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Adding generated mdf files and images for pynn based examples
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,191 @@ | ||
| HH: | ||
| format: ModECI MDF v0.4 | ||
| graphs: | ||
| HH: | ||
| notes: 'Example: HH' | ||
| nodes: | ||
| pop0: | ||
| metadata: | ||
| color: 1 0 0 | ||
| radius: 20 | ||
| region: region1 | ||
| parameters: | ||
| cm: | ||
| value: | ||
| - 0.2 | ||
| i_offset: | ||
| value: | ||
| - 0.05 | ||
| tau_syn_E: | ||
| value: | ||
| - 0.2 | ||
| tau_syn_I: | ||
| value: | ||
| - 2.0 | ||
| v_init: | ||
| value: | ||
| - -65.0 | ||
| v_offset: | ||
| value: | ||
| - -63.0 | ||
| e_rev_E: | ||
| value: | ||
| - 0.0 | ||
| e_rev_I: | ||
| value: | ||
| - -80.0 | ||
| e_rev_K: | ||
| value: | ||
| - -90.0 | ||
| e_rev_Na: | ||
| value: | ||
| - 50.0 | ||
| e_rev_leak: | ||
| value: | ||
| - -65.0 | ||
| g_leak: | ||
| value: | ||
| - 0.01 | ||
| gbar_K: | ||
| value: | ||
| - 6.0 | ||
| gbar_Na: | ||
| value: | ||
| - 20.0 | ||
| MSEC: | ||
| value: | ||
| - 0.001 | ||
| MVOLT: | ||
| value: | ||
| - 0.001 | ||
| NFARAD: | ||
| value: | ||
| - 1.0e-09 | ||
| spike: | ||
| value: | ||
| - 0 | ||
| v: | ||
| default_initial_value: v_init * MVOLT | ||
| time_derivative: (MVOLT * (iMemb / cm) / MSEC) + (iSyn | ||
| / (cm * NFARAD)) | ||
| m: | ||
| time_derivative: (alpham * (1 - m) - betam * m) / MSEC | ||
| default_initial_value: | ||
| - 0 | ||
| h: | ||
| time_derivative: (alphah * (1 - h) - betah * h) / MSEC | ||
| default_initial_value: | ||
| - 0 | ||
| n: | ||
| time_derivative: (alphan * (1 - n) - betan * n) / MSEC | ||
| default_initial_value: | ||
| - 0 | ||
| iSyn: | ||
| value: synapses_i | ||
| iLeak: | ||
| value: g_leak * (e_rev_leak - (v / MVOLT)) | ||
| iNa: | ||
| value: gbar_Na * (m * m * m) * h * (e_rev_Na - (v / MVOLT)) | ||
| iK: | ||
| value: gbar_K * (n * n * n * n) * (e_rev_K - (v / MVOLT)) | ||
| iMemb: | ||
| value: iLeak + iNa + iK + i_offset | ||
| alpham: | ||
| value: 0.32 * (13 - (v / MVOLT) + v_offset) / (numpy.exp((13 | ||
| - (v / MVOLT) + v_offset) / 4.0) - 1) | ||
| betam: | ||
| value: 0.28 * ((v / MVOLT) - v_offset - 40) / (numpy.exp(((v | ||
| / MVOLT) - v_offset - 40) / 5.0) - 1) | ||
| alphah: | ||
| value: 0.128 * numpy.exp((17 - (v / MVOLT) + v_offset) | ||
| / 18.0) | ||
| betah: | ||
| value: 4.0 / (1 + numpy.exp((40 - (v / MVOLT) + v_offset) | ||
| / 5)) | ||
| alphan: | ||
| value: 0.032 * (15 - (v / MVOLT) + v_offset) / (numpy.exp((15 | ||
| - (v / MVOLT) + v_offset) / 5) - 1) | ||
| betan: | ||
| value: 0.5 * numpy.exp((10 - (v / MVOLT) + v_offset) / | ||
| 40) | ||
| input_ports: | ||
| spike_in_E: | ||
| shape: | ||
| - 1 | ||
| reduce: add | ||
| spike_in_I: | ||
| shape: | ||
| - 1 | ||
| reduce: add | ||
| synapses_i: {} | ||
| output_ports: | ||
| spike: | ||
| value: spike | ||
| v: | ||
| value: v | ||
| m: | ||
| value: m | ||
| h: | ||
| value: h | ||
| n: | ||
| value: n | ||
| notes: "Cell: [Cell(notes=None, id='testcell', parameters={'i_offset':\ | ||
| \ 0.05}, neuroml2_source_file=None, lems_source_file=None,\ | ||
| \ neuroml2_cell=None, pynn_cell='HH_cond_exp', arbor_cell=None,\ | ||
| \ bindsnet_node=None)] is defined in None and in Lems is:\ | ||
| \ Component, id: testcell, type: HH_cond_exp,\n parameters:\ | ||
| \ {'cm': '0.2', 'i_offset': 0.05, 'tau_syn_E': '0.2', 'tau_syn_I':\ | ||
| \ '2.', 'v_init': '-65.', 'v_offset': '-63.', 'e_rev_E': '0.',\ | ||
| \ 'e_rev_I': '-80.', 'e_rev_K': '-90.', 'e_rev_Na': '50.',\ | ||
| \ 'e_rev_leak': '-65.', 'g_leak': '0.01', 'gbar_K': '6.',\ | ||
| \ 'gbar_Na': '20.'}\n parent: None\n" | ||
| InputList_stim: | ||
| parameters: | ||
| delay: | ||
| value: | ||
| - 0.2 | ||
| duration: | ||
| value: | ||
| - 0.6 | ||
| amplitude: | ||
| value: | ||
| - 0.0 | ||
| weight: | ||
| value: | ||
| - 0.0 | ||
| i: | ||
| conditions: | ||
| condition_0: | ||
| test: t < delay | ||
| value: '0' | ||
| condition_1: | ||
| test: t >= delay and t < duration + delay | ||
| value: weight * amplitude | ||
| condition_2: | ||
| test: t >= duration + delay | ||
| value: '0' | ||
| t: | ||
| default_initial_value: 0 | ||
| time_derivative: '1' | ||
| input_ports: | ||
| spike_input: | ||
| shape: | ||
| - 1 | ||
| reduce: add | ||
| output_ports: | ||
| i: | ||
| value: i | ||
| notes: "Cell: [InputSource(notes=None, id='i_clamp', parameters={'amplitude':\ | ||
| \ 'input_amp', 'start': 200.0, 'stop': 800.0}, neuroml2_source_file=None,\ | ||
| \ neuroml2_input=None, lems_source_file=None, pynn_input='DCSource')]\ | ||
| \ is defined in None and in Lems is: Component, id: i_clamp,\ | ||
| \ type: pulseGenerator,\n parameters: {'delay': '200.0ms',\ | ||
| \ 'duration': '600.0ms', 'amplitude': '0.0nA'}\n parent:\ | ||
| \ None\n" | ||
| edges: | ||
| Edge InputList_stim to pop0: | ||
| name: Edge InputList_stim to pop0 | ||
| sender_port: i | ||
| receiver_port: synapses_i | ||
| sender: InputList_stim | ||
| receiver: pop0 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,24 @@ | ||
| <neuroml xmlns="http://www.neuroml.org/schema/neuroml2" xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.xsd" id="HH"> | ||
| <notes>Generated by NeuroMLlite v0.5.5 | ||
| Generated network: HH | ||
| Generation seed: 1234 | ||
| NeuroMLlite parameters: | ||
| input_amp = 0</notes> | ||
| <pulseGenerator id="i_clamp" delay="200.0ms" duration="600.0ms" amplitude="0.0nA"/> | ||
| <HH_cond_exp id="testcell" cm="0.2" i_offset="0.05" tau_syn_E="0.2" tau_syn_I="2." v_init="-65." v_offset="-63." e_rev_E="0." e_rev_I="-80." e_rev_K="-90." e_rev_Na="50." e_rev_leak="-65." g_leak="0.01" gbar_K="6." gbar_Na="20."/> | ||
| <alphaCurrSynapse id="ampaSyn" tau_syn="20."/> | ||
| <network id="HH"> | ||
| <notes>Example: HH</notes> | ||
| <property tag="recommended_dt_ms" value="0.01"/> | ||
| <property tag="recommended_duration_ms" value="1000.0"/> | ||
| <population id="pop0" component="testcell" size="1" type="populationList"> | ||
| <property tag="color" value="1 0 0"/> | ||
| <property tag="radius" value="20"/> | ||
| <property tag="region" value="region1"/> | ||
| <instance id="0"> | ||
| <location x="966.453535692138757" y="44.073259917535268" z="7.491470058587191"/> | ||
| </instance> | ||
| </population> | ||
| <inputList id="stim" population="pop0" component="i_clamp"/> | ||
| </network> | ||
| </neuroml> |
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