QCB Scientific Programming 2019
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Scientific Programming for QCB
General Info
Practical 1
Practical 2
Practical 3
Practical 4
Practical 5
Practical 6
Practical 7
Practical 8
Practical 9
Practical 10
Practical 11
Midterm simulation
Index
QCB Scientific Programming 2019
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Index
Scientific Programming for QCB
General Info
Timetable and lecture rooms
Tutoring
Slides
Acknowledgements
Practical 1
Slides
Setting up the environment
The console
Visual Studio Code
The debugger
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
Midterm simulation
Before you start
Problem 1
Problem 2
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Index
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