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Matteo Cantarelli tarelli

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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: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
@tarelli
tarelli / gist:2c47ae47930e0571453c
Created February 10, 2015 12:52
Instance types meeting notes
var giovanni={}
giovanni.X=4
4
giovanni.Y=5
5
giovanni
Object {X: 4, Y: 5}
gioInstance.getType= function(){return this.target};
function (){return this.target}
@tarelli
tarelli / gist:10278549
Last active May 17, 2016 17:34
Deploy JARs to Github/Maven
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 / gist:9793438
Last active August 29, 2015 13:57
Geppetto-Sibernetic Script
from __future__ import with_statement
import os
import urllib
import tempfile, shutil, zipfile, re, sys
from fabric.api import local, lcd, hide, show, settings
import os.path as op
import sys
@tarelli
tarelli / Plot one var against another
Created February 7, 2014 01:18
/*******************************************************************************
* The MIT License (MIT)
*
* Copyright (c) 2011, 2013 OpenWorm.
* http://openworm.org
*
* All rights reserved. This program and the accompanying materials
* are made available under the terms of the MIT License
* which accompanies this distribution, and is available at
* http://opensource.org/licenses/MIT
@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>