cheelee

# WCON data source: https://zenodo.org/record/1034927/files/unc-80%20(e1069)%20nRHO-1%20QT309%20on%20food%20L_2011_11_11__13_12___3___4.wcon.zip
#
# WCON is kind of broken right now, so I won't bother to describe the software stack. To get it to work, some hackery involving dependencies are required.
# https://github.com/openworm/tracker-commons
#
from wcon import WCONWorms
# Assuming file properly renamed
>>> worm = WCONWorms.load_from_file('../static/example.wcon')
Loading file: ../static/example.wcon
# Loaded object's data field is a PANDAS dataframe

cheelee

Downloading: http://repository.springsource.com/maven/bundles/release/org/geppetto/core/0.2.7/core-0.2.7.pom
Downloading: http://repository.springsource.com/maven/bundles/external/org/geppetto/core/0.2.7/core-0.2.7.pom
Downloading: http://repository.springsource.com/maven/libraries/release/org/geppetto/core/0.2.7/core-0.2.7.pom
Downloading: http://repository.springsource.com/maven/libraries/external/org/geppetto/core/0.2.7/core-0.2.7.pom
Downloading: https://repo.maven.apache.org/maven2/org/geppetto/core/0.2.7/core-0.2.7.pom
[WARNING] The POM for org.geppetto:core:jar:0.2.7 is missing, no dependency information available
Downloading: http://repository.springsource.com/maven/bundles/release/org/geppetto/core/0.2.7/core-0.2.7.jar
Downloading: http://repository.springsource.com/maven/bundles/external/org/geppetto/core/0.2.7/core-0.2.7.jar
Downloading: http://repository.springsource.com/maven/libraries/release/org/geppetto/core/0.2.7/core-0.2.7.jar
Downloading: http://repository.springsource.com/maven/libraries/e

cheelee

Python 2.7 - via homebrew
Virgo server for Tomcat - http://www.eclipse.org/downloads/download.php?file=/virgo/release/VP/3.6.4.RELEASE/virgo-tomcat-server-3.6.4.RELEASE.zip 
gunzip -a virgo-tomcat-server-3.6.4.RELEASE.zip -d /usr/local
Maven - via homebrew
Tomcat - via homebrew

export MVN_HOME="$(brew --prefix maven)/libexec"
export JAVA_HOME="$(/usr/libexec/java_home -v 1.7)"
export SERVER_HOME="$(/usr/local/virgo-tomcat-server-3.7.1.RELEASE)"

cheelee

Arya:temp cheelee$ python test-exec-good.py
BEFORE - bar
6
INSIDE - num
7
AFTER - bar
7
Arya:temp cheelee$ python3 test-exec-good.py
BEFORE - bar
6

cheelee

import sys

def foo(op, val):
    num = [1];
    exec('num[0] = num[0] ' + op + ' val;');
    print("INSIDE - num");
    print(num[0]);
    return num[0];

if len(sys.argv) != 2:

cheelee

Arya:temp cheelee$ python test-exec-nogood.py
BEFORE - bar
6
INSIDE - num
7
AFTER - bar
7
Arya:temp cheelee$ python3 test-exec-nogood.py
BEFORE - bar
6

cheelee

import sys

def foo(op, val):
    num = 1;
    exec('num = num ' + op + ' val;');
    print("INSIDE - num");
    print(num);
    return num;

if len(sys.argv) != 2:

cheelee

// Testing embedded C++ code in blogspot via gist. Making this comment extra long so I can either see this wrap or the scroll bar.
int foo=0;
int bar(int x) {
  return 5*x;
}
class Foobar {
  public:
    Foobar() {};
    ~Foobar() {};
    void foobar() {};

cheelee

# AWS EC2 t2.micro instances seem to get stuck on matplotlib using this - may be low on memory or disk space? (1Gb each)
# Test sequence successfully completed on a VirtualBox image of Ubuntu 14.04 LTS running on Mac OS X with no real resource limits
# Pre-instructions: UPDATE SYSTEM
#export LC_ALL=en_US.UTF-8 # Only needed for AWS EC2
#export LANG=en_US.UTF-8   # Only needed for AWS EC2
sudo apt-get -y update
sudo apt-get -y upgrade
sudo apt-get -y dist-upgrade

cheelee

(hh_tutorial)cheelee@OwatWcon:~/pyNeuroML/examples/test_data$ pynml-channelanalysis -ivCurve HHCellNetwork.net.nml
pyNeuroML >>> 
pyNeuroML >>> Analysing channels from files: ['HHCellNetwork.net.nml']
pyNeuroML >>> 
pyNeuroML >>> Skipping passiveChan in HHCellNetwork.net.nml as it has no channels (probably passive conductance)
Traceback (most recent call last):
  File "/home/cheelee/miniconda3/envs/hh_tutorial/bin/pynml-channelanalysis", line 9, in <module>
    load_entry_point('pyNeuroML==0.1.12', 'console_scripts', 'pynml-channelanalysis')()
  File "/home/cheelee/miniconda3/envs/hh_tutorial/lib/python3.5/site-packages/pyneuroml/analysis/NML2ChannelAnalysis.py", line 616, in main
    run(a=args)