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
(by Titus Brown)
https://github.com/swcarpentry/2013-04-az/blob/master/swc-computer-diagram.png
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.
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Main Python Docs
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Global Module Index
- Built in modules like os, sys, datetime, math, random...
- http://docs.python.org/modindex.html
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Built-in Functions
- Built-in, always available functions like open, range, enumerate,
zip...
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- Fast arrays, used by almost every scientific Python package
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- Minimization, fitting, solvers, statistics, and more
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- 2D and 3D plotting, maps
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AstroPy for astronomy
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Biopython for bioinformatics
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Sage for mathematic analysis
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SymPy for symbolic mathematics
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pandas data analysis and stats for categorical and time series data
- 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
- 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
- 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
- An example http://ged.msu.edu/papers/2012-diginorm/
- 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 ...