Matteo Cantarelli tarelli
tarelli
/ terraform_functionality.sh
Created
March 22, 2024 16:59
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| rm -rf / |
tarelli
/ gist:a2cc07bfeb74aeb74eed836d2f133d0d
Created
September 27, 2018 16:55
NEURON installation
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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 |
tarelli
/ gist:4711f73ab805e8b06d72874ce303c076
Created
June 22, 2018 16:35
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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 |
tarelli
/ JS analysis IV + FI
Created
May 30, 2017 12:44
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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(); |
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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> |
tarelli
/ not working
Last active
January 4, 2017 14:40
Debugging Virgo 3.6.4 Spring and Jackson 2 (https://www.eclipse.org/forums/index.php/m/1751093/#msg_1751093)
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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 |
tarelli
/ geppetto.vm and dashboard.vm
Last active
November 29, 2016 16:40
OSB Geppetto Channel configuration
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| window.EMBEDDED = true; | |
| window.EMBEDDEDURL = "http://0.0.0.0:3000/"; |
tarelli
/ nmlException.txt
Created
February 13, 2016 13:29
NML input String which generates the exception
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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 |
tarelli
/ gist:66f24490e62b0d210491
Created
February 10, 2016 18:36
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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 |
tarelli
/ gist:adbe0524ac4bb9adb2e9
Created
January 20, 2016 12:53
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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) |
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