PPB18

Programming in Python for Biologists

Timetable (provisional)


Mon, Jul 23rd
Getting Started - Day #1
09:30 - 11:00 Welcome, introductions & expectations.
Warm-up with Diagnostic questionnaire and Q&A session.
Introduction to the working environment.
11:00 - 11:30 Coffee Break
11:30 - 12:30 Python shell
  • Variables
  • Importing modules
  • Python types: integers, floating
  • math
12:30 - 14:00 Lunch Break
14:00 - 16:00 Python Programs
  • Running a program
  • Input and output
16:00 - 16:30 Tea Break
16:30 - 18:00 Reading and writing files
  • Reading input from a file
  • Writing to files
  • Commenting your code
    • Tue, Jul 24th
    09:30 - 11:00 Morning Wrap-up (what have we done so far?)
    Repeating Things
    • for loops
    • while loops
    • Python types: strings
    • Manipulating strings
    11:00 - 11:30 Coffee Break
    11:30 - 12:30 Parsing Data Records I
    • File formats in bioinformatics
    • if conditions
    • Parsing FASTA files
    12:30 - 14:00 Lunch Break
    14:00 - 16:00 Parsing Data Records II
    • Python types: Lists
    • More on parsing
    16:00 - 16:30 Tea Break
    16:30 - 18:00 Parsing Data Records III
    • More on parsing
    Wed, Jul 25th
    09:30 - 11:00 Morning Wrap-up (what have we done so far?)
    Functions
    • Built-ins
    • Namespaces
    • Functions
    • Python types: Tuples
    11:00 - 11:30 Coffee Break
    11:30 - 12:30 Debugging
    • Errors and Exceptions
    • Error handling
    • try...except
    12:30 - 14:00 Lunch Break
    14:00 - 16:00 Data Columns
    • Useful built-in functions
    • String concatenation
    • String formatting
    16:00 - 16:30 Tea Break
    16:30 - 18:00 Tabular Data
    • Lists of lists
    • Taranspose a table
    • Sorting
    Thu, Jul 26th
    09:30 - 11:00 Morning Wrap-up (what have we done so far?)
    Searching--> Data Searching
    • Python types:dictionaries
    • Python types: sets
    11:00 - 11:30 Coffee Break
    11:30 - 12:30 Pipelines
    • Running a program from Python
    • subprocess and os.systems modules
    • sys.argv
    12:30 - 14:00 Lunch Break
    14:00 - 16:00 Python Libraries
    Participants will be split in 4 groups. Each group will practice on a different Python Library (e.g., BioPython, re - pattern matching, matplotlib, rpy2, pandas) and present the outcome of their practice to other groups.
    16:00 - 16:30 Tea Break
    16:30 - 18:00 Python Libraries (continued)
    Fri, Jul 27th
    Reflective practice - Day #5
    09:30 - 11:00 Practice with feedback
    • Review of the course and Q&A session
    • Practice with feedback on difficult exercises
    11:00 - 11:30 Coffee Break
    11:30 - 12:30 Practice with feedback
    • More practice with feedback
    • Write your own script(s)
    12:30 - 14:00 Lunch Break
    14:00 - 16:00 Practice with feedback and final Wrap-up
    • More practice with feedback
    • Write your own script(s)
    • Outcomes versus expectations
    • Final Wrap-up session
    Course Homepage

    Instituto Gulbenkian de Ciência,

    Apartado 14, 2781-901 Oeiras, Portugal

    GTPB Homepage

    IGC Homepage

    Last updated:   Jun 16th 2018