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Matteo Cantarelli tarelli

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tarelli / gist:adbe0524ac4bb9adb2e9
Created January 20, 2016 12:53
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)
@tarelli
tarelli / Past LEMS component problem
Created January 18, 2016 10:13
Errors
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
@tarelli
tarelli / gist:6229869
Created August 14, 2013 10:35
This file has been truncated, but you can view the full file.
{"entities":[{"id":"LIQUID_sph","geometries":[{"type":"Particle","id":"p[1575]","position":{"x":12.524999618530273,"y":2.505000114440918,"z":57.11399841308594}},{"type":"Particle","id":"p[1576]","position":{"x":12.524999618530273,"y":2.505000114440918,"z":58.784000396728516}},{"type":"Particle","id":"p[1577]","position":{"x":12.524999618530273,"y":2.505000114440918,"z":60.45399856567383}},{"type":"Particle","id":"p[1578]","position":{"x":12.524999618530273,"y":2.505000114440918,"z":62.124000549316406}},{"type":"Particle","id":"p[1579]","position":{"x":12.524999618530273,"y":2.505000114440918,"z":63.79399871826172}},{"type":"Particle","id":"p[1580]","position":{"x":12.524999618530273,"y":2.505000114440918,"z":65.46399688720703}},{"type":"Particle","id":"p[1581]","position":{"x":12.524999618530273,"y":2.505000114440918,"z":67.13400268554688}},{"type":"Particle","id":"p[1582]","position":{"x":12.524999618530273,"y":2.505000114440918,"z":68.80400085449219}},{"type":"Particle","id":"p[1583]","position":{"x":12.524
@tarelli
tarelli / gist:5928415
Last active December 19, 2015 08:49
Geppetto Alpha Release 0.0.2
* Basic simulation XML specification
* Basic simulation lifecycle
* Start/Pause/Stop/Reset
* Simulators currently in development
* Fluid hydrodynamics simulator bundle (PCI-SPH)
* Neuronal simulator bundle (LEMS/NeuroML)
* WebGL Frontend
* 3D visualization
* Particle system
* Ball stick morphologies
@tarelli
tarelli / GEPPETTO.xml
Last active December 19, 2015 00:18
Geppetto integration sample scripts
<?xml version="1.0" encoding="UTF-8"?>
<tns:simulation xmlns:tns="http://www.openworm.org/simulationSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.openworm.org/simulationSchema ../../src/main/resources/schema/simulationSchema.xsd ">
<tns:configuration>
<tns:outputFormat>RAW</tns:outputFormat>
</tns:configuration>
<tns:entities>
<tns:entity>
<tns:id>muscle_cell</tns:id>
<tns:aspects>
<tns:aspect>
@tarelli
tarelli / gist:5441745
Last active December 16, 2015 13:29
Geppetto simulations
https://www.dropbox.com/s/iyr085zcegyis0n/sph-sim-config.xml?dl=1 23/04/13 Not working
https://www.dropbox.com/s/7vxeh6qbln9jesk/sph-sim-config-test.xml?dl=1
https://dl.dropboxusercontent.com/u/7538688/funzionare.xml?dl=1
@tarelli
tarelli / instructions
Last active December 10, 2015 02:39
Automatic Virgo startup
Save the script as /etc/init.d/virgo
chmod 755 /etc/init.d/virgo
Make a link to it from /etc/rc3.d such as:
cd /etc/rc5.d
sudo ln -s ../init.d/virgo S90virgo
use chmod -R 777 on the virgo folder
@tarelli
tarelli / ScriptOutput.txt
Created November 22, 2012 17:23
Output from running script
Matteos-MacBook-Pro:~ matteocantarelli$ python build_server_package.py
['http://ftp.osuosl.org/pub/eclipse//virgo/milestone/VP/3.6.0.M01/virgo-tomcat-server-3.6.0.M01.zip', 'https://github.com/openworm/org.openworm.simulationengine.core/archive/master.zip', 'https://github.com/openworm/org.openworm.simulationengine/archive/master.zip', 'https://github.com/openworm/org.openworm.simulationengine.samplesimulation/archive/master.zip', 'https://github.com/openworm/org.openworm.simulationengine.frontend/archive/master.zip', 'https://github.com/openworm/org.openworm.simulationengine.samplesolver/archive/master.zip', 'https://github.com/openworm/org.openworm.simulationengine.model.sph/archive/master.zip', 'https://github.com/openworm/org.openworm.simulationengine.solver.sph/archive/master.zip', 'https://github.com/openworm/org.openworm.simulationengine.simulator.sph/archive/master.zip', 'https://github.com/openworm/org.openworm.simulationengine.simulation/archive/master.zip', 'https://github.com/openworm/org.openwor
@tarelli
tarelli / gist:5487c69b79e14c43033b
Created May 7, 2015 08:55
Update Geppetto
org.geppetto/utilities/source_setup/python gitall.py pull //make sure everything is updated
org.geppetto/mvn install //this will download all the new libraries required (if any)
org.geppetto/utilities/source_setup/python update_server.py eclipse //this will copy everything to virgo
@tarelli
tarelli / gist:6d23d9fa33eca5b6d253
Created May 6, 2015 15:05
Setup NEURON
import os
import sys
from subprocess import check_output as co
from distutils.core import run_setup
class working_dir(object):
"""Context manager for changing the current working directory"""
def __init__(self, newPath):
self.newPath = newPath