STEM: DNA Biology and Bioinformatics

Resources for working with Linux, Python, and your Raspberry Pi

CGRB Jupyter Hub: https://web-dev.cgrb.oregonstate.edu/J-STEM/hub/login (this will disappear after camp; please be sure to download your Notebook files)

Python3 Language Documentation (and tutorials): https://docs.python.org/3.4/

Raspberry Pi (main site): https://www.raspberrypi.org

Raspberry Pi Docs: https://www.raspberrypi.org/documentation/

Raspbian Documentation: https://www.raspbian.org/

Linux Commands for installing needed modules/libraries/applications: 

• MatPlotLib (Python graphing and plotting tools): sudo pip3 install matplotlib
• BioPython (Python bioinformatics packages): sudo pip3 install biopython
• ClustalW (Linux genetic sequence clustering program): sudo apt-get install clustalw

Helpful Linux commands for your Pi:

• Download & install open-source software: sudo apt-get install <package_name>
• Download & install python modules/libraries: sudo pip3 install <module_name>
• Launch your local Jupyter Notebook: jupyter notebook
• Shutdown your Pi: sudo shutdown -h now (can also be done from the Raspbian GUI menu)

Crown Gall Microbiome analysis output files:

http://changlab.cgrb.oregonstate.edu/sites/default/files/PCoA_plot.png

http://changlab.cgrb.oregonstate.edu/sites/default/files/makeplot_class.png

http://changlab.cgrb.oregonstate.edu/sites/default/files/makeplot_order.png

http://changlab.cgrb.oregonstate.edu/sites/default/files/makeplot_family...

http://changlab.cgrb.oregonstate.edu/sites/default/files/makeplot_phylum...

http://changlab.cgrb.oregonstate.edu/sites/default/files/makeplot_genus.png

If you have any questions about Python or running your Raspberry Pi, please contact preecej[at]science[dot]oregonstate[dot]edu.