View gist:a2cc07bfeb74aeb74eed836d2f133d0d
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10523 git clone --branch 7.6.2 https://github.com/neuronsimulator/nrn | |
10524 cd nrn | |
10525 ./configure --without-x --with-nrnpython=python3 --without-paranrn --prefix="/Users/matteocantarelli/.pyenv/versions/netpynePython37/bin/nrn/" --without-iv | |
10526 ./build.sh | |
10527 ./configure --without-x --with-nrnpython=python3 --without-paranrn --prefix="/Users/matteocantarelli/.pyenv/versions/netpynePython37/bin/nrn/" --without-iv | |
10528 cd src/nrnpython | |
10529 cp ~/Documents/Development/nrn/src/nrnpython/setup.cfg . | |
10530 cd .. | |
10531 history | grep make | |
10532 make --silent -j4 |
View gist:4711f73ab805e8b06d72874ce303c076
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nwb.group1.time | |
nwb.group1.stimulus_1 | |
nwb.group1.stimulus_2 | |
group1.stimulus_3 | |
group1.stimulus_4 | |
group1.stimulus_5 | |
group2.time | |
group2.stimulus_1 | |
group2.stimulus_2 |
View JS analysis IV + FI
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window.plotIV = function(protocolName, e){ | |
e.preventDefault(); | |
// figure out if we have any protocol and organize into a map | |
var experiments = Project.getExperiments(); | |
var protocolExperimentsMap = {}; | |
for(var i=0; i<experiments.length; i++){ | |
if(experiments[i].getName().startsWith('[P]')){ | |
// parse protocol pattern | |
var experimentName = experiments[i].getName(); |
View BigCA1.net.nml.xmi
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<?xml version="1.0" encoding="ASCII"?> | |
<gep:GeppettoModel xmi:version="2.0" xmlns:xmi="http://www.omg.org/XMI" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:gep="https://raw.githubusercontent.com/openworm/org.geppetto.model/development/src/main/resources/geppettoModel.ecore" xmlns:gep_1="https://raw.githubusercontent.com/openworm/org.geppetto.model/development/src/main/resources/geppettoModel.ecore#//types" xmlns:gep_2="https://raw.githubusercontent.com/openworm/org.geppetto.model/development/src/main/resources/geppettoModel.ecore#//values"> | |
<libraries> | |
<types xsi:type="gep_1:CompositeType" id="hd__vhalflmin73" name="hd__vhalflmin73" superType="//@libraries.0/@types.1"> | |
<variables id="conductance" name="Conductance" types="//@libraries.1/@types.0" static="true"> | |
<initialValues key="//@libraries.1/@types.0"> | |
<value xsi:type="gep_2:PhysicalQuantity" value="10.0"> | |
<unit unit="pS"/> | |
</value> | |
</initialValues> |
View not working
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osgi> ss ckson | |
"Framework is launched." | |
id State Bundle | |
82 ACTIVE com.fasterxml.jackson.core.jackson-core_2.8.5 | |
89 ACTIVE jackson-core-asl_1.9.13 | |
90 ACTIVE jackson-mapper-asl_1.9.13 | |
145 ACTIVE com.fasterxml.jackson.core.jackson-annotations_2.8.5 | |
146 ACTIVE com.fasterxml.jackson.core.jackson-databind_2.8.5 |
View geppetto.vm and dashboard.vm
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window.EMBEDDED = true; | |
window.EMBEDDEDURL = "http://0.0.0.0:3000/"; |
View nmlException.txt
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<neuroml xmlns="http://www.neuroml.org/schema/neuroml2" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.githubusercontent.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2beta4.xsd" id="network_t3"> | |
<notes> | |
Network structure (NeuroML 2beta4) for project: t3 saved with neuroConstruct v1.7.1 on: 19:48:05, 22-Oct-15 | |
Cell Group: CG_C04_RS_sm contains 20 cells | |
Cell Group: CG_C04_AxAx_sm contains 10 cells | |
Cell Group: CG_C04_Bask_sm contains 10 cells | |
Cell Group: CG_C04_LTS_sm contains 10 cells | |
Cell Group: CG_C04_FRB_sm contains 6 cells | |
Network connection: RS_RS_gap_sm contains 24 individual synaptic connections | |
Network connection: AxAx_AxAx_gap_sm contains 20 individual synaptic connections |
View gist:66f24490e62b0d210491
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WARN : org.geppetto.core.recordings.GeppettoRecordingCreator - Creating variable net1(net1).muscle(SingleCompMuscleCell)[0].biophys(biophys).membraneProperties(membraneProperties).ca_boyle_all(ca_boyle_all).iDensity(StateVariable) 0 | |
WARN : org.geppetto.core.recordings.GeppettoRecordingCreator - Creating variable net1(net1).muscle(SingleCompMuscleCell)[0].caConc(StateVariable) 1 | |
WARN : org.geppetto.core.recordings.GeppettoRecordingCreator - Creating variable net1(net1).muscle(SingleCompMuscleCell)[0].biophys(biophys).membraneProperties(membraneProperties).k_fast_all(k_fast_all).iDensity(StateVariable) 2 | |
WARN : org.geppetto.core.recordings.GeppettoRecordingCreator - Creating variable time(StateVariable) 3 | |
WARN : org.geppetto.core.recordings.GeppettoRecordingCreator - Creating variable net1(net1).neuron(generic_iaf_cell)[0].v(StateVariable) 4 | |
WARN : org.geppetto.core.recordings.GeppettoRecordingCreator - Creating variable net1(net1).muscle(SingleCompMuscleCell)[0].biophys(biophys).membraneProperties(membraneProp |
View gist:adbe0524ac4bb9adb2e9
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Valid paths | |
acnet2.pyramidals_48[4].soma.v (acnet2.pyramidals_48[4].soma.v might not always be possible because the name is optional) | |
acnet2.pyramidals_48[4].soma.spiking | |
acnet2.pyramidals_48[4].apical2.spiking | |
(Not for now, short/medium term) //acnet2.pyramidals_48[4].soma.bioPhys1.membraneProperties.Kdr_bask_soma_group.iDensity | |
acnet2.pyramidals_48[4].bioPhys1.membraneProperties.Kdr_bask_soma_group.erev (It's valid without the morphology because it's a parameter) |
View Past LEMS component problem
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server-3.6.3.RELEASE/geppettoTmp/RUN/projects/17/NEURONModel_18012016_101203/BackgroundRandomIClamps.mod at: | |
[2016-01-18 10:12:04.851] ERROR Thread-67 System.err java.lang.NumberFormatException: For input string: "null" | |
[2016-01-18 10:12:04.851] ERROR Thread-67 System.err at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65) | |
[2016-01-18 10:12:04.851] ERROR Thread-67 System.err at java.lang.Integer.parseInt(Integer.java:492) | |
[2016-01-18 10:12:04.851] ERROR Thread-67 System.err at java.lang.Integer.parseInt(Integer.java:527) | |
[2016-01-18 10:12:04.851] ERROR Thread-67 System.err at org.neuroml.export.utils.LEMSQua |
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