Index

• Scientific Programming for QCB
• General Info
  • Timetable and lecture rooms
  • Moodle
  • Zoom links
  • Slides
  • Acknowledgements
• Practical 1
  • Slides
  • Setting up the environment
  • Our toolbox
  • Installing Python3 in Linux
  • Installing Python3 in Windows/Mac
  • The console
  • Visual Studio Code
  • The debugger
  • A quick Jupyter primer (just for your information, skip if not interested)
  • Exercises
• Practical 2
  • Slides
  • Modules
  • Objects
  • Variables
  • Numeric types
  • Strings
  • Exercises
• Practical 3
  • Slides
  • Lists
  • Tuples
  • Exercises
• Practical 4
  • Slides
  • Execution flow
  • Conditionals
  • Loops
  • Exercises
• Practical 5
  • Slides
  • More on loops
  • Dictionaries
  • Exercises
• Practical 6
  • Slides
  • Functions
  • Namespace and variable scope
  • Argument passing
  • File input and output
  • Exercises
• Practical 7
  • Slides
  • Functions
  • Getting input from the command line
  • Argparse
  • Exercises
• Practical 8
  • Slides
  • Libraries installation
  • Pandas
  • Series
  • Plotting data
  • Pandas DataFrames
  • Exercises
• Practical 9
  • Slides
  • Numpy
  • Numpy ndarray
  • Random arrays
  • Numpy to and from pandas
  • Reshaping
  • Iterating over arrays and Indexing
  • Broadcasting and arithmetic functions
  • Filtering
  • Linear algebra
  • Matplotlib
  • Exercises
• Practical 10
  • Slides
  • Biopython
  • Installation of Biopython
  • General overview
  • Sequence objects
  • Looping, slicing and concatenation
  • Sequence annotation
  • Sequence I/O
  • Multiple sequence alignment
  • Exercises
• Practical 11
  • Slides
  • Biopython
  • BLAST
  • Getting data from NCBI
  • Getting data from ExPASy
  • 3D structure and PDB
  • Exercises
• Material
• Midterm
  • Before you start
  • Problem 1
  • Problem 2
  • A possible solution