MIB Python Club! 🐍

This is the repository for MIB Python club!

We have:

Meetings:

• Every Friday @ 12 - check the MIB slack #python channel for links
• scope - scientific data analysis with python, command line kung fu, machine learning, virtual drug screening, hacking & more!

Tutorials

• Basic bits - what's going on, dna translation using dictionaries
• Back to basics - some useful basic bits including: string stuff, dictionary lookups, bash, numpy, graph theoy (with networkx), classes - all with the protein (p450 bm3) from Basic bits
• UV-Vis data analysis - pandas, matplotlib - using real data from a UV-Vis spectrometer experiment on p450 bm3
• COVID-19 data - pandas, matplotlib - download and plot global COVID-19 infection rates
• Curve fitting - scipy michaelis-menten kinetics for enzyme binding
• Curve fitting - growth curve - fitting the gomperz equation to bacterial growth and bootstrapping to estimate uncertainty - thank you Steve for this one
• Cheminformatics - some basic rdkit
• Biopython cheat sheet
• List comprehensions - for loops in one line - really useful
• the linux/mac command line - 4 sessions on the unix command line, connecting to remote linux servers and hacking!

tutorials
├── basics
│   ├── BackToBasics.ipynb
│   ├── BasicBitsPython.ipynb
│   ├── Curve-Fitting.ipynb
│   ├── ListComprehensions.ipynb
│   └── plate-data-with-pandas.ipynb
├── data
├── design-of-experiments
│   └── Design-of-Experiments.ipynb
├── Growth-Curve
│   └── growthCurve.ipynb
├── intro-to
│   ├── IntroToBiopython.ipynb
│   ├── IntroToCheminformatics.ipynb
│   └── IntroToDataWranglingWithPandas.ipynb
├── PL-Pro
│   ├── PL-Pro-Part1-DataAcquisition.ipynb
│   └── PL-Pro-Part2-Featurization.ipynb
├── tutorial-data
│   ├── curve-fitting
│   │   └── DataGenerator.ipynb
│   └── titrations
└── uv-vis
    ├── CAMS-workshop-scipy
    │   ├── __pycache__
    │   └── scipy.ipynb
    └── uv-vis-data.ipynb

Resources

I've dumped some useful resources into this file for topics including, but not limited to:

• Links to Tutorials
• Videos
• Cheat sheets
• Curated lists of machine learning + biology papers