References and Resources

Restructured Text

Restructured Text (reST) and Sphinx CheatSheet

Sphinx Markup Constructs

Quick reStructuredText

reST – reStructuredText

Read text table with numpy

Data visualization on the web and D3.js

Online book: Interactive Data Visualization for the web

Mike Bostock’s website

Nested Selections

Working with Transitions

Let’s make a bar chart

Let’s make a map

Stroke Dash Interpolation

Animate path in D3

Point-Along-Path Interpolation

Python programming

Online book: Python cookbook

Python Module of the week

IPython cookbook

David Beazley’s website

Book: Python for Data Analysis

HTML5, CSS, and Javascript programming

Learning Javascript Design Patterns, by Addy Osmani

Javascript Documenation on MDN

Javascript: the Good Parts, by Douglas Crockford

WebSocket tutorial on HTML5 Rocks

Varialble vs. Properties in Javascript

BioInformatics

Tutorials from Homolog.us – Bioinformatics website

`Data formats used at UCSC genome browser project<http://genome.ucsc.edu/FAQ/FAQformat.html>`_

Tools provided from UCSC genome browser project

The bigbed indexed binary format for genome annotation

The bigwig indexed binary format for dense, continuous genome bioinformatics data

The wig data format

The bedgraph data format

A comprehensive index of R packages and documentation from CRAN, Bioconductor, GitHub and R-Forge

H3k4me3 data