Basic programming for drug discovery - Python

How to set up the Python for this course:

1. Install anaconda
2. Create a new environment using conda_env_BPiDD_2019.yml:
   • Option 1: Use anaconda navigator to import the environment untested
   • Option 2: Create the environment with the command line: conda env create -f environment.yml
3. Online using Binder. This takes around 10 minutes to get ready, but does not require any kind of setup on your end. Click here to get started: []

Recommended resources

• Interactive tutorial at DataCamp (only free parts)
• Interactive tutorial at Learn Python (skip advanced part)
• Python for Biologists: covers same topics that were covered in the Python basics part of the course LACDR course
• Python data science handbook
• Matplotlib tutorial
• Interactive Python (jupyter and jupyterlab)
• Seaborn tutorial
• Effective Pandas
• Cheat sheets (Python)
• Python Graph Gallery
• Markdown for jupyter

Recommended Python libraries

Data visualization

• matplotlib
• seaborn
• ggplot: similar to R's ggplot
• plotly and bokeh: interactive plots

Statistics

• scipy
• statsmodels

Machine learning

• scikit-learn

Image analysis

• scikit-image
• mahotas

Recommended IDEs

IDEs are usefull for developing code.

• PyCharm, free community edition or free pro version for academic use
• Spyder (included in Anaconda)