russelljjarvis

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Mac OS X 10.9.x (Mavericks)

Shell
#!/usr/bin/env sh

Python

russelljjarvis

Click here for Fedora 24

The current kernel of Fedora 21 doesn't support the Wifi chip used on my Mac Book Pro. Proprietary Broadcom drivers are packaged and available in the rpmfusion repo.

Verify that your card is a Broadcom using: lspci -vnn -d 14e4:

Sample output:

02:00.0 Network controller [0280]: Broadcom Corporation BCM4360 802.11ac Wireless Network Adapter [14e4:43a0] (rev 03)

russelljjarvis

Hi Rick,

As discussed I am trying to integrate the GA development code I initially made here.

With sciunit judge, in order to use it to optomize the Allen Brian Institute example here.

Today I was occupied with fixing minor problems such as getting pyneuroml and allenbrainsdk into the dockerbuild I have made, that builds on scidash/neuronunit-scoop-deap. I am currently trying to replicate the AIBS.ipynb using the said docker image as substrate. Incidentally when I try to run the AIBS notebook it gets stuck on the line: NameError: name 'vm' is not defined. When reading over the code vm does not appear to be declared anywhere, I am not sure how it enters the name space in the notebook. Perhaps it comes from an imported module.

I did not get the sense that vm is used in a way that has consequences for the variables that I want to optomize so now I have commented out

russelljjarvis

int bluePin=6;
int lightPulsePin=5;
int solenoidPin=10;
int odorPulsePin=11;

//int matlabData[]={0,0,0,0,0,0,0};

float matlabData2[]={0,0,0,0,0,0,0};
unsigned long previousMillis = 0;        // will store last time LED was updated
unsigned long interval_odor_on = 0;

russelljjarvis

                                                                                                                                                                                                                          
#!pip install -e +git https://github.com/ckreibich/scholar.py                                                                                                                                                                                 
import sys
from scholar_scrape import scholar
import pandas as pd

unicode = str # pylint: disable-msg=W0622                                                                                                                                                                                                     
encode = lambda s: unicode(s) # pylint: disable-msg=C0103                                                                                                                                                                                ''' 

russelljjarvis

A quick and dirty syntax translation / conversion reference guide to ease the transition between Python and Julia. This is not meant as a reference to the language. For that you should read the manual.

Some important differences

• Arrays in Julia are indexed starting from 1.
• In Julia classes (i.e. types) don't own methods. Methods are implementations of generic functions and are invoked in a "static style", i.e. instead of Python's str1.rstrip(), we will have rstrip( str1 ), instead of file1.close(), close( file1 ).

Some important similarities.

russelljjarvis

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russelljjarvis

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russelljjarvis

import numpy as np
import matplotlib.pyplot as plt
import scipy.stats as scs

def z_val(sig_level=0.05, two_tailed=True):
    """Returns the z value for a given significance level"""
    z_dist = scs.norm()
    if two_tailed:
        sig_level = sig_level/2
        area = 1 - sig_level

russelljjarvis

'''
Author information. This is an extension to the Utils class from Allen Brain API. 
The parallel wiring related functions are written by Russell Jarvis rjjarvis@asu.edu
'''


from allensdk.model.biophys_sim.neuron.hoc_utils import HocUtils
import logging
import glob
from mpi4py import MPI