Jupman
latest
Scientific Programming for QCB
General Info
Timetable and lecture rooms
Moodle
Zoom links
Slides
Acknowledgements
Practical 1
Slides
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
Practical 2
Slides
Modules
Objects
Variables
Numeric types
Integers
Booleans
Real numbers
Strings
Methods for the str object
Exercises
Practical 3
Slides
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
Exercises
Practical 4
Slides
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
Practical 5
Slides
More on loops
Ternary operator
Break and continue
Continue statement
Break statement
List comprehension
Dictionaries
Functions working on dictionaries
Dictionary methods
Exercises
Practical 6
Slides
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
Practical 7
Slides
Functions
Getting input from the command line
Argparse
Exercises
Practical 8
Slides
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
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
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
Practical 11
Slides
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
Material
Midterm
Before you start
Problem 1
Problem 2
Available material for exams
Download the data
A possible solution
Jupman
Scientific Programming for QCB
General Info
Timetable and lecture rooms
Moodle
Zoom links
Slides
Acknowledgements
Practical 1
Slides
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
Practical 2
Slides
Modules
Objects
Variables
Numeric types
Integers
Booleans
Real numbers
Strings
Methods for the str object
Exercises
Practical 3
Slides
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
Exercises
Practical 4
Slides
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
Practical 5
Slides
More on loops
Ternary operator
Break and continue
Continue statement
Break statement
List comprehension
Dictionaries
Functions working on dictionaries
Dictionary methods
Exercises
Practical 6
Slides
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
Practical 7
Slides
Functions
Getting input from the command line
Argparse
Exercises
Practical 8
Slides
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
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
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
Practical 11
Slides
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
Material
Midterm
Before you start
Problem 1
Problem 2
Available material for exams
Download the data
A possible solution
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