Resources

The purpose of this repository is to compile resources for newer members to explore useful programs, learn new languages, etc. Older members if you see something useful, feel free to simply include links, etc. in the README.

Python

1. Useful Sources to Learn Python:

• This is an intro course from UC Berkeley (CS61a) going over Python and the basics of CS. Reading links and resources are useful for those with no previous experience in programming. https://cs61a.org/

2. Visualizing in Python:

• Python Data Science Online Handbook (really good examples/explanations of machine learning, PCA, etc.): https://jakevdp.github.io/PythonDataScienceHandbook/
• Visualizing with Seaborn: https://jakevdp.github.io/PythonDataScienceHandbook/04.14-visualization-with-seaborn.html
  • Changing default visuals for Seaborn: https://seaborn.pydata.org/tutorial/aesthetics.html
  • KDE bandwidth cross-validation (important if your distribtion is not normal): https://jakevdp.github.io/PythonDataScienceHandbook/05.13-kernel-density-estimation.html
• Plotting pandas dataframes using Seaborn + other miscellaneous packages: https://tomaugspurger.github.io/modern-6-visualization.html

3. UCI Data Science Workshop jupyter notebooks: https://github.com/UCIDataScienceInitiative

Terminal

1. Vim cheat sheet (terminal): https://vim.rtorr.com/

2. Useful website which explains commands and flags: https://explainshell.com/

3. Useful terminal shortcuts: https://www.techrepublic.com/article/20-terminal-shortcuts-developers-need-to-know/

AMBER

1. Official AMBER tutorials: http://ambermd.org/tutorials/Introductory.php

2. Additional AMBER tutorials from the Rizzo lab (not the official ones): http://ringo.ams.sunysb.edu/index.php/AMBER_Tutorials

3. Cpptraj

• Go to this folder in your amber setup for a LOT of cpptraj code examples (didn't find this till 2nd year, learn from our mistakes -_-): amber16-with-patches/AmberTools/test/cpptraj

Programs

1. Text editor: http://www.sublimetext.com/
2. Mac terminal emulator (better than default): https://iterm2.com/
3. LigPLOT+ (ligand-protein diagrams): https://www.ebi.ac.uk/thornton-srv/software/LigPlus/
4. Chimera (visualization software): https://www.cgl.ucsf.edu/chimera/download.html
5. VMD (visualization software): http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD

Useful Papers:

1. Comparison of clustering algorithms:

• Shao, Jianyin, et al. "Clustering molecular dynamics trajectories: 1. Characterizing the performance of different clustering algorithms." Journal of chemical theory and computation 3.6 (2007): 2312-2334.
• Wolf, Antje, and Karl N. Kirschner. "Principal component and clustering analysis on molecular dynamics data of the ribosomal L11· 23S subdomain." Journal of molecular modeling 19.2 (2013): 539-549.

If you still use Windows...

Why you should just stop:

1. https://www.lifewire.com/operating-systems-unix-vs-windows-2180225
2. https://www.techrepublic.com/blog/10-things/10-things-linux-does-better-than-windows/