qingpeng / SoftwareCarpentryWuhan

SoftwareCarpentryWuhan

Some materials

matplotlib: https://github.com/qingpeng/SoftwareCarpentryWuhan/blob/master/matplot.pdf?raw=true

Shell/Linux Command https://www.dropbox.com/sh/rugyzvalqztvuay/htJfb23Eqk

python slides: http://blog.yeyanbo.com/slides/python.html#1

How computers work

(by Titus Brown)

https://github.com/swcarpentry/2013-04-az/blob/master/swc-computer-diagram.png

Python

Python is a programming language gaining popularity in the sciences. It's open source, free, and an array of existing libraries mean you can often find code that will do some task for you.

Useful Python Links

Core Python

• Main Python Docs

  • http://docs.python.org/

• Global Module Index

  • Built in modules like os, sys, datetime, math, random...
  • http://docs.python.org/modindex.html

• Built-in Functions

  • Built-in, always available functions like open, range, enumerate,

zip...

• http://docs.python.org/library/functions.html

Python in Science

• NumPy

  • Fast arrays, used by almost every scientific Python package

• SciPy

  • Minimization, fitting, solvers, statistics, and more

• matplotlib

  • 2D and 3D plotting, maps

• AstroPy for astronomy

• Biopython for bioinformatics

• Sage for mathematic analysis

• SymPy for symbolic mathematics

• pandas data analysis and stats for categorical and time series data

Install Python

• It's already there! (Linux, Mac OS)
• Python Official Installer
  • To get the newest version.
  • Support Windows, Linux, Mac OS, etc.
• Enthought Python Distribution - Canopy
  • Commercial, not free, but has academic license(free)
  • With many third-party packages like numpy, matplotlib,ipython(notbook)
  • Mac OS, Windows, Linux
  • Easy install and update
• ActiveState ActivePython
  • Commercial, with free version, has good IDEs(not free)
  • Windows, Mac OS, Linux
• Python(x,y)
  • Windows, Linux
  • With many third-party packages like numpy, matplotlib, ipython(notebook)
  • totally free

Install Python packages

• Python package installer
  • "pip install package" to install
  • The Python Package Index is a repository of software for the Python programming language. There are currently 32576 packages here
• Not in Python Package Index?
  • Go to homepage
  • download source code and read "README"
  • install as instructed

Install Linux

• Ubuntu
• BioUbuntu(including many bioinformatics software)
• Virtual Machine
• Amazon Cloud Computing
  • not free, you use , you pay
  • free Tire for beginner
  • a tutorial http://ged.msu.edu/angus/tutorials-2013/day1.html

Reproducibility

• An example http://ged.msu.edu/papers/2012-diginorm/

Some Useful Links

• Software Carpentry Github Repo
  • workshop materials
• Software Carpentry Website
  • lost of tutorials
• GED Lab Angus
  • a bunch of course/workshop materials, tutorials, etc.
• SeqAnswers
  • online forum
• BioStars
• Many more ...
• Google