Full.net.nml @@ -4,7 +4,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: All cells diff --git a/examples/c302_B_IClamp.net.nml b/examples/c302_B_IClamp.net.nml index 3d84983d..3c2a4dfb 100644 --- a/examples/c302_B_IClamp.net.nml +++ b/examples/c302_B_IClamp.net.nml @@ -4,7 +4,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['ADAL', 'PVCL'] diff --git a/examples/c302_B_Muscles.net.nml b/examples/c302_B_Muscles.net.nml index 3c4764eb..917db5e7 100644 --- a/examples/c302_B_Muscles.net.nml +++ b/examples/c302_B_Muscles.net.nml @@ -4,7 +4,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['AS1', 'AS10', 'AS11', 'AS2', 'AS3', 'AS4', 'AS5', 'AS6', 'AS7', 'AS8', 'AS9', 'AVFL', 'AVFR', 'AVKR', 'AVL', 'CEPVL', 'CEPVR', 'DA1', 'DA2', 'DA3', 'DA4', 'DA5', 'DA6', 'DA7', 'DA8', 'DA9', 'DB1', 'DB2', 'DB3', 'DB4', 'DB5', 'DB6', 'DB7', 'DD1', 'DD2', 'DD3', 'DD4', 'DD5', 'DD6', 'DVB', 'HSNL', 'HSNR', 'IL1DL', 'IL1DR', 'IL1L', 'IL1R', 'IL1VL', 'IL1VR', 'PDA', 'PDB', 'PVNL', 'PVNR', 'RID', 'RIML', 'RIMR', 'RIVL', 'RIVR', 'RMDDL', 'RMDDR', 'RMDL', 'RMDR', 'RMDVL', 'RMDVR', 'RMED', 'RMEL', 'RMER', 'RMEV', 'RMFL', 'RMGL', 'RMGR', 'RMHL', 'RMHR', 'SMBDL', 'SMBDR', 'SMBVL', 'SMBVR', 'SMDDL', 'SMDDR', 'SMDVL', 'SMDVR', 'URADL', 'URADR', 'URAVL', 'URAVR', 'VA1', 'VA10', 'VA11', 'VA12', 'VA2', 'VA3', 'VA4', 'VA5', 'VA6', 'VA7', 'VA8', 'VA9', 'VB1', 'VB10', 'VB11', 'VB2', 'VB3', 'VB4', 'VB5', 'VB6', 'VB7', 'VB8', 'VB9', 'VC1', 'VC2', 'VC3', 'VC4', 'VC5', 'VC6', 'VD1', 'VD10', 'VD11', 'VD12', 'VD13', 'VD2', 'VD3', 'VD4', 'VD5', 'VD6', 'VD7', 'VD8', 'VD9', 'AVAL', 'AVAR', 'AVBL', 'AVBR', 'AVDL', 'AVDR', 'PVCL', 'PVCR'] diff --git a/examples/c302_B_Oscillator.net.nml b/examples/c302_B_Oscillator.net.nml index 78d43723..7e28da25 100644 --- a/examples/c302_B_Oscillator.net.nml +++ b/examples/c302_B_Oscillator.net.nml @@ -4,7 +4,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['DB2', 'VB2', 'DD2', 'VD2', 'DB3', 'VB3', 'DD3', 'VD3', 'DA2', 'VA2', 'DA3', 'VA3', 'AVBL', 'AVBR'] diff --git a/examples/c302_B_Pharyngeal.net.nml b/examples/c302_B_Pharyngeal.net.nml index b7fefa27..0c4ff09e 100644 --- a/examples/c302_B_Pharyngeal.net.nml +++ b/examples/c302_B_Pharyngeal.net.nml @@ -4,7 +4,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['M1', 'M2L', 'M2R', 'M3L', 'M3R', 'M4', 'M5', 'I1L', 'I1R', 'I2L', 'I2R', 'I3', 'I4', 'I5', 'I6', 'MI', 'NSML', 'NSMR', 'MCL', 'MCR'] diff --git a/examples/c302_B_Social.net.nml b/examples/c302_B_Social.net.nml index 544d24c7..3d9f08c0 100644 --- a/examples/c302_B_Social.net.nml +++ b/examples/c302_B_Social.net.nml @@ -4,7 +4,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['RMGR', 'ASHR', 'ASKR', 'AWBR', 'IL2R', 'RMHR', 'URXR'] diff --git a/examples/c302_B_Syns.net.nml b/examples/c302_B_Syns.net.nml index 08f9491c..3aafe3ad 100644 --- a/examples/c302_B_Syns.net.nml +++ b/examples/c302_B_Syns.net.nml @@ -4,7 +4,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['URYDL', 'SMDDR', 'VD12', 'VB11', 'AS2', 'AIZL', 'ASHL'] diff --git a/examples/c302_C0_Full.net.nml b/examples/c302_C0_Full.net.nml index f9fcf995..007c9b20 100644 --- a/examples/c302_C0_Full.net.nml +++ b/examples/c302_C0_Full.net.nml @@ -4,7 +4,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: All cells diff --git a/examples/c302_C0_IClamp.net.nml b/examples/c302_C0_IClamp.net.nml index 6a8ccb4e..ca4ea2c6 100644 --- a/examples/c302_C0_IClamp.net.nml +++ b/examples/c302_C0_IClamp.net.nml @@ -4,7 +4,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['ADAL', 'PVCL'] diff --git a/examples/c302_C0_Muscles.net.nml b/examples/c302_C0_Muscles.net.nml index 6e6041b7..8b3f0ecd 100644 --- a/examples/c302_C0_Muscles.net.nml +++ b/examples/c302_C0_Muscles.net.nml @@ -4,7 +4,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['AS1', 'AS10', 'AS11', 'AS2', 'AS3', 'AS4', 'AS5', 'AS6', 'AS7', 'AS8', 'AS9', 'AVFL', 'AVFR', 'AVKR', 'AVL', 'CEPVL', 'CEPVR', 'DA1', 'DA2', 'DA3', 'DA4', 'DA5', 'DA6', 'DA7', 'DA8', 'DA9', 'DB1', 'DB2', 'DB3', 'DB4', 'DB5', 'DB6', 'DB7', 'DD1', 'DD2', 'DD3', 'DD4', 'DD5', 'DD6', 'DVB', 'HSNL', 'HSNR', 'IL1DL', 'IL1DR', 'IL1L', 'IL1R', 'IL1VL', 'IL1VR', 'PDA', 'PDB', 'PVNL', 'PVNR', 'RID', 'RIML', 'RIMR', 'RIVL', 'RIVR', 'RMDDL', 'RMDDR', 'RMDL', 'RMDR', 'RMDVL', 'RMDVR', 'RMED', 'RMEL', 'RMER', 'RMEV', 'RMFL', 'RMGL', 'RMGR', 'RMHL', 'RMHR', 'SMBDL', 'SMBDR', 'SMBVL', 'SMBVR', 'SMDDL', 'SMDDR', 'SMDVL', 'SMDVR', 'URADL', 'URADR', 'URAVL', 'URAVR', 'VA1', 'VA10', 'VA11', 'VA12', 'VA2', 'VA3', 'VA4', 'VA5', 'VA6', 'VA7', 'VA8', 'VA9', 'VB1', 'VB10', 'VB11', 'VB2', 'VB3', 'VB4', 'VB5', 'VB6', 'VB7', 'VB8', 'VB9', 'VC1', 'VC2', 'VC3', 'VC4', 'VC5', 'VC6', 'VD1', 'VD10', 'VD11', 'VD12', 'VD13', 'VD2', 'VD3', 'VD4', 'VD5', 'VD6', 'VD7', 'VD8', 'VD9', 'AVAL', 'AVAR', 'AVBL', 'AVBR', 'AVDL', 'AVDR', 'PVCL', 'PVCR'] diff --git a/examples/c302_C0_Oscillator.net.nml b/examples/c302_C0_Oscillator.net.nml index 58d78d9f..f4c44b16 100644 --- a/examples/c302_C0_Oscillator.net.nml +++ b/examples/c302_C0_Oscillator.net.nml @@ -4,7 +4,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['DB2', 'VB2', 'DD2', 'VD2', 'DB3', 'VB3', 'DD3', 'VD3', 'DA2', 'VA2', 'DA3', 'VA3', 'AVBL', 'AVBR'] diff --git a/examples/c302_C0_Pharyngeal.net.nml b/examples/c302_C0_Pharyngeal.net.nml index e1a2ae98..3019c4d7 100644 --- a/examples/c302_C0_Pharyngeal.net.nml +++ b/examples/c302_C0_Pharyngeal.net.nml @@ -4,7 +4,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['M1', 'M2L', 'M2R', 'M3L', 'M3R', 'M4', 'M5', 'I1L', 'I1R', 'I2L', 'I2R', 'I3', 'I4', 'I5', 'I6', 'MI', 'NSML', 'NSMR', 'MCL', 'MCR'] diff --git a/examples/c302_C0_Social.net.nml b/examples/c302_C0_Social.net.nml index f7c32993..0ab8f1ec 100644 --- a/examples/c302_C0_Social.net.nml +++ b/examples/c302_C0_Social.net.nml @@ -4,7 +4,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['RMGR', 'ASHR', 'ASKR', 'AWBR', 'IL2R', 'RMHR', 'URXR'] diff --git a/examples/c302_C0_Syns.net.nml b/examples/c302_C0_Syns.net.nml index 0bda841e..a44bf231 100644 --- a/examples/c302_C0_Syns.net.nml +++ b/examples/c302_C0_Syns.net.nml @@ -4,7 +4,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['URYDL', 'SMDDR', 'VD12', 'VB11', 'AS2', 'AIZL', 'ASHL'] diff --git a/examples/c302_C1_Full.net.nml b/examples/c302_C1_Full.net.nml index 56f9be3b..caafc550 100644 --- a/examples/c302_C1_Full.net.nml +++ b/examples/c302_C1_Full.net.nml @@ -4,7 +4,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: All cells diff --git a/examples/c302_C1_IClamp.net.nml b/examples/c302_C1_IClamp.net.nml index f2884925..a2e54c8e 100644 --- a/examples/c302_C1_IClamp.net.nml +++ b/examples/c302_C1_IClamp.net.nml @@ -4,7 +4,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['ADAL', 'PVCL'] diff --git a/examples/c302_C1_Muscles.net.nml b/examples/c302_C1_Muscles.net.nml index f37bef69..fe630c3c 100644 --- a/examples/c302_C1_Muscles.net.nml +++ b/examples/c302_C1_Muscles.net.nml @@ -4,7 +4,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['AS1', 'AS10', 'AS11', 'AS2', 'AS3', 'AS4', 'AS5', 'AS6', 'AS7', 'AS8', 'AS9', 'AVFL', 'AVFR', 'AVKR', 'AVL', 'CEPVL', 'CEPVR', 'DA1', 'DA2', 'DA3', 'DA4', 'DA5', 'DA6', 'DA7', 'DA8', 'DA9', 'DB1', 'DB2', 'DB3', 'DB4', 'DB5', 'DB6', 'DB7', 'DD1', 'DD2', 'DD3', 'DD4', 'DD5', 'DD6', 'DVB', 'HSNL', 'HSNR', 'IL1DL', 'IL1DR', 'IL1L', 'IL1R', 'IL1VL', 'IL1VR', 'PDA', 'PDB', 'PVNL', 'PVNR', 'RID', 'RIML', 'RIMR', 'RIVL', 'RIVR', 'RMDDL', 'RMDDR', 'RMDL', 'RMDR', 'RMDVL', 'RMDVR', 'RMED', 'RMEL', 'RMER', 'RMEV', 'RMFL', 'RMGL', 'RMGR', 'RMHL', 'RMHR', 'SMBDL', 'SMBDR', 'SMBVL', 'SMBVR', 'SMDDL', 'SMDDR', 'SMDVL', 'SMDVR', 'URADL', 'URADR', 'URAVL', 'URAVR', 'VA1', 'VA10', 'VA11', 'VA12', 'VA2', 'VA3', 'VA4', 'VA5', 'VA6', 'VA7', 'VA8', 'VA9', 'VB1', 'VB10', 'VB11', 'VB2', 'VB3', 'VB4', 'VB5', 'VB6', 'VB7', 'VB8', 'VB9', 'VC1', 'VC2', 'VC3', 'VC4', 'VC5', 'VC6', 'VD1', 'VD10', 'VD11', 'VD12', 'VD13', 'VD2', 'VD3', 'VD4', 'VD5', 'VD6', 'VD7', 'VD8', 'VD9', 'AVAL', 'AVAR', 'AVBL', 'AVBR', 'AVDL', 'AVDR', 'PVCL', 'PVCR'] diff --git a/examples/c302_C1_Oscillator.net.nml b/examples/c302_C1_Oscillator.net.nml index ec74b475..aaafb42e 100644 --- a/examples/c302_C1_Oscillator.net.nml +++ b/examples/c302_C1_Oscillator.net.nml @@ -4,7 +4,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['DB2', 'VB2', 'DD2', 'VD2', 'DB3', 'VB3', 'DD3', 'VD3', 'DA2', 'VA2', 'DA3', 'VA3', 'AVBL', 'AVBR'] diff --git a/examples/c302_C1_Pharyngeal.net.nml b/examples/c302_C1_Pharyngeal.net.nml index 08b6ff49..0bafa0e7 100644 --- a/examples/c302_C1_Pharyngeal.net.nml +++ b/examples/c302_C1_Pharyngeal.net.nml @@ -4,7 +4,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['M1', 'M2L', 'M2R', 'M3L', 'M3R', 'M4', 'M5', 'I1L', 'I1R', 'I2L', 'I2R', 'I3', 'I4', 'I5', 'I6', 'MI', 'NSML', 'NSMR', 'MCL', 'MCR'] diff --git a/examples/c302_C1_Social.net.nml b/examples/c302_C1_Social.net.nml index e49915e1..be3ddea6 100644 --- a/examples/c302_C1_Social.net.nml +++ b/examples/c302_C1_Social.net.nml @@ -4,7 +4,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['RMGR', 'ASHR', 'ASKR', 'AWBR', 'IL2R', 'RMHR', 'URXR'] diff --git a/examples/c302_C1_Syns.net.nml b/examples/c302_C1_Syns.net.nml index 4f7a953a..590e84c0 100644 --- a/examples/c302_C1_Syns.net.nml +++ b/examples/c302_C1_Syns.net.nml @@ -4,7 +4,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['URYDL', 'SMDDR', 'VD12', 'VB11', 'AS2', 'AIZL', 'ASHL'] diff --git a/examples/c302_C2_FW.net.nml b/examples/c302_C2_FW.net.nml index e90a823a..4be23047 100644 --- a/examples/c302_C2_FW.net.nml +++ b/examples/c302_C2_FW.net.nml @@ -4,7 +4,7 @@ Parameters and setting used to generate this network: Data reader: UpdatedSpreadsheetDataReader2 - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['AVBL', 'AVBR', 'DB1', 'DB2', 'DB3', 'DB4', 'DB5', 'DB6', 'DB7', 'VD1', 'VD2', 'VD3', 'VD4', 'VD5', 'VD6', 'VD7', 'VD8', 'VD9', 'VD10', 'VD11', 'VD12', 'VD13', 'VB1', 'VB2', 'VB3', 'VB4', 'VB5', 'VB6', 'VB7', 'VB8', 'VB9', 'VB10', 'VB11', 'DD1', 'DD2', 'DD3', 'DD4', 'DD5', 'DD6'] diff --git a/examples/c302_C2_Full.net.nml b/examples/c302_C2_Full.net.nml index 79bc0e70..8bb0caa4 100644 --- a/examples/c302_C2_Full.net.nml +++ b/examples/c302_C2_Full.net.nml @@ -4,7 +4,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: All cells diff --git a/examples/c302_C2_IClamp.net.nml b/examples/c302_C2_IClamp.net.nml index e81720be..6282f9ba 100644 --- a/examples/c302_C2_IClamp.net.nml +++ b/examples/c302_C2_IClamp.net.nml @@ -4,7 +4,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['ADAL', 'PVCL'] diff --git a/examples/c302_C2_Muscles.net.nml b/examples/c302_C2_Muscles.net.nml index 5f8633be..40f2c276 100644 --- a/examples/c302_C2_Muscles.net.nml +++ b/examples/c302_C2_Muscles.net.nml @@ -4,7 +4,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['AS1', 'AS10', 'AS11', 'AS2', 'AS3', 'AS4', 'AS5', 'AS6', 'AS7', 'AS8', 'AS9', 'AVFL', 'AVFR', 'AVKR', 'AVL', 'CEPVL', 'CEPVR', 'DA1', 'DA2', 'DA3', 'DA4', 'DA5', 'DA6', 'DA7', 'DA8', 'DA9', 'DB1', 'DB2', 'DB3', 'DB4', 'DB5', 'DB6', 'DB7', 'DD1', 'DD2', 'DD3', 'DD4', 'DD5', 'DD6', 'DVB', 'HSNL', 'HSNR', 'IL1DL', 'IL1DR', 'IL1L', 'IL1R', 'IL1VL', 'IL1VR', 'PDA', 'PDB', 'PVNL', 'PVNR', 'RID', 'RIML', 'RIMR', 'RIVL', 'RIVR', 'RMDDL', 'RMDDR', 'RMDL', 'RMDR', 'RMDVL', 'RMDVR', 'RMED', 'RMEL', 'RMER', 'RMEV', 'RMFL', 'RMGL', 'RMGR', 'RMHL', 'RMHR', 'SMBDL', 'SMBDR', 'SMBVL', 'SMBVR', 'SMDDL', 'SMDDR', 'SMDVL', 'SMDVR', 'URADL', 'URADR', 'URAVL', 'URAVR', 'VA1', 'VA10', 'VA11', 'VA12', 'VA2', 'VA3', 'VA4', 'VA5', 'VA6', 'VA7', 'VA8', 'VA9', 'VB1', 'VB10', 'VB11', 'VB2', 'VB3', 'VB4', 'VB5', 'VB6', 'VB7', 'VB8', 'VB9', 'VC1', 'VC2', 'VC3', 'VC4', 'VC5', 'VC6', 'VD1', 'VD10', 'VD11', 'VD12', 'VD13', 'VD2', 'VD3', 'VD4', 'VD5', 'VD6', 'VD7', 'VD8', 'VD9', 'AVAL', 'AVAR', 'AVBL', 'AVBR', 'AVDL', 'AVDR', 'PVCL', 'PVCR'] diff --git a/examples/c302_C2_Oscillator.net.nml b/examples/c302_C2_Oscillator.net.nml index 20851cbd..063796e2 100644 --- a/examples/c302_C2_Oscillator.net.nml +++ b/examples/c302_C2_Oscillator.net.nml @@ -4,7 +4,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['DB2', 'VB2', 'DD2', 'VD2', 'DB3', 'VB3', 'DD3', 'VD3', 'DA2', 'VA2', 'DA3', 'VA3', 'AVBL', 'AVBR'] diff --git a/examples/c302_C2_Pharyngeal.net.nml b/examples/c302_C2_Pharyngeal.net.nml index 66caaf9e..29f5f252 100644 --- a/examples/c302_C2_Pharyngeal.net.nml +++ b/examples/c302_C2_Pharyngeal.net.nml @@ -4,7 +4,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['M1', 'M2L', 'M2R', 'M3L', 'M3R', 'M4', 'M5', 'I1L', 'I1R', 'I2L', 'I2R', 'I3', 'I4', 'I5', 'I6', 'MI', 'NSML', 'NSMR', 'MCL', 'MCR'] diff --git a/examples/c302_C2_Social.net.nml b/examples/c302_C2_Social.net.nml index 8fc58516..d6ac9cee 100644 --- a/examples/c302_C2_Social.net.nml +++ b/examples/c302_C2_Social.net.nml @@ -4,7 +4,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['RMGR', 'ASHR', 'ASKR', 'AWBR', 'IL2R', 'RMHR', 'URXR'] diff --git a/examples/c302_C2_Syns.net.nml b/examples/c302_C2_Syns.net.nml index 3da60252..92701b7e 100644 --- a/examples/c302_C2_Syns.net.nml +++ b/examples/c302_C2_Syns.net.nml @@ -4,7 +4,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['URYDL', 'SMDDR', 'VD12', 'VB11', 'AS2', 'AIZL', 'ASHL'] diff --git a/examples/c302_C_Full.net.nml b/examples/c302_C_Full.net.nml index 7a00de2b..b9588302 100644 --- a/examples/c302_C_Full.net.nml +++ b/examples/c302_C_Full.net.nml @@ -4,7 +4,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: All cells diff --git a/examples/c302_C_IClamp.net.nml b/examples/c302_C_IClamp.net.nml index 613af16e..558ffad6 100644 --- a/examples/c302_C_IClamp.net.nml +++ b/examples/c302_C_IClamp.net.nml @@ -4,7 +4,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['ADAL', 'PVCL'] diff --git a/examples/c302_C_Muscles.net.nml b/examples/c302_C_Muscles.net.nml index 584e49d7..d797794f 100644 --- a/examples/c302_C_Muscles.net.nml +++ b/examples/c302_C_Muscles.net.nml @@ -4,7 +4,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['AS1', 'AS10', 'AS11', 'AS2', 'AS3', 'AS4', 'AS5', 'AS6', 'AS7', 'AS8', 'AS9', 'AVFL', 'AVFR', 'AVKR', 'AVL', 'CEPVL', 'CEPVR', 'DA1', 'DA2', 'DA3', 'DA4', 'DA5', 'DA6', 'DA7', 'DA8', 'DA9', 'DB1', 'DB2', 'DB3', 'DB4', 'DB5', 'DB6', 'DB7', 'DD1', 'DD2', 'DD3', 'DD4', 'DD5', 'DD6', 'DVB', 'HSNL', 'HSNR', 'IL1DL', 'IL1DR', 'IL1L', 'IL1R', 'IL1VL', 'IL1VR', 'PDA', 'PDB', 'PVNL', 'PVNR', 'RID', 'RIML', 'RIMR', 'RIVL', 'RIVR', 'RMDDL', 'RMDDR', 'RMDL', 'RMDR', 'RMDVL', 'RMDVR', 'RMED', 'RMEL', 'RMER', 'RMEV', 'RMFL', 'RMGL', 'RMGR', 'RMHL', 'RMHR', 'SMBDL', 'SMBDR', 'SMBVL', 'SMBVR', 'SMDDL', 'SMDDR', 'SMDVL', 'SMDVR', 'URADL', 'URADR', 'URAVL', 'URAVR', 'VA1', 'VA10', 'VA11', 'VA12', 'VA2', 'VA3', 'VA4', 'VA5', 'VA6', 'VA7', 'VA8', 'VA9', 'VB1', 'VB10', 'VB11', 'VB2', 'VB3', 'VB4', 'VB5', 'VB6', 'VB7', 'VB8', 'VB9', 'VC1', 'VC2', 'VC3', 'VC4', 'VC5', 'VC6', 'VD1', 'VD10', 'VD11', 'VD12', 'VD13', 'VD2', 'VD3', 'VD4', 'VD5', 'VD6', 'VD7', 'VD8', 'VD9', 'AVAL', 'AVAR', 'AVBL', 'AVBR', 'AVDL', 'AVDR', 'PVCL', 'PVCR'] diff --git a/examples/c302_C_Oscillator.net.nml b/examples/c302_C_Oscillator.net.nml index c289a301..690943d1 100644 --- a/examples/c302_C_Oscillator.net.nml +++ b/examples/c302_C_Oscillator.net.nml @@ -4,7 +4,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['DB2', 'VB2', 'DD2', 'VD2', 'DB3', 'VB3', 'DD3', 'VD3', 'DA2', 'VA2', 'DA3', 'VA3', 'AVBL', 'AVBR'] diff --git a/examples/c302_C_Pharyngeal.net.nml b/examples/c302_C_Pharyngeal.net.nml index f4afce2d..2ee21b63 100644 --- a/examples/c302_C_Pharyngeal.net.nml +++ b/examples/c302_C_Pharyngeal.net.nml @@ -4,7 +4,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['M1', 'M2L', 'M2R', 'M3L', 'M3R', 'M4', 'M5', 'I1L', 'I1R', 'I2L', 'I2R', 'I3', 'I4', 'I5', 'I6', 'MI', 'NSML', 'NSMR', 'MCL', 'MCR'] diff --git a/examples/c302_C_Social.net.nml b/examples/c302_C_Social.net.nml index aada7b81..2de2f451 100644 --- a/examples/c302_C_Social.net.nml +++ b/examples/c302_C_Social.net.nml @@ -4,7 +4,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['RMGR', 'ASHR', 'ASKR', 'AWBR', 'IL2R', 'RMHR', 'URXR'] diff --git a/examples/c302_C_Syns.net.nml b/examples/c302_C_Syns.net.nml index c5f6046e..02241ba2 100644 --- a/examples/c302_C_Syns.net.nml +++ b/examples/c302_C_Syns.net.nml @@ -4,7 +4,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['URYDL', 'SMDDR', 'VD12', 'VB11', 'AS2', 'AIZL', 'ASHL'] diff --git a/examples/c302_D1_Full.net.nml b/examples/c302_D1_Full.net.nml index 540e534d..36f4b6ed 100644 --- a/examples/c302_D1_Full.net.nml +++ b/examples/c302_D1_Full.net.nml @@ -4,7 +4,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: All cells diff --git a/examples/c302_D1_IClamp.net.nml b/examples/c302_D1_IClamp.net.nml index b259492f..bbde7ff3 100644 --- a/examples/c302_D1_IClamp.net.nml +++ b/examples/c302_D1_IClamp.net.nml @@ -4,7 +4,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['ADAL', 'PVCL'] diff --git a/examples/c302_D1_Muscles.net.nml b/examples/c302_D1_Muscles.net.nml index 0bf4e242..e3dcfca7 100644 --- a/examples/c302_D1_Muscles.net.nml +++ b/examples/c302_D1_Muscles.net.nml @@ -4,7 +4,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['AS1', 'AS10', 'AS11', 'AS2', 'AS3', 'AS4', 'AS5', 'AS6', 'AS7', 'AS8', 'AS9', 'AVFL', 'AVFR', 'AVKR', 'AVL', 'CEPVL', 'CEPVR', 'DA1', 'DA2', 'DA3', 'DA4', 'DA5', 'DA6', 'DA7', 'DA8', 'DA9', 'DB1', 'DB2', 'DB3', 'DB4', 'DB5', 'DB6', 'DB7', 'DD1', 'DD2', 'DD3', 'DD4', 'DD5', 'DD6', 'DVB', 'HSNL', 'HSNR', 'IL1DL', 'IL1DR', 'IL1L', 'IL1R', 'IL1VL', 'IL1VR', 'PDA', 'PDB', 'PVNL', 'PVNR', 'RID', 'RIML', 'RIMR', 'RIVL', 'RIVR', 'RMDDL', 'RMDDR', 'RMDL', 'RMDR', 'RMDVL', 'RMDVR', 'RMED', 'RMEL', 'RMER', 'RMEV', 'RMFL', 'RMGL', 'RMGR', 'RMHL', 'RMHR', 'SMBDL', 'SMBDR', 'SMBVL', 'SMBVR', 'SMDDL', 'SMDDR', 'SMDVL', 'SMDVR', 'URADL', 'URADR', 'URAVL', 'URAVR', 'VA1', 'VA10', 'VA11', 'VA12', 'VA2', 'VA3', 'VA4', 'VA5', 'VA6', 'VA7', 'VA8', 'VA9', 'VB1', 'VB10', 'VB11', 'VB2', 'VB3', 'VB4', 'VB5', 'VB6', 'VB7', 'VB8', 'VB9', 'VC1', 'VC2', 'VC3', 'VC4', 'VC5', 'VC6', 'VD1', 'VD10', 'VD11', 'VD12', 'VD13', 'VD2', 'VD3', 'VD4', 'VD5', 'VD6', 'VD7', 'VD8', 'VD9', 'AVAL', 'AVAR', 'AVBL', 'AVBR', 'AVDL', 'AVDR', 'PVCL', 'PVCR'] diff --git a/examples/c302_D1_Oscillator.net.nml b/examples/c302_D1_Oscillator.net.nml index 6f82416f..fd8bbea2 100644 --- a/examples/c302_D1_Oscillator.net.nml +++ b/examples/c302_D1_Oscillator.net.nml @@ -4,7 +4,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['DB2', 'VB2', 'DD2', 'VD2', 'DB3', 'VB3', 'DD3', 'VD3', 'DA2', 'VA2', 'DA3', 'VA3', 'AVBL', 'AVBR'] diff --git a/examples/c302_D1_Pharyngeal.net.nml b/examples/c302_D1_Pharyngeal.net.nml index a8530b71..e9acf9fb 100644 --- a/examples/c302_D1_Pharyngeal.net.nml +++ b/examples/c302_D1_Pharyngeal.net.nml @@ -4,7 +4,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['M1', 'M2L', 'M2R', 'M3L', 'M3R', 'M4', 'M5', 'I1L', 'I1R', 'I2L', 'I2R', 'I3', 'I4', 'I5', 'I6', 'MI', 'NSML', 'NSMR', 'MCL', 'MCR'] diff --git a/examples/c302_D1_Social.net.nml b/examples/c302_D1_Social.net.nml index 8e58edce..d0a7d58d 100644 --- a/examples/c302_D1_Social.net.nml +++ b/examples/c302_D1_Social.net.nml @@ -4,7 +4,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['RMGR', 'ASHR', 'ASKR', 'AWBR', 'IL2R', 'RMHR', 'URXR'] diff --git a/examples/c302_D1_Syns.net.nml b/examples/c302_D1_Syns.net.nml index 7ddff9b8..cc7ee744 100644 --- a/examples/c302_D1_Syns.net.nml +++ b/examples/c302_D1_Syns.net.nml @@ -4,7 +4,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['URYDL', 'SMDDR', 'VD12', 'VB11', 'AS2', 'AIZL', 'ASHL'] diff --git a/examples/c302_D_Full.net.nml b/examples/c302_D_Full.net.nml index 7c2596fe..187d47ac 100644 --- a/examples/c302_D_Full.net.nml +++ b/examples/c302_D_Full.net.nml @@ -4,7 +4,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: All cells diff --git a/examples/c302_D_IClamp.net.nml b/examples/c302_D_IClamp.net.nml index fd24595e..596eceb3 100644 --- a/examples/c302_D_IClamp.net.nml +++ b/examples/c302_D_IClamp.net.nml @@ -4,7 +4,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['ADAL', 'PVCL'] diff --git a/examples/c302_D_Muscles.net.nml b/examples/c302_D_Muscles.net.nml index 236f2bb3..e21c495c 100644 --- a/examples/c302_D_Muscles.net.nml +++ b/examples/c302_D_Muscles.net.nml @@ -4,7 +4,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['AS1', 'AS10', 'AS11', 'AS2', 'AS3', 'AS4', 'AS5', 'AS6', 'AS7', 'AS8', 'AS9', 'AVFL', 'AVFR', 'AVKR', 'AVL', 'CEPVL', 'CEPVR', 'DA1', 'DA2', 'DA3', 'DA4', 'DA5', 'DA6', 'DA7', 'DA8', 'DA9', 'DB1', 'DB2', 'DB3', 'DB4', 'DB5', 'DB6', 'DB7', 'DD1', 'DD2', 'DD3', 'DD4', 'DD5', 'DD6', 'DVB', 'HSNL', 'HSNR', 'IL1DL', 'IL1DR', 'IL1L', 'IL1R', 'IL1VL', 'IL1VR', 'PDA', 'PDB', 'PVNL', 'PVNR', 'RID', 'RIML', 'RIMR', 'RIVL', 'RIVR', 'RMDDL', 'RMDDR', 'RMDL', 'RMDR', 'RMDVL', 'RMDVR', 'RMED', 'RMEL', 'RMER', 'RMEV', 'RMFL', 'RMGL', 'RMGR', 'RMHL', 'RMHR', 'SMBDL', 'SMBDR', 'SMBVL', 'SMBVR', 'SMDDL', 'SMDDR', 'SMDVL', 'SMDVR', 'URADL', 'URADR', 'URAVL', 'URAVR', 'VA1', 'VA10', 'VA11', 'VA12', 'VA2', 'VA3', 'VA4', 'VA5', 'VA6', 'VA7', 'VA8', 'VA9', 'VB1', 'VB10', 'VB11', 'VB2', 'VB3', 'VB4', 'VB5', 'VB6', 'VB7', 'VB8', 'VB9', 'VC1', 'VC2', 'VC3', 'VC4', 'VC5', 'VC6', 'VD1', 'VD10', 'VD11', 'VD12', 'VD13', 'VD2', 'VD3', 'VD4', 'VD5', 'VD6', 'VD7', 'VD8', 'VD9', 'AVAL', 'AVAR', 'AVBL', 'AVBR', 'AVDL', 'AVDR', 'PVCL', 'PVCR'] diff --git a/examples/c302_D_Oscillator.net.nml b/examples/c302_D_Oscillator.net.nml index 9fa1c718..f9785628 100644 --- a/examples/c302_D_Oscillator.net.nml +++ b/examples/c302_D_Oscillator.net.nml @@ -4,7 +4,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['DB2', 'VB2', 'DD2', 'VD2', 'DB3', 'VB3', 'DD3', 'VD3', 'DA2', 'VA2', 'DA3', 'VA3', 'AVBL', 'AVBR'] diff --git a/examples/c302_D_Pharyngeal.net.nml b/examples/c302_D_Pharyngeal.net.nml index acf1956b..1b69f91c 100644 --- a/examples/c302_D_Pharyngeal.net.nml +++ b/examples/c302_D_Pharyngeal.net.nml @@ -4,7 +4,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['M1', 'M2L', 'M2R', 'M3L', 'M3R', 'M4', 'M5', 'I1L', 'I1R', 'I2L', 'I2R', 'I3', 'I4', 'I5', 'I6', 'MI', 'NSML', 'NSMR', 'MCL', 'MCR'] diff --git a/examples/c302_D_Social.net.nml b/examples/c302_D_Social.net.nml index ec2d540c..27f42af7 100644 --- a/examples/c302_D_Social.net.nml +++ b/examples/c302_D_Social.net.nml @@ -4,7 +4,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['RMGR', 'ASHR', 'ASKR', 'AWBR', 'IL2R', 'RMHR', 'URXR'] diff --git a/examples/c302_D_Syns.net.nml b/examples/c302_D_Syns.net.nml index 926af51f..0d8c7610 100644 --- a/examples/c302_D_Syns.net.nml +++ b/examples/c302_D_Syns.net.nml @@ -4,7 +4,7 @@ Parameters and setting used to generate this network: Data reader: SpreadsheetDataReader - c302 version: 0.7.12 + c302 version: 0.8.0 owmeta version: 0.12.3 owmeta_core version: 0.13.5 Cells: ['URYDL', 'SMDDR', 'VD12', 'VB11', 'AS2', 'AIZL', 'ASHL'] diff --git a/examples/test/Comparison.ipynb b/examples/test/Comparison.ipynb index 8e18a84f..22a63a3a 100644 --- a/examples/test/Comparison.ipynb +++ b/examples/test/Comparison.ipynb @@ -2,7 +2,7 @@ "cells": [ { "cell_type": "code", - "execution_count": 3, + "execution_count": 1, "id": "481d3c70-313a-4979-8475-d4a0089a8a0b", "metadata": { "tags": [] @@ -13,31 +13,17 @@ "output_type": "stream", "text": [ "\n", - "****** Importing dataset SpreadsheetData using c302.SpreadsheetDataReader ******\n", - "c302 >>> Opened Excel file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/CElegansNeuronTables.xls\n", - "c302 >>> Opened Excel file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/CElegansNeuronTables.xls\n", - "c302 >>> Opened Excel file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/CElegansNeuronTables.xls\n", - "c302 >>> Opened Excel file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/CElegansNeuronTables.xls\n", - "c302 >>> Opened Excel file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/CElegansNeuronTables.xls\n", - "c302 >>> Opened Excel file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/CElegansNeuronTables.xls\n", - "c302 >>> Opened Excel file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/CElegansNeuronTables.xls\n", - "c302 >>> Opened Excel file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/CElegansNeuronTables.xls\n", - "c302 >>> Opened Excel file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/CElegansNeuronTables.xls\n", - "c302 >>> Opened Excel file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/CElegansNeuronTables.xls\n", - "c302 >>> Opened Excel file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/CElegansNeuronTables.xls\n", - "c302 >>> Opened Excel file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/CElegansNeuronTables.xls\n", + "****** Importing dataset SSData using c302.SpreadsheetDataReader ******\n", + "c302 >>> Opened Excel file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/CElegansNeuronTables.xls\n", + "c302 >>> Opened Excel file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/CElegansNeuronTables.xls\n", "\n", - "****** Importing dataset UpdSpreadsheetData using c302.UpdatedSpreadsheetDataReader ******\n", - "c302 >>> Opened file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/herm_full_edgelist.csv\n", - "c302 >>> Opened file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/herm_full_edgelist.csv\n", - "c302 >>> Opened file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/herm_full_edgelist.csv\n", - "c302 >>> Opened file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/herm_full_edgelist.csv\n", + "****** Importing dataset UpdSSData using c302.UpdatedSpreadsheetDataReader ******\n", + "c302 >>> Opened file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/herm_full_edgelist.csv\n", + "c302 >>> Opened file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/herm_full_edgelist.csv\n", "\n", - "****** Importing dataset UpdSpreadsheetData2 using c302.UpdatedSpreadsheetDataReader2 ******\n", - "c302 >>> Opened file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/herm_full_edgelist_MODIFIED.csv\n", - "c302 >>> Opened file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/herm_full_edgelist_MODIFIED.csv\n", - "c302 >>> Opened file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/herm_full_edgelist_MODIFIED.csv\n", - "c302 >>> Opened file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/herm_full_edgelist_MODIFIED.csv\n", + "****** Importing dataset UpdSSData2 using c302.UpdatedSpreadsheetDataReader2 ******\n", + "c302 >>> Opened file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/herm_full_edgelist_MODIFIED.csv\n", + "c302 >>> Opened file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/herm_full_edgelist_MODIFIED.csv\n", "\n", "****** Importing dataset OpenWorm using c302.OpenWormReader ******\n", "c302 >>> Initialising OpenWormReader\n", @@ -45,136 +31,97 @@ "c302 >>> Total connections found 5805 \n", "c302 >>> Total cells 397 (254 with connections)\n", "c302 >>> Total connections found 926 \n", - "c302 >>> Total cells 397 (254 with connections)\n", - "c302 >>> Total connections found 926 \n", - "c302 >>> Total cells 397 (254 with connections)\n", - "c302 >>> Total connections found 926 \n", - "c302 >>> Total cells 397 (254 with connections)\n", - "c302 >>> Total connections found 926 \n", - "c302 >>> Total cells 397 (254 with connections)\n", - "c302 >>> Total connections found 926 \n", - "c302 >>> Total cells 397 (254 with connections)\n", - "c302 >>> Total connections found 926 \n", - "c302 >>> Total cells 397 (254 with connections)\n", - "c302 >>> Total connections found 926 \n", - "c302 >>> Total cells 397 (254 with connections)\n", - "c302 >>> Total connections found 926 \n", - "c302 >>> Total cells 397 (254 with connections)\n", - "c302 >>> Total connections found 926 \n", - "c302 >>> Total cells 397 (254 with connections)\n", - "c302 >>> Total connections found 926 \n", - "c302 >>> Total cells 397 (254 with connections)\n", - "c302 >>> Total connections found 926 \n", - "c302 >>> Total cells 397 (254 with connections)\n", - "c302 >>> Total connections found 926 \n", - "c302 >>> Total cells 397 (254 with connections)\n", - "c302 >>> Total connections found 926 \n", - "c302 >>> Total cells 397 (254 with connections)\n", - "c302 >>> Total connections found 926 \n", - "c302 >>> Total cells 397 (254 with connections)\n", - "c302 >>> Total connections found 926 \n", - "c302 >>> Total cells 397 (254 with connections)\n", - "c302 >>> Total connections found 926 \n", - "c302 >>> Total cells 397 (254 with connections)\n", - "c302 >>> Total connections found 926 \n", - "c302 >>> Total cells 397 (254 with connections)\n", - "c302 >>> Total connections found 926 \n", - "c302 >>> Total cells 397 (254 with connections)\n", - "c302 >>> Total connections found 926 \n", - "c302 >>> Total cells 397 (254 with connections)\n", - "c302 >>> Total connections found 926 \n", - "c302 >>> Total cells 397 (254 with connections)\n", - "c302 >>> Total connections found 926 \n", - "c302 >>> Total cells 397 (254 with connections)\n", - "c302 >>> Total connections found 926 \n", - "c302 >>> Total cells 397 (254 with connections)\n", - "c302 >>> Total connections found 926 \n", "\n", - "****** Importing dataset WormNeuroAtlas using c302.WormNeuroAtlasReader ******\n", - "c302 >>> Initialising WormNeuroAtlasReader\n", + "****** Importing dataset White_A using c302.White_A ******\n", + "c302 >>> Opened file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/aconnectome_white_1986_A.csv\n", + "c302 >>> Opened file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/aconnectome_white_1986_A.csv\n", "\n", - "****** Importing dataset Varshney using c302.VarshneyDataReader ******\n", - "c302 >>> Opened the Excel file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/NeuronConnectFormatted.xlsx\n", - "c302 >>> Opened Excel file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/NeuronConnectFormatted.xlsx\n", - "c302 >>> Opened Excel file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/NeuronConnectFormatted.xlsx\n", + "****** Importing dataset White_L4 using c302.White_L4 ******\n", + "c302 >>> Opened file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/aconnectome_white_1986_L4.csv\n", + "c302 >>> Opened file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/aconnectome_white_1986_L4.csv\n", "\n", - "****** Importing dataset Witvliet(1) using c302.W_SpreadsheetDataReader ******\n", - "c302 >>> Opened Excel file..: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/witvliet_2020_7.xlsx\n", - "c302 >>> Opened Excel file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/witvliet_2020_7.xlsx\n", - "c302 >>> Opened Excel file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/witvliet_2020_7.xlsx\n", + "****** Importing dataset White_whole using c302.White_whole ******\n", + "c302 >>> Opened file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/aconnectome_white_1986_whole.csv\n", + "c302 >>> Opened file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/aconnectome_white_1986_whole.csv\n", "\n", - "****** Importing dataset Witvliet(2) using c302.W_SpreadsheetDataReader ******\n", - "c302 >>> Opened Excel file..: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/witvliet_2020_8.xlsx\n", - "c302 >>> Opened Excel file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/witvliet_2020_8.xlsx\n", - "c302 >>> Opened Excel file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/witvliet_2020_8.xlsx\n", + "****** Importing dataset Varshney using c302.VarshneyDataReader ******\n", + "c302 >>> Opened the Excel file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/NeuronConnectFormatted.xlsx\n", + "c302 >>> Opened Excel file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/NeuronConnectFormatted.xlsx\n", "\n", - "****** Importing dataset White(A) using c302.WhiteDataReader ******\n", - "c302 >>> Opened file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/aconnectome_white_1986_A.csv\n", - "c302 >>> Opened file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/aconnectome_white_1986_A.csv\n", - "c302 >>> Opened file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/aconnectome_white_1986_A.csv\n", + "****** Importing dataset Witvliet1 using c302.WitvlietDataReader1 ******\n", + "c302 >>> Opened the Excel file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/witvliet_2020_7.xlsx\n", + "c302 >>> Opened Excel file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/witvliet_2020_7.xlsx\n", "\n", - "****** Importing dataset White(L4) using c302.WhiteDataReader ******\n", - "c302 >>> Opened file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/aconnectome_white_1986_L4.csv\n", - "c302 >>> Opened file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/aconnectome_white_1986_L4.csv\n", - "c302 >>> Opened file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/aconnectome_white_1986_L4.csv\n", + "****** Importing dataset Witvliet2 using c302.WitvlietDataReader2 ******\n", + "c302 >>> Opened the Excel file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/witvliet_2020_8.xlsx\n", + "c302 >>> Opened Excel file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/witvliet_2020_8.xlsx\n", "\n", - "****** Importing dataset White(Whole) using c302.WhiteDataReader ******\n", - "c302 >>> Opened file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/aconnectome_white_1986_whole.csv\n", - "c302 >>> Opened file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/aconnectome_white_1986_whole.csv\n", - "c302 >>> Opened file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/aconnectome_white_1986_whole.csv\n", - "c302 >>> Opened file: c:\\Users\\vyasi\\anaconda3\\envs\\ProWorm\\lib\\site-packages\\c302/data/aconnectome_white_1986_whole.csv\n" + "****** Importing dataset WormNeuroAtlas using c302.WormNeuroAtlasReader ******\n", + "*This version of the NeuroAtlas does not include the CAN neurons. This will be fixed soon.\n", + "*In loading the anatomical connectome, the following conventions are used to allow for its comparison with the other datasets: AWCL->AWCOFF and AWCR->AWCON\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "/opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/wormneuroatlas/WormBase.py:52: UserWarning: Wormbase.org updated its database to a new version (WS291). The version of Worm Neuro Atlas that you are using has been built for the wormbase database version WS287. To ensure reproducible results, upgrade Worm Neuro Atlas with `python -m pip install --upgrade wormneuroatlas` If this warning persists after upgrading, let the developers know by opening an issue here: https://github.com/francescorandi/wormneuroatlas/issues. NOTE: You can still use Worm Neuro Atlas in the meantime. The metadata accessible via wormneuroatlas.WormBase.get_metadata() and wormneuroatlas.NeuroAtlas.get_metadata() contain the version of wormbase that you are currently using, so make sure you save the metadata alongside your results. \n", + " warnings.warn(w)\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "c302 >>> Initialising WormNeuroAtlasReader\n", + "\n", + "Finished loading all the data from the readers!\n" ] } ], "source": [ "\n", "import c302\n", - "from c302.NeuroMLUtilities import analyse_connections\n", + "from c302.ConnectomeReader import analyse_connections\n", + "from c302.ConnectomeReader import check_neurons\n", "\n", "all_data = {}\n", - "all_data[\"Values\"] =[\"Num Neurons\", \"Num Muscles\", \"Num N->N conns\", \"Num N with ->M\", \"Num N->M conns\", \"N neurotransmitters\", \"M neurotransmitters\"]\n", + "all_data[\"Values\"] =[\"Num neurons\", \n", + " \"Missing neurons\", \n", + " \"Non neurons\", \n", + " \"Num muscles\", \n", + " \"Num N->N conns\", \n", + " \"Num N with ->M\", \n", + " \"Num N->M conns\", \n", + " \"N->N neurotrans.\", \n", + " \"N->M neurotrans.\"]\n", "\n", - "readers = {\"SpreadsheetData\": \"c302.SpreadsheetDataReader\", \n", - " \"UpdSpreadsheetData\": \"c302.UpdatedSpreadsheetDataReader\",\n", - " \"UpdSpreadsheetData2\": \"c302.UpdatedSpreadsheetDataReader2\",\n", + "readers = {\"SSData\": \"c302.SpreadsheetDataReader\", \n", + " \"UpdSSData\": \"c302.UpdatedSpreadsheetDataReader\",\n", + " \"UpdSSData2\": \"c302.UpdatedSpreadsheetDataReader2\",\n", " \"OpenWorm\": \"c302.OpenWormReader\",\n", - " \"WormNeuroAtlas\": \"c302.WormNeuroAtlasReader\",\n", + " \"White_A\": \"c302.White_A\", \n", + " \"White_L4\": \"c302.White_L4\", \n", + " \"White_whole\": \"c302.White_whole\",\n", " \"Varshney\": \"c302.VarshneyDataReader\",\n", - " \"Witvliet(1)\": \"c302.W_SpreadsheetDataReader\",\n", - " \"Witvliet(2)\": \"c302.W_SpreadsheetDataReader\",\n", - " \"White(A)\": \"c302.WhiteDataReader\",\n", - " \"White(L4)\": \"c302.WhiteDataReader\",\n", - " \"White(Whole)\": \"c302.WhiteDataReader\"}\n", + " \"Witvliet1\": \"c302.WitvlietDataReader1\",\n", + " \"Witvliet2\": \"c302.WitvlietDataReader2\",\n", + " \"WormNeuroAtlas\": \"c302.WormNeuroAtlasReader\",\n", + " }\n", "\n", + "def shorten_neurotransmitter(nt):\n", + " return nt.replace('Acetylcholine', 'ACh').replace('Serotonin', '5HT').replace('Glutamate', 'Glu')\\\n", + " .replace('Tyramine', 'Tyr').replace('FMRFamide','FMRFam').replace('Generic_', 'Gen_')\n", "\n", "for name, reader in readers.items():\n", "\n", " print(\"\\n****** Importing dataset %s using %s ******\"% (name, reader))\n", " \n", - " if name == \"Witvliet(1)\":\n", - " exec(f\"from {reader} import WitvlietDataReader1\")\n", - " data_reader_instance = eval(f\"WitvlietDataReader1\")\n", - " cells, neuron_conns = data_reader_instance.read_data(include_nonconnected_cells=True)\n", - " elif name == \"Witvliet(2)\":\n", - " exec(f\"from {reader} import WitvlietDataReader2\")\n", - " data_reader_instance = eval(f\"WitvlietDataReader2\")\n", - " cells, neuron_conns = data_reader_instance.read_data(include_nonconnected_cells=True)\n", - " elif name == \"White(A)\":\n", - " exec(f\"from {reader} import White_A\")\n", - " data_reader_instance = eval(f\"White_A\")\n", - " cells, neuron_conns = data_reader_instance.read_data(include_nonconnected_cells=True)\n", - " elif name == \"White(L4)\":\n", - " exec(f\"from {reader} import White_L4\")\n", - " data_reader_instance = eval(f\"White_L4\")\n", - " cells, neuron_conns = data_reader_instance.read_data(include_nonconnected_cells=True)\n", - " elif name == \"White(Whole)\":\n", - " exec(f\"from {reader} import White_whole\")\n", - " data_reader_instance = eval(f\"White_whole\")\n", - " cells, neuron_conns = data_reader_instance.read_data(include_nonconnected_cells=True)\n", - " else:\n", - " exec(\"from %s import read_data, read_muscle_data\"%reader)\n", - " cells, neuron_conns = read_data(include_nonconnected_cells=True)\n", "\n", + " exec(\"from %s import read_data, read_muscle_data\"%reader)\n", + " cells, neuron_conns = read_data(include_nonconnected_cells=True)\n", + "\n", + " preferred, not_in_preferred, missing_preferred = check_neurons(cells)\n", "\n", " neuron_nts = {}\n", " for c in neuron_conns:\n", @@ -187,32 +134,11 @@ " neuron_nts[nt] +=1\n", " \n", " nts_info = ''\n", - " for nts in sorted(neuron_nts.keys()):\n", - " nts_info+='%s (%i)
'%(nts, neuron_nts[nts])\n", + " for nt in sorted(neuron_nts.keys()):\n", + " nts_info+='%s (%i)
'%(shorten_neurotransmitter(nt), neuron_nts[nt])\n", "\n", - " if name == \"Witvliet(1)\":\n", - " exec(f\"from {reader} import WitvlietDataReader1\")\n", - " data_reader_instance = eval(f\"WitvlietDataReader1\")\n", - " neurons2muscles, muscles, muscle_conns = data_reader_instance.read_muscle_data()\n", - " elif name == \"Witvliet(2)\":\n", - " exec(f\"from {reader} import WitvlietDataReader2\")\n", - " data_reader_instance = eval(f\"WitvlietDataReader2\")\n", - " neurons2muscles, muscles, muscle_conns = data_reader_instance.read_muscle_data()\n", - " elif name == \"White(A)\":\n", - " exec(f\"from {reader} import White_A\")\n", - " data_reader_instance = eval(f\"White_A\")\n", - " neurons2muscles, muscles, muscle_conns = data_reader_instance.read_muscle_data()\n", - " elif name == \"White(L4)\":\n", - " exec(f\"from {reader} import White_L4\")\n", - " data_reader_instance = eval(f\"White_L4\")\n", - " neurons2muscles, muscles, muscle_conns = data_reader_instance.read_muscle_data()\n", - " elif name == \"White(Whole)\":\n", - " exec(f\"from {reader} import White_whole\")\n", - " data_reader_instance = eval(f\"White_whole\")\n", - " neurons2muscles, muscles, muscle_conns = data_reader_instance.read_muscle_data()\n", - " else:\n", - " neurons2muscles, muscles, muscle_conns = read_muscle_data()\n", - " \n", + " \n", + " neurons2muscles, muscles, muscle_conns = read_muscle_data()\n", " \n", " muscle_nts = {}\n", " for c in muscle_conns:\n", @@ -225,23 +151,26 @@ " muscle_nts[nt] +=1\n", " \n", " m_nts_info = ''\n", - " for nts in sorted(muscle_nts):\n", - " m_nts_info+='%s (%i)
'%(nts, muscle_nts[nts])\n", + " for nt in sorted(muscle_nts):\n", + " m_nts_info+='%s (%i)
'%(shorten_neurotransmitter(nt), muscle_nts[nt])\n", "\n", "\n", - " all_data[name] =[len(cells),\n", + " all_data[name] =[len(preferred),\n", + " len(missing_preferred), \n", + " len(not_in_preferred), \n", " len(muscles), \n", " len(neuron_conns), \n", " len(neurons2muscles), \n", " len(muscle_conns),\n", " nts_info,\n", " m_nts_info]\n", - "\n" + "\n", + "print('\\nFinished loading all the data from the readers!')" ] }, { "cell_type": "code", - "execution_count": 4, + "execution_count": 2, "id": "2308051a-0a24-44db-a481-fc0d0f2af4fb", "metadata": { "tags": [] @@ -254,44 +183,72 @@ " \n", " \n", " Values\n", - " SpreadsheetData\n", - " UpdSpreadsheetData\n", - " UpdSpreadsheetData2\n", + " SSData\n", + " UpdSSData\n", + " UpdSSData2\n", " OpenWorm\n", - " WormNeuroAtlas\n", + " White_A\n", + " White_L4\n", + " White_whole\n", " Varshney\n", - " Witvliet(1)\n", - " Witvliet(2)\n", - " White(A)\n", - " White(L4)\n", - " White(Whole)\n", + " Witvliet1\n", + " Witvliet2\n", + " WormNeuroAtlas\n", " \n", " \n", " \n", " \n", - " Num Neurons\n", + " Num neurons\n", " 302\n", " 302\n", " 302\n", " 302\n", - " 300\n", + " 182\n", + " 180\n", + " 301\n", " 279\n", - " 225\n", - " 222\n", - " 191\n", - " 185\n", - " 311\n", + " 181\n", + " 180\n", + " 300\n", + " \n", + " \n", + " Missing neurons\n", + " 0\n", + " 0\n", + " 0\n", + " 0\n", + " 120\n", + " 122\n", + " 1\n", + " 23\n", + " 121\n", + " 122\n", + " 2\n", + " \n", + " \n", + " Non neurons\n", + " 0\n", + " 0\n", + " 0\n", + " 0\n", + " 9\n", + " 5\n", + " 8\n", + " 0\n", + " 9\n", + " 7\n", + " 0\n", " \n", " \n", - " Num Muscles\n", + " Num muscles\n", " 97\n", " 95\n", " 95\n", " 95\n", - " 0\n", - " 1\n", " 32\n", " 32\n", + " 1\n", + " 1\n", " 32\n", " 32\n", " 0\n", @@ -302,13 +259,13 @@ " 5806\n", " 5821\n", " 5805\n", - " 1650\n", - " 6264\n", - " 2493\n", - " 2496\n", " 1694\n", " 1593\n", - " 2961\n", + " 2847\n", + " 6264\n", + " 2251\n", + " 2274\n", + " 5701\n", " \n", " \n", " Num N with ->M\n", @@ -316,12 +273,12 @@ " 254\n", " 254\n", " 159\n", - " 0\n", + " 38\n", + " 38\n", + " 114\n", " 115\n", " 58\n", " 47\n", - " 38\n", - " 38\n", " 0\n", " \n", " \n", @@ -330,40 +287,40 @@ " 1118\n", " 1118\n", " 926\n", - " 0\n", + " 205\n", + " 176\n", + " 114\n", " 153\n", " 230\n", " 216\n", - " 205\n", - " 176\n", " 0\n", " \n", " \n", - " N neurotransmitters\n", - " Acetylcholine (394)
Acetylcholine_Tyramine (29)
Dopamine (120)
FMRFamide (247)
GABA (200)
Generic_GJ (1084)
Glutamate (962)
Octapamine (20)
Serotonin (178)
Serotonin_Acetylcholine (104)
Serotonin_Glutamate (25)
\n", - " Acetylcholine (3581)
GABA (57)
Generic_GJ (2168)
\n", - " Acetylcholine (3596)
GABA (57)
Generic_GJ (2168)
\n", - " Acetylcholine (2008)
Acetylcholine_GJ (222)
Acetylcholine_Tyramine (29)
Acetylcholine_Tyramine_GJ (13)
Dopamine (98)
Dopamine_GJ (13)
FMRFamide (170)
FMRFamide_GJ (90)
FRMFemide (45)
FRMFemide_GJ (33)
GABA (182)
GABA_GJ (76)
Generic_GJ (1356)
Glutamate (824)
Glutamate_GJ (324)
Octapamine (19)
Octapamine_GJ (4)
Serotonin (163)
Serotonin_Acetylcholine (91)
Serotonin_Acetylcholine_GJ (13)
Serotonin_GJ (20)
Serotonin_Glutamate (11)
Serotonin_Glutamate_GJ (1)
\n", - " Generic_GJ (1650)
\n", - " Chemical_Synapse (5233)
Generic_GJ (1031)
\n", - " Chemical_Synapse (2202)
Generic_GJ (291)
\n", - " Chemical_Synapse (2186)
Generic_GJ (310)
\n", - " Acetylcholine (1424)
Generic_GJ (270)
\n", - " Acetylcholine (1304)
Generic_GJ (289)
\n", - " Acetylcholine (2333)
GABA (53)
Generic_GJ (575)
\n", + " N->N neurotrans.\n", + " ACh (394)
ACh_Tyr (29)
Dopamine (120)
FMRFam (247)
GABA (200)
Gen_GJ (1084)
Glu (962)
Octapamine (20)
5HT (178)
5HT_ACh (104)
5HT_Glu (25)
\n", + " ACh (3581)
GABA (57)
Gen_GJ (2168)
\n", + " ACh (3596)
GABA (57)
Gen_GJ (2168)
\n", + " ACh (2008)
ACh_GJ (222)
ACh_Tyr (29)
ACh_Tyr_GJ (13)
Dopamine (98)
Dopamine_GJ (13)
FMRFam (170)
FMRFam_GJ (90)
FRMFemide (45)
FRMFemide_GJ (33)
GABA (182)
GABA_GJ (76)
Gen_GJ (1356)
Glu (824)
Glu_GJ (324)
Octapamine (19)
Octapamine_GJ (4)
5HT (163)
5HT_ACh (91)
5HT_ACh_GJ (13)
5HT_GJ (20)
5HT_Glu (11)
5HT_Glu_GJ (1)
\n", + " ACh (1424)
Gen_GJ (270)
\n", + " ACh (1304)
Gen_GJ (289)
\n", + " ACh (2237)
GABA (35)
Gen_GJ (575)
\n", + " Gen_CS (5233)
Gen_GJ (1031)
\n", + " Gen_CS (1979)
Gen_GJ (272)
\n", + " Gen_CS (1970)
Gen_GJ (304)
\n", + " ACh (2017)
GABA (631)
Gen_CS (431)
Gen_GJ (1650)
Glu (972)
\n", " \n", " \n", - " M neurotransmitters\n", - " **MISSING** (2)
Acetylcholine (377)
Acetylcholineplus_Tyramine (6)
Dopamine (1)
FMRFamide (3)
FRMFemide (5)
GABA (126)
Glutamate (35)
Serotonin (1)
Serotoninplus_Acetylcholine (8)
\n", - " Acetylcholine (808)
GABA (116)
Generic_GJ (194)
\n", - " Acetylcholine (808)
GABA (116)
Generic_GJ (194)
\n", - " Acetylcholine (924)
Generic_GJ (2)
\n", - " \n", - " Chemical_Synapse (153)
\n", - " Chemical_Synapse (230)
\n", - " Chemical_Synapse (216)
\n", - " Acetylcholine (205)
\n", - " Acetylcholine (176)
\n", + " N->M neurotrans.\n", + " **MISSING** (2)
ACh (377)
AChplus_Tyr (6)
Dopamine (1)
FMRFam (3)
FRMFemide (5)
GABA (126)
Glu (35)
5HT (1)
5HTplus_ACh (8)
\n", + " ACh (808)
GABA (116)
Gen_GJ (194)
\n", + " ACh (808)
GABA (116)
Gen_GJ (194)
\n", + " ACh (924)
Gen_GJ (2)
\n", + " ACh (205)
\n", + " ACh (176)
\n", + " ACh (96)
GABA (18)
\n", + " Gen_CS (153)
\n", + " Gen_CS (230)
\n", + " Gen_CS (216)
\n", " \n", " \n", " \n", @@ -373,7 +330,7 @@ "" ] }, - "execution_count": 4, + "execution_count": 2, "metadata": {}, "output_type": "execute_result" } @@ -391,18 +348,216 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 5, "id": "8a6f79cf-8fb4-4c04-b319-03456f64d298", "metadata": { "tags": [] }, - "outputs": [], - "source": [] + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\n", + "=== Generating using reader SpreadsheetDataReader\n", + "c302 >>> Set default parameters for C\n", + "c302 >>> Set default parameters for C\n", + "c302 >>> Set default parameters for C\n", + "c302 >>> Set default parameters for C1\n", + "c302 >>> Opened Excel file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/CElegansNeuronTables.xls\n", + "c302 >>> Opened Excel file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/CElegansNeuronTables.xls\n", + "c302 >>> Writing generated network to: /Users/padraig/c302/examples/test/images/c302_C1_Oscillator.net.nml\n", + "c302 >>> Saving connectivity figure to: ./images/SSData_exc_to_neurons.png\n", + "c302 >>> Saving connectivity figure to: ./images/SSData_inh_to_neurons.png\n", + "c302 >>> Saving connectivity figure to: ./images/SSData_elec_neurons_neurons.png\n", + "\n", + "=== Generating using reader UpdatedSpreadsheetDataReader\n", + "c302 >>> Set default parameters for C\n", + "c302 >>> Set default parameters for C\n", + "c302 >>> Set default parameters for C\n", + "c302 >>> Set default parameters for C1\n", + "c302 >>> Opened file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/herm_full_edgelist.csv\n", + "c302 >>> Opened file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/herm_full_edgelist.csv\n", + "c302 >>> Writing generated network to: /Users/padraig/c302/examples/test/images/c302_C1_Oscillator.net.nml\n", + "c302 >>> Saving connectivity figure to: ./images/UpdSSData_exc_to_neurons.png\n", + "c302 >>> Saving connectivity figure to: ./images/UpdSSData_inh_to_neurons.png\n", + "c302 >>> Saving connectivity figure to: ./images/UpdSSData_elec_neurons_neurons.png\n", + "\n", + "=== Generating using reader UpdatedSpreadsheetDataReader2\n", + "c302 >>> Set default parameters for C\n", + "c302 >>> Set default parameters for C\n", + "c302 >>> Set default parameters for C\n", + "c302 >>> Set default parameters for C1\n", + "c302 >>> Opened file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/herm_full_edgelist_MODIFIED.csv\n", + "c302 >>> Opened file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/herm_full_edgelist_MODIFIED.csv\n", + "c302 >>> Writing generated network to: /Users/padraig/c302/examples/test/images/c302_C1_Oscillator.net.nml\n", + "c302 >>> Saving connectivity figure to: ./images/UpdSSData2_exc_to_neurons.png\n", + "c302 >>> Saving connectivity figure to: ./images/UpdSSData2_inh_to_neurons.png\n", + "c302 >>> Saving connectivity figure to: ./images/UpdSSData2_elec_neurons_neurons.png\n", + "\n", + "=== Generating using reader OpenWormReader\n", + "c302 >>> Set default parameters for C\n", + "c302 >>> Set default parameters for C\n", + "c302 >>> Set default parameters for C\n", + "c302 >>> Set default parameters for C1\n", + "c302 >>> Initialising OpenWormReader\n", + "c302 >>> Total cells 302 (300 with connections)\n", + "c302 >>> Total connections found 5805 \n", + "c302 >>> Total cells 397 (254 with connections)\n", + "c302 >>> Total connections found 926 \n", + "c302 >>> Writing generated network to: /Users/padraig/c302/examples/test/images/c302_C1_Oscillator.net.nml\n", + "c302 >>> Saving connectivity figure to: ./images/OpenWorm_exc_to_neurons.png\n", + "c302 >>> Saving connectivity figure to: ./images/OpenWorm_inh_to_neurons.png\n", + "c302 >>> Saving connectivity figure to: ./images/OpenWorm_elec_neurons_neurons.png\n", + "\n", + "=== Generating using reader White_A\n", + "c302 >>> Set default parameters for C\n", + "c302 >>> Set default parameters for C\n", + "c302 >>> Set default parameters for C\n", + "c302 >>> Set default parameters for C1\n", + "c302 >>> Opened file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/aconnectome_white_1986_A.csv\n", + "c302 >>> No matching cell for CEPshVL\n", + "c302 >>> No matching cell for CEPshDR\n", + "c302 >>> No matching cell for CEPshVR\n", + "c302 >>> Opened file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/aconnectome_white_1986_A.csv\n", + "c302 >>> Writing generated network to: /Users/padraig/c302/examples/test/images/c302_C1_Oscillator.net.nml\n", + "c302 >>> Saving connectivity figure to: ./images/White_A_elec_neurons_neurons.png\n", + "\n", + "=== Generating using reader White_L4\n", + "c302 >>> Set default parameters for C\n", + "c302 >>> Set default parameters for C\n", + "c302 >>> Set default parameters for C\n", + "c302 >>> Set default parameters for C1\n", + "c302 >>> Opened file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/aconnectome_white_1986_L4.csv\n", + "c302 >>> No matching cell for CEPshVL\n", + "c302 >>> No matching cell for CEPshVR\n", + "c302 >>> Opened file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/aconnectome_white_1986_L4.csv\n", + "c302 >>> Writing generated network to: /Users/padraig/c302/examples/test/images/c302_C1_Oscillator.net.nml\n", + "c302 >>> Saving connectivity figure to: ./images/White_L4_elec_neurons_neurons.png\n", + "\n", + "=== Generating using reader White_whole\n", + "c302 >>> Set default parameters for C\n", + "c302 >>> Set default parameters for C\n", + "c302 >>> Set default parameters for C\n", + "c302 >>> Set default parameters for C1\n", + "c302 >>> Opened file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/aconnectome_white_1986_whole.csv\n", + "c302 >>> No matching cell for pm1\n", + "c302 >>> No matching cell for pm4\n", + "c302 >>> Opened file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/aconnectome_white_1986_whole.csv\n", + "c302 >>> Writing generated network to: /Users/padraig/c302/examples/test/images/c302_C1_Oscillator.net.nml\n", + "c302 >>> Saving connectivity figure to: ./images/White_whole_exc_to_neurons.png\n", + "c302 >>> Saving connectivity figure to: ./images/White_whole_inh_to_neurons.png\n", + "c302 >>> Saving connectivity figure to: ./images/White_whole_elec_neurons_neurons.png\n", + "\n", + "=== Generating using reader VarshneyDataReader\n", + "c302 >>> Set default parameters for C\n", + "c302 >>> Set default parameters for C\n", + "c302 >>> Set default parameters for C\n", + "c302 >>> Set default parameters for C1\n", + "c302 >>> Opened the Excel file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/NeuronConnectFormatted.xlsx\n", + "c302 >>> Opened Excel file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/NeuronConnectFormatted.xlsx\n", + "c302 >>> Writing generated network to: /Users/padraig/c302/examples/test/images/c302_C1_Oscillator.net.nml\n", + "c302 >>> Saving connectivity figure to: ./images/VarshneyData_exc_to_neurons.png\n", + "c302 >>> Saving connectivity figure to: ./images/VarshneyData_elec_neurons_neurons.png\n", + "\n", + "=== Generating using reader WitvlietDataReader1\n", + "c302 >>> Set default parameters for C\n", + "c302 >>> Set default parameters for C\n", + "c302 >>> Set default parameters for C\n", + "c302 >>> Set default parameters for C1\n", + "c302 >>> Opened the Excel file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/witvliet_2020_7.xlsx\n", + "c302 >>> No matching cell for CEPshVL\n", + "c302 >>> No matching cell for CEPshDL\n", + "c302 >>> No matching cell for CEPshDR\n", + "c302 >>> No matching cell for CEPshVR\n", + "c302 >>> Opened Excel file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/witvliet_2020_7.xlsx\n", + "c302 >>> Writing generated network to: /Users/padraig/c302/examples/test/images/c302_C1_Oscillator.net.nml\n", + "c302 >>> Saving connectivity figure to: ./images/WitvlietData1_elec_neurons_neurons.png\n", + "\n", + "=== Generating using reader WitvlietDataReader2\n", + "c302 >>> Set default parameters for C\n", + "c302 >>> Set default parameters for C\n", + "c302 >>> Set default parameters for C\n", + "c302 >>> Set default parameters for C1\n", + "c302 >>> Opened the Excel file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/witvliet_2020_8.xlsx\n", + "c302 >>> No matching cell for CEPshVL\n", + "c302 >>> No matching cell for CEPshDL\n", + "c302 >>> No matching cell for CEPshDR\n", + "c302 >>> No matching cell for CEPshVR\n", + "c302 >>> Opened Excel file: /opt/homebrew/anaconda3/envs/py39n/lib/python3.9/site-packages/c302/data/witvliet_2020_8.xlsx\n", + "c302 >>> Writing generated network to: /Users/padraig/c302/examples/test/images/c302_C1_Oscillator.net.nml\n", + "c302 >>> Saving connectivity figure to: ./images/WitvlietData2_elec_neurons_neurons.png\n", + "\n", + "=== Generating using reader WormNeuroAtlasReader\n", + "c302 >>> Set default parameters for C\n", + "c302 >>> Set default parameters for C\n", + "c302 >>> Set default parameters for C\n", + "c302 >>> Set default parameters for C1\n", + "c302 >>> Initialising WormNeuroAtlasReader\n", + "c302 >>> Writing generated network to: /Users/padraig/c302/examples/test/images/c302_C1_Oscillator.net.nml\n", + "c302 >>> Saving connectivity figure to: ./images/WormNeuroAtlas_exc_to_neurons.png\n", + "c302 >>> Saving connectivity figure to: ./images/WormNeuroAtlas_inh_to_neurons.png\n", + "c302 >>> Saving connectivity figure to: ./images/WormNeuroAtlas_elec_neurons_neurons.png\n", + "Finished generation of images!\n" + ] + } + ], + "source": [ + "\n", + "from neuroml.loaders import read_neuroml2_file\n", + " \n", + "parameter_set = 'C1'\n", + "\n", + "from c302.c302_Oscillator import setup\n", + "from c302.c302_utils import generate_conn_matrix\n", + "\n", + "import matplotlib.pyplot as plt\n", + "\n", + "plt.ioff()\n", + "\n", + "for reader_module in readers.values():\n", + " \n", + " reader = reader_module[5:]\n", + " \n", + " print(\"\\n=== Generating using reader %s\"%reader)\n", + " setup(parameter_set, \n", + " generate=True, \n", + " target_directory='images',\n", + " data_reader=reader,\n", + " verbose=False)\n", + "\n", + " nml_filename = 'c302_%s_Oscillator.net.nml'%parameter_set\n", + "\n", + " nml_doc = read_neuroml2_file('images/%s'%nml_filename)\n", + " nml_doc.networks[0].id = reader.replace('Reader','').replace('Spreadsheet','SS').replace('Updated','Upd')\n", + "\n", + " generate_conn_matrix(nml_doc, save_fig_dir='./images', figsize=(6,6))\n", + " \n", + "print('Finished generation of images!')\n" + ] + }, + { + "cell_type": "markdown", + "id": "d3640706-413a-4729-850f-8073402aebd6", + "metadata": {}, + "source": [ + "|EXC|INH|GJ|\n", + "|-|-|-|\n", + "|![exc](./images/SSData_exc_to_neurons.png)|![inh](./images/SSData_inh_to_neurons.png)|![gj](./images/SSData_elec_neurons_neurons.png)|\n", + "|![exc](./images/UpdSSData_exc_to_neurons.png)|![inh](./images/UpdSSData_inh_to_neurons.png)|![gj](./images/UpdSSData_elec_neurons_neurons.png)|\n", + "|![exc](./images/UpdSSData2_exc_to_neurons.png)|![inh](./images/UpdSSData2_inh_to_neurons.png)|![gj](./images/UpdSSData2_elec_neurons_neurons.png)|\n", + "|![exc](./images/OpenWorm_exc_to_neurons.png)|![inh](./images/OpenWorm_inh_to_neurons.png)|![gj](./images/OpenWorm_elec_neurons_neurons.png)|\n", + "|![exc](./images/White_whole_exc_to_neurons.png)|![inh](./images/White_whole_inh_to_neurons.png)|![gj](./images/White_whole_elec_neurons_neurons.png)|\n", + "|![exc](./images/VarshneyData_exc_to_neurons.png)|![inh](./images/VarshneyData_inh_to_neurons.png)|![gj](./images/VarshneyData_elec_neurons_neurons.png)|\n", + "|![exc](./images/WitvlietData2_exc_to_neurons.png)|![inh](./images/WitvlietData2_inh_to_neurons.png)|![gj](./images/WitvlietData2_elec_neurons_neurons.png)|\n", + "|![exc](./images/WormNeuroAtlas_exc_to_neurons.png)|![inh](./images/WormNeuroAtlas_inh_to_neurons.png)|![gj](./images/WormNeuroAtlas_elec_neurons_neurons.png)|\n", + "\n" + ] }, { "cell_type": "code", "execution_count": null, - "id": "74790762-7d9e-49dc-8d5c-ffcab50bf9ec", + "id": "2b476857-b458-485b-8da7-88546f0fc308", "metadata": {}, "outputs": [], "source": [] @@ -424,7 +579,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.18" + "version": "3.9.16" } }, "nbformat": 4, diff --git a/examples/test/images/OpenWorm_elec_neurons_neurons.png b/examples/test/images/OpenWorm_elec_neurons_neurons.png new file mode 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b/examples/test/images/WormNeuroAtlas_inh_to_neurons.png new file mode 100644 index 00000000..dd893fa1 Binary files /dev/null and b/examples/test/images/WormNeuroAtlas_inh_to_neurons.png differ diff --git a/examples/test/test_nwa.py b/examples/test/test_nwa.py index c967db25..e5b906dc 100644 --- a/examples/test/test_nwa.py +++ b/examples/test/test_nwa.py @@ -10,14 +10,16 @@ # will merge bilateral pairs of neurons (AVAL/R as AVA). # atlas = wa.NeuroAtlas(merge_bilateral=True, merge_dorsoventral=False, # merge_numbered=False, merge_AWC=False) + metadata = atlas.get_metadata() + for m in metadata: print("\n%s:"%(m,)) for e in metadata[m]: print(" %s:\t%s"%(e,metadata[m][e])) -test_cells = ['ADAL','ADEL','RIAL', 'VD9'] +test_cells = ['ADAL','ADEL','RIAL', 'VA3', 'VD3'] for c in test_cells: atlas.everything_about(c) @@ -27,8 +29,6 @@ def get_info(a): print("Array %s, %s"%(a.dtype, a.shape)) print(a) -gj = atlas.get_gap_junctions() -print(get_info(gj)) for index in range(len(atlas.neuron_ids)): neuron = atlas.neuron_ids[index] @@ -36,10 +36,32 @@ def get_info(a): print("Index %i: %s = %s"%(index, neuron, ai)) assert(index==ai) +print("------ Gap junctions: ------ ") +gj = atlas.get_gap_junctions() +print(get_info(gj)) + +print("------ Chem syns: ------ ") +cs = atlas.get_chemical_synapses() +print(get_info(cs)) + +print("------ Anatomical conn: ------ ") +ac = atlas.get_anatomical_connectome() +print(get_info(ac)) + + +syn_sign = wa.SynapseSign() + +for nt in ['Glu', 'ACh', 'GABA']: + ns = syn_sign.get_neurons_producing(nt, mode='dominant') + print("------ Neurons producing %s as dominant NT (%i) ------ "%(nt, len(ns))) + print(ns) + ns = syn_sign.get_neurons_producing(nt, mode='alternative') + print("------ Neurons producing %s as alternative NT (%i) ------ "%(nt, len(ns))) + print(ns) + for c in test_cells: print("------------ ") print("Connection info on %s, ais: %s"%(c, atlas.ids_to_ai(c))) - print(c)