elijahc

In walking through the math to derive the equation they use in their code to maintain/model the X(t) neuron state vector I realized I was not using an appropriate time step size. After correcting the step size the model appears to make better predictions as quantified by mean Pearson Correlation Coefficient

N = 1000

214 Cells in Experiment 500964514

Using 50 cell ids: [ 7 11 26 28 40 41 45 47 49 50 54 63 68 69 70 76 77 82

elijahc

Download cuda-8.run file
Download Nvidia-367.18-driver.run file

Remove old drivers (apt remove --purge nvidia*)
Remove old nvidia.deb packages (just in case that's necessary?)
Remove my cuda folders (/usr/local/cuda*) (again, just in case)

reboot
Graphics probably won't work now (they didn't for me), so use tty (ctrl-alt-1) or ssh (might want to set that up before doing all this)
(I might have run the Nvidia-367.18.run file here, followed with a reboot, but I can't remember)

elijahc

##VGG19 model for Keras

This is the Keras model of the 19-layer network used by the VGG team in the ILSVRC-2014 competition.

It has been obtained by directly converting the Caffe model provived by the authors.

Details about the network architecture can be found in the following arXiv paper:

Very Deep Convolutional Networks for Large-Scale Image Recognition

K. Simonyan, A. Zisserman

elijahc

import json

...

# Parse arguments
parser = argparse.ArgumentParser(description='RNN for modeling neuron populations')
...
FLAGS = parser.parse_args()
return FLAGS

elijahc

#!/usr/bin/env python
import json
import urllib2
import os
import sys
import pexpect
import time

usr,pts = str(sys.argv[1]).split('.')

elijahc

Startup

$ cd /home/webapps2/vertex
$ unicorn_rails -c config/unicorn.rb
$ bundle exec sidekiq
$ sudo service nginx restart

# Redis should always be running, but in case its not and you have the permissions, I believe this is how you would start it.

$ sudo service redis start

elijahc

class Blink < Sinatra::Base
  require 'rbc'

  get '/user/:id' do |id|
    @user = User.find(id)
    haml :users_show
  end

  get '/user/:id/destroy' do |id, status|
    restrict! :to_below => 3

elijahc

# This file is auto-generated from the current state of the database. Instead
# of editing this file, please use the migrations feature of Active Record to
# incrementally modify your database, and then regenerate this schema definition.
#
# Note that this schema.rb definition is the authoritative source for your
# database schema. If you need to create the application database on another
# system, you should be using db:schema:load, not running all the migrations
# from scratch. The latter is a flawed and unsustainable approach (the more migrations
# you'll amass, the slower it'll run and the greater likelihood for issues).
#

elijahc

CentOS 6

Install Ruby

Using RVM (probably the most popular way)

$ \curl -sSL https://get.rvm.io | bash -s stable

OR

elijahc

require 'resque-status'
module Importer
  require_relative 'importer_base'
  require 'rbc'

  class Pipe < ImporterBase

    def initialize(key, options={})
      @key = key
      @options = options