Zsailer

Resample function until convergence

Python function that will rerun a function until its output convergences. The output must be numerical values. It can been an int, float, list, or array. Requires numpy.

This method runs the function in chunks (N=sample_size). It calculates the mean and standard deviation of the total set of samples after each chunk. If the mean and standard deviation of the total set is relatively close (see rtol) the last iteration, the sampling is assumed to have converged.

Zsailer

import networkx as nx

def draw_networkx_nodes_ellipses(G, pos,
    nodelist=None,
    node_height=1,
    node_width=2,
    node_angle=0,
    node_color='r',
    node_shape='o',
    alpha=1.0,

Zsailer

import matplotlib

def prettify(ax, legend_loc=4):
    """ A simple wrapper to make matplotlib figures prettier."""
    
    # Change default colors to something softer. 
    colors = {
        'b': '#0066CC',
        'r': '#CC0000',
        'm': '#660066',

Zsailer

%% Document type
\documentclass[12pt]{article}

%% Start of preamble
\usepackage{amsmath}        % Advanced math extension
\usepackage{amssymb}        % Advanced math symbols
\usepackage{array}          % Advanced tables
%\usepackage{bm}            % Allows bold greek letters in math mode
%\usepackage{caption}       % Allows customization of caption appearance
\usepackage[margin=1in]{geometry}   % Management of document margins and size

Zsailer

// Metadata for networks and trajectories from the following paper:
// "Darwinian Evolution Can Follow Only Very Few Mutational Paths to Fitter Proteins"
// Weinreich, D., et.al
// http://www.sciencemag.org/content/312/5770/111.short

{
  "directed": true,
  "nodes": [
    {
      "value": 1.0152510120727598,

Zsailer

Tasks for the day

1. Read the introduction to D3.js here.
2. Work through these tutorials:

• Let’s Make a Bar Chart, Parts I
• Part II
• Part III

Try to implement these bar charts directly in the d3app boilerplate code you've been using. Download a fresh project if you need here 3. Read about D3 transitions here.

Zsailer

Creating an open source D3-Backbone app on Github

Github is where you'll host all your projects publically. It's the platform we'll use to write and share applications, and it allows us to work on these projects in parallel. It will make it easier for me to help you, since all your code is availabe for me to oversee online.

Getting started.

Navigate to the directory where you'd like to keep all your projects. The commands below will download the boilerplate code and prepare it for development. Anytime you see <project_name>, replace it with whatever name you're like to give the project (no spaces!).

git clone https://github.com/Zsailer/d3app 

Zsailer

Zsailer

IPython Web Services

This documentation describes the current API for IPython Notebook's web-services. In handling HTTP request, we pass all information between the server and client using JSON standard models. Each standard model is shown at the beginning of the sections below. This format adheres to the principles described in RESTful web-services.

• Notebooks
  • List notebooks in root directory
  • Create new notebook
  • List notebooks in named directory
  • Open the named noteboko in subdirectory
  • Change notebook's standard model and save modified notebook
  • Delete a notebook in subdirectory

Zsailer

{   "path": "foo/bar", 
    "notebooks":[{{"kernel_id":"###","name":"Notebook1","notebook_id":"###"}},{...}], 
    "directories": ["sub-directory1", "sub-directory2", ...],
    "files":["file1","file2",...]
    }