Zsailer

Architecture of IPython notebook's Dashboard

The tables below show the current RESTful web service architecture implemented in IPython notebook. The listed URL's use the HTTP verbs to return representations of the desired resource.

We are in the process of creating a new dashboard architecture for the IPython notebook, which will allow the user to navigate through multiple directory files to find desired notebooks.

Current Architecture

This chart shows the web-services in the single directory IPython notebook.

Zsailer

A Multi-directory IPython notebook dashboard

Author: Zach Sailer <[email protected]>

Created: 2013-4-10

Updated: 2013-4-10

Abstract

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

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

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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 

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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

// 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

%% 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

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',