Python for
                                                                                                              Biologists
                                                                                                               Monga
                                Python for Biologists1                                                     Python
                                                                                                           Python
                                                                                                           fundamentals
                                                                                                            Assignment
                                                                                                            Basic operations
                                           Mattia Monga                                                    Flow of
                                                                                                           control
                                                                                                            Selections
                                           Dip. di Informatica                                              Repetitions
                               Universit`a degli Studi di Milano, Italia                                   Functions
                                       mattia.monga@unimi.it                                               Composite
                                                                                                           objects
                                                                                                            Tuples and lists
                                         September 2021                                                    Software
                                                                                                           Dictionaries
                                                                                                           Sets
          1                                                                                                Comprehensions
           cba2021M.Monga. Creative Commons Attribuzione — Condividi allo stesso modo 4.0
     Internazionale. http://creativecommons.org/licenses/by-sa/4.0/deed.it                                 Files
                                                                                                           Exercises
                                                                                                           Types,
                                                                                                           docstrings,
                                                                                                           doctests
                                                                                                           Abstracting
                                                                                                           similarities
                                                                                                           Procedural
                                                                                                           encapsulation
                                                                                                           OO
                                                                                                           encapsulation
                                                                                                           Simulations
                                                                                                           Third-party
                                                                                                           libraries
                                                                                                           NumPy
                                                                                                           ndarr⌋
                                                                                                           ay
                                                                                                            Creation
                                                                                                            Indexing
                                                                                                            Vectorization
                                                                                                            Array operations
                                                                                                           Random
                                                                                                           numbers
                                                                                                           Monte Carlo
                                                                                                           Matplotlib
                                                                                                            Graphical commands
                                                                                                            OOplotting
                                                                                                           Pandas
                                                                                                      1
                                                                                                             Python for
                                                                                                              Biologists
                                                                                                               Monga
                                                                                                           Python
                                                                                                           Python
                                                                                                           fundamentals
                                                                                                            Assignment
                                                                                                            Basic operations
     Lecture I: Programming in Python for biologists                                                       Flow of
                                                                                                           control
                                                                                                            Selections
                                                                                                            Repetitions
                                                                                                           Functions
                                                                                                           Composite
                                                                                                           objects
                                                                                                            Tuples and lists
                                                                                                           Software
                                                                                                           Dictionaries
                                                                                                           Sets
                                                                                                           Comprehensions
                                                                                                           Files
                                                                                                           Exercises
                                                                                                           Types,
                                                                                                           docstrings,
                                                                                                           doctests
                                                                                                           Abstracting
                                                                                                           similarities
                                                                                                           Procedural
                                                                                                           encapsulation
                                                                                                           OO
                                                                                                           encapsulation
                                                                                                           Simulations
                                                                                                           Third-party
                                                                                                           libraries
                                                                                                           NumPy
                                                                                                           ndarr⌋
                                                                                                           ay
                                                                                                            Creation
                                                                                                            Indexing
                                                                                                            Vectorization
                                                                                                            Array operations
                                                                                                           Random
                                                                                                           numbers
                                                                                                           Monte Carlo
                                                                                                           Matplotlib
                                                                                                            Graphical commands
                                                                                                            OOplotting
                                                                                                           Pandas
                                                                                                      2
   Programming in Python (for quantitative
   biologists)
                                                                                                             Python for
     The course introduces imperative programming by referring to                                             Biologists
     the Python language.                                                                                      Monga
                                                                                                           Python
       1   Python3 and its object-oriented
                                                                                                           Python
           features;                                                                                       fundamentals
                                                                                                            Assignment
       2   Python3 libraries that can be useful                                                             Basic operations
           in scientific computation and data                                                              Flow of
                                                                                                           control
           analysis, in particular NumPy and                                                                Selections
                                                                                                            Repetitions
           pandas.                                                                                         Functions
                                                                                                           Composite
                                                                                                           objects
       This course is a shortened/adapted version of the one I teach                                        Tuples and lists
                              in the “Quantitative Biology”:                                               Software
                       mattiamon.ga/pyqb                                                                   Dictionaries
                                                                                                           Sets
                                                                                                           Comprehensions
                                                                                                           Files
                                                                                                           Exercises
                                                                                                           Types,
                                                                                                           docstrings,
                                                                                                           doctests
                                                                                                           Abstracting
                                                                                                           similarities
                                                                                                           Procedural
                                                                                                           encapsulation
                                                                                                           OO
                                                                                                           encapsulation
                                                                                                           Simulations
                                                                                                           Third-party
                                                                                                           libraries
                                                                                                           NumPy
                                                                                                           ndarr⌋
                                                                                                           ay
                                                                                                            Creation
                                                                                                            Indexing
                                                                                                            Vectorization
                                                                                                            Array operations
                                                                                                           Random
                                                                                                           numbers
                                                                                                           Monte Carlo
                                                                                                           Matplotlib
                                                                                                            Graphical commands
                                                                                                            OOplotting
                                                                                                           Pandas
                                                                                                      3
   Course schedule
                                                                                                             Python for
                                                                                                              Biologists
                                                                                                               Monga
                                                                                                           Python
            5 lectures, 4 hours each                                                                       Python
                                                                                                           fundamentals
            Wewill explore different setups:                                                                Assignment
                                                                                                            Basic operations
                    a “scaffolded” one for the first steps (1-2 lectures)                                  Flow of
                    the plain python interpreter (2-3 lectures)                                            control
                    the notebooks popular in scientific practice (1 lecture)                                Selections
                                                                                                            Repetitions
     It’s very important that you try to do the exercises by                                               Functions
     yourselves!                                                                                           Composite
                                                                                                           objects
                                                                                                            Tuples and lists
                                                                                                           Software
                                                                                                           Dictionaries
                                                                                                           Sets
                                                                                                           Comprehensions
                                                                                                           Files
                                                                                                           Exercises
                                                                                                           Types,
                                                                                                           docstrings,
                                                                                                           doctests
                                                                                                           Abstracting
                                                                                                           similarities
                                                                                                           Procedural
                                                                                                           encapsulation
                                                                                                           OO
                                                                                                           encapsulation
                                                                                                           Simulations
                                                                                                           Third-party
                                                                                                           libraries
                                                                                                           NumPy
                                                                                                           ndarr⌋
                                                                                                           ay
                                                                                                            Creation
                                                                                                            Indexing
                                                                                                            Vectorization
                                                                                                            Array operations
                                                                                                           Random
                                                                                                           numbers
                                                                                                           Monte Carlo
                                                                                                           Matplotlib
                                                                                                            Graphical commands
                                                                                                            OOplotting
                                                                                                           Pandas
                                                                                                      4