YAML Configuration#

The MiV-Simulator leverages a YAML-based configuration format to declaratively describe complex neural systems. The user-specified configuration files are used to generate concrete instantiations of the system used in the simulation. For example, a YAML user configuration may describe the number and distribution of neurons which is used during network construction to determine the exact sampled soma positions.

The different configuration templates that are used for simulation construction are described below.

Simulation Configuration#

../MiV-Simulator-Cases/1-construction/config/Microcircuit_Small.yaml#
 1## Model configuration of microcircuit network
 2Model Name: Microcircuit_Small
 3Dataset Name: Microcircuit_Small
 4Definitions: !include Definitions.yaml
 5Global Parameters: !include Global.yaml
 6Geometry: !include Geometry_Small.yaml
 7Random Seeds: !include Random.yaml
 8Connection Generator: !include Microcircuit_Connections.yaml
 9Cell Data: MiV_Cells_Microcircuit_Small_20220410.h5
10Connection Data: MiV_Connections_Microcircuit_Small_20220410.h5
11Recording: !include Recording.yaml
12Stimulus: !include Input_Configuration.yaml
13Analysis: !include Analysis_Configuration.yaml
14Cell Types:
15  PYR:
16    template: PoolosPyramidalCell
17    synapses:
18      density: !include PYR_synapse_density.yaml
19  OLM:
20    template: OLMCell
21    synapses:
22      density: !include OLM_synapse_density.yaml
23  PVBC:
24    template: PVBasketCell
25    synapses:
26      density: !include PVBC_synapse_density.yaml
27  STIM:
28    template: VecStim
29    spike train:
30      namespace: Input Spikes
31      attribute: Spike Train
../MiV-Simulator-Cases/1-construction/config/Connection_Velocity.yaml#
1PYR: 250.0
2STIM: 250.0
3PVBC: 250.0
4OLM: 250.0
../MiV-Simulator-Cases/1-construction/config/Definitions.yaml#
 1# Common definitions used in model configuration of neuron and network models
 2SWC Types:
 3  soma:   1
 4  axon:   2
 5  basal:  3
 6  apical: 4
 7  trunk:  5
 8  tuft:   6
 9  ais:    7
10  hillock: 8
11Synapse Types:
12  excitatory:    0
13  inhibitory:    1
14  modulatory:    2
15Synapse Mechanisms:
16  AMPA:    0
17  GABA_A:  1
18  GABA_B:  2
19  NMDA:    30
20Layers:
21  Hilus: 0
22  GCL:   1  ## Granule cell
23  IML:   2  ## Inner molecular
24  MML:   3  ## Middle molecular
25  OML:   4  ## Outer molecular
26  SO:    5  ## Oriens
27  SP:    6  ## Pyramidale
28  SL:    7  ## Lucidum
29  SR:    8  ## Radiatum
30  SLM:   9  ## Lacunosum-moleculare
31Populations:
32  STIM: 0
33  PYR:  100
34  PVBC:  101
35  OLM:  102
36Input Selectivity Types:
37  random: 0
38  constant: 1
../MiV-Simulator-Cases/1-construction/config/Geometry_Small.yaml#
 1# 80 neurons
 2# 200 um electrode spacing
 3# 30 um electrode size
 4Parametric Surface:
 5  Origin:
 6    U: median
 7    V: median
 8    L: max
 9  Layer Extents:
10    SO:  [[0.0,0.0,0.0], [1000.0,1000.0,100.0]]
11    SP:  [[0.0,0.0,100.0],[1000.0,1000.0,150.0]]
12    SR:  [[0.0,0.0,150.0], [1000.0,1000.0,350.0]]
13    SLM: [[0.0, 0.0,350.0], [1000.0, 1000.0, 450.0]]
14  Rotation: [0.0, 0.0, 0.0]
15# Range of 
16Cell Constraints: # Constraint in Z-Height
17  PC:
18    SP: [100., 120.] # Lee, ..., Soltesz. Neuron 2014
19  PVBC:
20    SR: [150., 200.0] # Booker, Vida. Cell & Tissue Research 2018
21Cell Distribution:
22  STIM:
23    SO:  0
24    SP:  10
25    SR:  0
26    SLM: 0
27  PYR:
28    SO:  0
29    SP:  80
30    SR:  0
31    SLM: 0
32  PVBC: #5530
33    SO:  35
34    SP:  10
35    SR:  8
36    SLM: 0
37  OLM: #1640
38    SO:  44
39    SP:  0
40    SR:  0
41    SLM: 0

Synapse / Dentrites Configuration#

../MiV-Simulator-Cases/1-construction/config/Microcircuit_Connections.yaml#
  1Synapse Mechanisms:
  2  AMPA: LinExp2Syn
  3  NMDA: LinExp2SynNMDA
  4  GABA_A: LinExp2Syn
  5  GABA_B: LinExp2Syn
  6Synapse Parameter Rules: !include Synapse_Parameter_Rules.yaml
  7Axon Extent: !include Axon_Extent.yaml
  8Connection Velocity: !include Connection_Velocity.yaml
  9Synapses:
 10  PYR:
 11    STIM:
 12      type: excitatory
 13      sections: [soma, basal, apical, apical]
 14      layers: [SP, SO, SR, SLM]
 15      proportions: [0.5, 0.5, 0.5, 0.5]
 16      mechanisms:
 17        AMPA:
 18          tau_rise: 0.5
 19          tau_decay: 3.0
 20          e: 0
 21          g_unit: 0.00001
 22          weight: 1.0
 23        NMDA:
 24          g_unit: 0.00001
 25          weight: 1.0
 26    PYR:
 27      type: excitatory
 28      sections: [soma, basal, apical, apical]
 29      layers: [SP, SO, SR, SLM]
 30      proportions: [0.5, 0.5, 0.5, 0.5]
 31      mechanisms:
 32        AMPA:
 33          tau_rise: 0.5
 34          tau_decay: 3.0
 35          e: 0
 36          g_unit: 0.00001
 37          weight: 1.0
 38        NMDA:
 39          g_unit: 0.00001
 40          weight: 1.0
 41    PVBC:
 42      type: inhibitory
 43      sections: [soma, basal, apical, ais, ais]
 44      layers: [SP, SO, SR, SP, SR]
 45      proportions: [1.0, 0.5, 1.0, 1.0, 1.0]
 46      mechanisms:
 47        GABA_A:
 48          tau_rise: 0.30
 49          tau_decay: 6.2
 50          e: -60
 51          g_unit: 0.005
 52          weight: 1.0
 53    OLM:
 54      type: inhibitory
 55      sections: [soma, basal, apical]
 56      layers: [SO, SO, SLM]
 57      proportions: [1.0, 0.5, 1.0]
 58      mechanisms:
 59        GABA_A:
 60          tau_rise: 0.50
 61          tau_decay: 9.0
 62          e: -60
 63          g_unit: 0.0033
 64          weight: 1.0
 65  PVBC:
 66    PYR:
 67      type: excitatory
 68      sections: [soma, apical, apical, basal]
 69      layers: [SP, SLM, SR, SO]
 70      proportions: [0.5, 0.5, 0.5, 0.5]
 71      mechanisms:
 72        AMPA:
 73          tau_rise: 0.5
 74          tau_decay: 3.0
 75          e: 0
 76          g_unit: 0.0005
 77          weight: 1.0
 78    STIM:
 79      type: excitatory
 80      sections: [soma, apical, apical, basal]
 81      layers: [SP, SLM, SR, SO]
 82      proportions: [0.5, 0.5, 0.5, 0.5]
 83      mechanisms:
 84        AMPA:
 85          tau_rise: 0.5
 86          tau_decay: 3.0
 87          e: 0
 88          g_unit: 0.0002
 89          weight: 0.1
 90    PVBC:
 91      type: inhibitory
 92      sections: [soma, apical, apical, basal]
 93      layers: [SP, SP, SR, SO]
 94      proportions: [1.0, 1.0, 1.0, 1.0]
 95      mechanisms:
 96        GABA_A:
 97          tau_rise: 0.08
 98          tau_decay: 4.8
 99          e: -60
100          g_unit: 0.001
101          weight: 1.0
102    OLM:
103      type: inhibitory
104      sections: [apical]
105      layers: [SLM]
106      proportions: [1.0]
107      mechanisms:
108        GABA_A:
109          tau_rise: 0.08
110          tau_decay: 4.8
111          e: -60
112          g_unit: 0.001
113          weight: 1.0
114  OLM:
115    PYR:
116      type: excitatory
117      sections: [apical, basal, basal]
118      layers: [SLM, SR, SO]
119      proportions: [1.0, 1.0, 1.0]
120      mechanisms:
121        AMPA:
122          tau_rise: 0.5
123          tau_decay: 3.0
124          e: 0
125          g_unit: 0.001
126          weight: 1.0
127    PVBC:
128      type: inhibitory
129      sections: [basal, soma, apical]
130      layers: [SO, SP, SR]
131      proportions: [1.0, 1.0, 1.0]
132      mechanisms:
133        GABA_A:
134          tau_rise: 0.08
135          tau_decay: 4.8
136          e: -60
137          g_unit: 0.0001
138          weight: 1.0
../MiV-Simulator-Cases/1-construction/config/Axon_Extent.yaml#
 1# Axonal extent in um [S-T, M-L]
 2STIM:
 3  default:
 4    width: [1000.0, 1000.0]
 5    offset: [0,0]
 6PYR:
 7  default:
 8    width: [1000.0, 1000.0]
 9    offset: [0,0]
10PVBC: # soma in layer pyramidale, PV+
11  default:
12    width: [1000.0, 1000.0]
13    offset: [0,0]
14OLM: # soma in layer oriens, SOM+
15  default:
16    width: [840.0, 500.0]
17    offset: [0,0]
../MiV-Simulator-Cases/1-construction/config/OLM_synapse_density.yaml#
 1## OLM cell synapse density configuration
 2# number of inhibitory and excitatory connections from conndata_403.data
 3# total dendritic length of 2000 um estimated from https://onlinelibrary.wiley.com/doi/full/10.1111/ejn.14549
 4# Assumed synapses distributed evenly across layers
 5
 6basal:
 7  excitatory:
 8    SO:
 9      mean: 3.60
10      variance: 0.1
11  inhibitory:
12    SO:
13      mean: 1.06
14      variance: 0.1
../MiV-Simulator-Cases/1-construction/config/PVBC_synapse_density.yaml#
 1## PV Basket Cell (PVBC) synapse density configuration
 2
 3## https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6782984/
 4
 5apical:
 6  excitatory:
 7    SLM:
 8      mean: 1.43
 9      variance: 0.1
10    SR:
11      mean: 4.16
12      variance: 0.1
13
14  inhibitory:
15    SLM:
16      mean: 0.27
17      variance: 0.1
18    SR:
19      mean: 0.16
20      variance: 0.1
21basal:
22  excitatory:
23    SO:
24      mean: 3.61
25      variance: 0.1
26  inhibitory:
27    SO:
28      mean: 3.44
29      variance: 0.1
30soma:
31  inhibitory:
32    default:
33      mean: 0.18
34      variance: 0.1
35  excitatory:
36    default:
37      mean: 0.40
38      variance: 0.1
../MiV-Simulator-Cases/1-construction/config/PYR_synapse_density.yaml#
 1## PYR synapse density configuration.
 2## https://www.sciencedirect.com/science/article/pii/S0306452200004966?via%3Dihub
 3
 4apical:
 5  excitatory:
 6    SLM:
 7      mean: 0.90
 8      variance: 0.1
 9    SR:
10      mean: 3.52
11      variance: 0.1
12
13  inhibitory:
14    SLM:
15      mean: 0.15
16      variance: 0.1
17    SR:
18      mean: 0.11
19      variance: 0.1
20basal:
21  excitatory:
22    SO:
23      mean: 3.08
24      variance: 0.1
25  inhibitory:
26    SO:
27      mean: 0.11
28      variance: 0.1
29soma:
30  inhibitory:
31    default:
32      mean: 0.20
33      variance: 0.1
34  excitatory:
35    default:
36      mean: 0.0
37      variance: 0.1
38
39ais:
40  inhibitory: # Inhibitory https://www.ncbi.nlm.nih.gov/pubmed/20034063
41    default: # layer
42      mean: 0.68
43      variance: 0.01
../MiV-Simulator-Cases/1-construction/config/PYR_SoldadoMagraner.yaml#
 1##
 2## Conditioning by Subthreshold Synaptic Input Changes the Intrinsic
 3## Firing Pattern of CA3 Hippocampal Neurons.  Saray Soldado-Magraner,
 4## Federico Brandalise, Suraj Honnuraiah, Michael Pfeiffer, Marie
 5## Moulinier, Urs Gerber, Rodney Douglas. J Neurophysiology, 2019.
 6##
 7
 8soma:
 9  cable:
10    L:
11      value: 50.0      #Length of soma (um)
12    diam:
13      value: 50.0   #Diameter of soma (um)
14    Ra:
15      value: 150.0
16    cm:
17      value: 1.41
18  pas:
19    g:
20      value: 4.0e-5
21    e:
22      value: -60.0
23
24# Spiking conductances    
25  na3:
26    gbar:
27      value: 0.04
28  kdr:
29    gkdrbar:
30      value: 0.01
31  kap:
32    gkabar:
33      value: 0.07
34    
35# Firing pattern conductances 
36  km:
37    gbar:
38      value: 0.0006
39  kd:
40    gkdbar:
41      value: 0.00045
42  kd_slow:
43    gkdbar:
44      value: 0
45  cal:
46    gcalbar:
47      value: 0.001
48  can:
49    gcanbar:
50      value: 0.001
51  cat:
52    gcatbar:
53      value: 0.001
54  cagk:
55    gbar:
56      value: 0.0001
57  cacum:
58    depth:
59      value: 25.0
60
../MiV-Simulator-Cases/1-construction/config/Synapse_Parameter_Rules.yaml#
 1Exp2Syn:
 2    mech_file: exp2syn.mod
 3    mech_params:
 4      - tau1
 5      - tau2
 6      - e
 7    netcon_params:
 8      weight: 0
 9    netcon_state: {}
10LinExp2Syn:
11    mech_file: lin_exp2syn.mod
12    mech_params:
13      - tau_rise
14      - tau_decay
15      - e
16    netcon_params:
17      weight: 0
18      g_unit: 1
19    netcon_state: {}
20LinExp2SynNMDA:
21    mech_file: lin_exp2synNMDA.mod
22    mech_params:
23      - tau_rise
24      - tau_decay
25      - e
26      - mg
27      - Kd
28      - gamma
29      - vshift
30    netcon_params:
31      weight: 0
32      g_unit: 1
33    netcon_state: {}

Input / Stimulation Configuration#

../MiV-Simulator-Cases/1-construction/config/Input_Configuration.yaml#
 1Spatial Resolution: 3.0  # cm
 2Temporal Resolution: 1.0  # ms
 3Equilibration Duration: 250. # ms
 4
 5Selectivity Type Probabilities:
 6  STIM:
 7    constant: 1.0
 8  PYR:
 9    constant: 1.0
10  PVBC:
11    constant: 1.0
12  OLM:
13    constant: 1.0
14
15
16Peak Rate:
17  STIM:
18    constant: 80.0
19  PYR:
20    constant: 20.0
21  PVBC:
22    constant: 21.0
23  OLM:
24    constant: 10.0
25
26
27
28Global Oscillation:
29  frequency: 5.0 # oscillation frequency
30  Phase Distribution:  # parameters of phase distribution along septotemporal axis
31    slope: 16.5
32    offset: 0.0
33  Phase Modulation: # cell type-specific modulation
34    PYR:
35      phase range: [0, 150]
36      depth: 0.5
37    PVBC:
38      phase range: [180, 540]
39      depth: 0.8
40    OLM:
41      phase range: [200, 560]
42      depth: 0.8
43
44Arena:
45  A:
46    Domain:
47      vertices: [[-100, -100], [-100, 100], [100, 100], [100, -100]]
48      simplices: [[0,1], [1,2], [2,3], [3,0]]
49
50    Trajectory:
51      Diag:
52        path: [[-100, -100], [100, 100]]
53        run velocity: 30.  # cm/s
54
55
56    default run velocity: 30.  # cm/s
57
58  Calibration:
59    Domain:
60      vertices: [[-32.5, -32.5], [-32.5, 32.5], [32.5, 32.5], [32.5, -32.5]]
61      simplices: [[0,1], [1,2], [2,3], [3,0]]

Post-Process Configuration#

../MiV-Simulator-Cases/1-construction/config/Recording.yaml#
 1## Recording configuration for field potentials and intracellular quantities
 2Intracellular:
 3  Network default:
 4    fraction: 0.2
 5    dt: 0.1
 6    section quantity:
 7      v:
 8        swc types:
 9          - soma
10  Network clamp default:
11    dt: 0.025
12    section quantity:
13      v:
14        swc types:
15          - soma
16          - ais
17          - apical
18          - basal
19  Network clamp axial current:
20    dt: 0.025
21    section quantity:
22      start.v:
23        variable: v
24        loc:
25          - 1e-3
26          - 1e-3
27        swc types:
28          - apical
29          - basal
30      mid.v:
31        variable: v
32        loc:
33          - 0.5
34          - 0.5
35          - 0.5
36        swc types:
37          - soma
38          - apical
39          - basal
40  Network clamp inh synaptic:
41    dt: 0.1
42    reduce: True
43    section quantity:
44      v:
45        swc types:
46          - soma
47          - hillock
48          - apical
49          - basal
50    synaptic quantity:
51      i:
52        syn types:
53          - inhibitory
54  Network clamp exc synaptic:
55    dt: 0.1
56    reduce: True
57    section quantity:
58      v:
59        swc types:
60          - soma
61          - hillock
62          - apical
63          - basal
64    synaptic quantity:
65      i:
66        syn types:
67          - excitatory
68  Network clamp all synaptic:
69    dt: 0.5
70    reduce: True
71    section quantity:
72      v:
73        swc types:
74          - soma
75          - ais
76          - hillock
77          - apical
78          - basal
79    synaptic quantity:
80      i: {}
81LFP:
82  # Configuration for virtual local field potential recordings
83  Electrode 0:
84    rho: 333.0
85    position: [-1205.5, 2700.3, -211.7]
86    maxEDist: 100.
87    fraction: .1
88    dt: 0.1
89  Electrode 1:
90    rho: 333.0
91    position: [-1205.5, 2700.3, -411.7]
92    maxEDist: 100.
93    fraction: .1
94    dt: 0.1
../MiV-Simulator-Cases/1-construction/config/Analysis_Configuration.yaml#
 1Firing Rate Inference:
 2  Temporal Resolution: 1.  # ms
 3  BAKS Alpha: 4.7725100028345535
 4  BAKS Beta: 0.41969058927343522
 5  Pad Duration: 1000.  # ms
 6
 7Mutual Information:
 8  Spatial Resolution: 5.  # cm
 9
10Place Fields:
11  Minimum Width: 10.
12  Minimum Rate: 1.

Miscellaneous Configuration#

../MiV-Simulator-Cases/1-construction/config/Random.yaml#
 1## Random seeds used in model configuration of dentate gyrus network
 2Synapse Locations:                        0 ## Distributing synapse locations
 3Connectivity Clustering:             1.5e+6 ## Clustering of connections from same source
 4Distance-Dependent Connectivity:     2.0e+6 ## Generating distance-dependent connectivity
 5Input Selectivity:                   4.0e+6 ## Generating stimulus and proxy input cell selectivity features
 6Input Remap:                         5.0e+6 ## Remapping of stimulus input cells
 7Random Connectivity:                 6.0e+6 ## Computing random connectivity (not distance-dependent)
 8Normal Weights:                     15.0e+6 ## Normal weights
 9Synaptic Integration Optimization:  14.0e+6 ## Choosing synapses and branches for optimization of synaptic integration in GCs.
10EPSC Attenuation Optimization:      16.0e+6 ## Choosing branches for optimization of EPSC attenuation in GCs.
11Synapse Projection Partitions:      18.0e+6 ## Partitioning synapse locations by projection
12Intracellular Recording Sample:     24.0e+6 ## Selecting cells to sample intracellular quantities from
13Local Field Potential:              30.0e+6 ## Selecting cells to sample extracellular voltage from
14Input Spiketrains:                  50.0e+6 ## Spike trains of stimulus and proxy input cells
15Soma Locations:                     60.0e+6 ## Soma locations
16Gap Junctions:                      70.0e+6 ## Soma locations
../MiV-Simulator-Cases/1-construction/config/Global.yaml#
1celsius: 35.0