• Scientific Programming for QCB
• General Info
  • Timetable and lecture rooms
  • Tutoring
  • Equipment
  • Acknowledgements
• Module 1, Practical 1
  • Setting up the environment
    • Linux on windows
    • A dual boot system
  • Our toolbox
  • Installing Python3 in Linux
  • Installing Python3 in Windows/Mac
    • OPTION 1:
    • OPTION 2 (easier):
  • The console
  • Visual Studio Code
  • The debugger
  • A quick Jupyter primer (just for your information, skip if not interested)
    • Installation
  • Exercises
• Module 1, Practical 2
  • Modules
  • Objects
  • Variables
  • Numeric types
    • Integers
    • Booleans
    • Real numbers
  • Strings
    • Methods for the str object
  • Exercises
• Module 1, Practical 3
  • Lists
    • Operators for lists
    • Methods of the class list
    • From strings to lists, the split method
    • And back to strings with the join method
  • Tuples
  • Introduction to sets
  • Exercises
• Module 1, Practical 4
  • Execution flow
  • Conditionals
    • The basic if - else statement
    • The if - elif - else statement
  • Loops
    • For loop
    • Looping over a range
    • Nested for loops
    • While loops
  • Exercises
• Module 1, Practical 5
  • More on control structures
    • Ternary operator
    • Break and continue
      • Continue statement
      • Break statement
    • List comprehension
  • Dictionaries
    • Functions working on dictionaries
    • Dictionary methods
  • Exercises
• Module 1, Practical 6
  • Functions
  • Namespace and variable scope
  • Argument passing
    • Positional arguments
    • Passing arguments by keyword
    • Specifying default values
  • File input and output
    • Opening a file
    • Closing a file
    • Reading from a file
    • Writing to a file
    • String formatting with format
  • Exercises
• Module 1, Practical 7
  • Quick reminder on functions
  • Getting input from the command line
  • Argparse
  • Libraries installation for the next practicals
  • Exercises
• Module 1, Practical 8
  • Libraries installation
  • Pandas
  • Series
    • How to define and access a Series
    • Operator broadcasting
    • Filtering
    • Missing data
    • Computing stats
  • Plotting data
  • Pandas DataFrames
    • Define a DataFrame
    • Loading data from external files
    • Extract values by row and column
    • Broadcasting, filtering and computing stats
    • Merging DataFrames
    • Grouping
  • Exercises
• Module 1, Practical 9
  • 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
• Module 1, Practical 10
  • Biopython
  • Installation of Biopython
  • General overview
  • Sequence objects
  • Looping, slicing and concatenation
    • Complement and reverse complement
    • Transcription and translation
    • MutableSeq
  • Sequence annotation
  • Sequence I/O
    • BioSeqIO.parse()
    • Sequences as dictionaries
    • Writing sequence files
  • Multiple sequence alignment
    • Parsing multiple sequence alignments
    • Writing multiple sequence alignments
    • Manipulating alignments
    • Biopython’s pairwise2 alignment
  • Exercises
• Module 1, Practical 10b
  • Biopython
  • BLAST
    • The function qblast
    • Parsing qblast output
    • Saving results to file
    • Open a blast .XML file
    • The BLAST record class
  • Getting data from NCBI
  • Getting data from ExPASy
  • 3D structure and PDB
  • Exercises
• Module 1, Practical 11
  • Recursive functions
  • Exercise
• Module 1, MidTerm Simulation
  • Download the data
  • Problem 1
  • Problem 2
• Module 2, Tutoring
• Module 2, Practical 1
  • Object Oriented Programming
    • Classes, Methods and Objects
    • Self
    • Definition of a class
    • The life-cycle of classes and objects in a program:
  • Encapsulation
  • Special methods
  • Inheritance and overriding
    • Exercise
  • Lambda functions
  • Exercises
• Module 2, Practical 2
  • Testing
  • Unit testing
    • Exercise
  • Measuring time
    • Exercise
  • Measuring memory
    • Exercise
• Module 2, Practical 3
  • Complexity
  • Exercises
• Module 2, Practical 4
  • Regular expressions
    • Basic Patterns
    • Group extraction
    • Exercises
    • re.compile
    • Substitution
    • Exercise
  • Exercises
• Module 2, Announcement
• Module 2, Practical 5
  • Sorting algorithms
  • Selection sort
    • A base class for sorting algorithms
    • Exercise (implementation)
  • Insertion sort
    • Exercise (implementation)
  • Merge sort and Quick sort
    • Merge sort
    • Exercise (Implementation)
    • Quick sort
    • Exercise (Implementation)
  • Exercise (algorithm benchmark)
  • Exercise (Counting Sort)
• Module 2, Practical 6
  • Data structures
    • Abstract Data Types (ADTs)
      • ADT: Sequence
      • ADT: Set
    • Iterators in Python
    • Exercise (set implementation)
    • ADT: dictionary
  • Linked lists
    • Example: bidirectional linked list
    • Exercise (complete bidirectional list)
    • Exercise (circular list)
  • Stacks
    • Exercise
  • Queues
  • Collections
    • Exercise
• Module 2, Practical 7
  • Trees
  • ADT: Binary Tree
    • Exercise
  • Tree visit
    • Binary Tree visits: DFS
    • Binary Tree visits: BFS
    • Exercises
  • ADT: Generic Tree
    • Exercise (implementation)
• Module 2, Practical 8
  • Graphs
  • Graph ADT
  • Implementation as adjacency matrix
    • Exercises
  • Implementation as (adjacency) linked list
    • Exercises
• Module 2, Practical 9
  • Graphs recap
  • Visits
    • Depth First Search (DFS)
    • Exercises
    • Breadth First Search (BFS)
    • Exercise
  • Exercise
• Module 2, Practical 10
  • Dynamic programming
    • Excercise
  • Finding (the optimal) overlaps among DNA strings
    • Exercise
• Module 2, MidTerm Simulation
  • Theoretical part
    • Exercise 1
    • Exercise 2
  • Practical part
    • Exercise 3
    • Exercise 4