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View gist:a2cc07bfeb74aeb74eed836d2f133d0d
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
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
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();
@tarelli
tarelli / BigCA1.net.nml.xmi
Last active Jan 28, 2017
Geppetto XMIs for testing
View BigCA1.net.nml.xmi
<?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
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
@tarelli
tarelli / geppetto.vm and dashboard.vm
Last active Nov 29, 2016
OSB Geppetto Channel configuration
View geppetto.vm and dashboard.vm
window.EMBEDDED = true;
window.EMBEDDEDURL = "http://0.0.0.0:3000/";
@tarelli
tarelli / gist:10278549
Last active May 17, 2016
Deploy JARs to Github/Maven
View gist:10278549
mvn install:install-file -DgroupId=edu.ucar -DartifactId=netcdf -Dversion=4.3.20 -Dfile=/Users/matteocantarelli/Documents/Development/MetaCellWorkspace/Geppetto/org.geppetto.core/lib/netcdf-4.3.20.jar -Dpackaging=jar -DgeneratePom=true -DlocalRepositoryPath=/Users/matteocantarelli/Documents/Development/MetaCellWorkspace/Geppetto/org.geppetto.maven -DcreateChecksum=true
mvn install:install-file -DgroupId=org.jscience -DartifactId=jscience -Dversion=4.3.1 -Dfile=/Users/matteocantarelli/Documents/Development/MetaCellWorkspace/Geppetto/org.geppetto.core/lib/jscience-4.3.1.jar -Dpackaging=jar -DgeneratePom=true -DlocalRepositoryPath=/Users/matteocantarelli/Documents/Development/MetaCellWorkspace/Geppetto/org.geppetto.maven -DcreateChecksum=true
mvn install:install-file -DgroupId=org.scala-saddle -DartifactId=jhdf5 -Dversion=13.06.2 -Dfile=/Users/matteocantarelli/Desktop/jhdf5.jar/ -Dpackaging=jar -DgeneratePom=true -DlocalRepositoryPath=/Users/matteocantarelli/Documents/Development/MetaCellWorkspace/Geppetto
@tarelli
tarelli / nmlException.txt
Created Feb 13, 2016
NML input String which generates the exception
View nmlException.txt
<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
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
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)