bioinformatics zero to hero

Zero to Hero BioPython for Bioinformatics

Part 1: Learning Python Fundamentals

Module 1: Introduction to Python

• Overview of Python and its applications in bioinformatics.
• Installation and setup (Python, IDEs, Jupyter Notebook).
• Writing your first Python script.

Module 2: Python Syntax and Basics

• Variables and data types.
• Basic operators (arithmetic, logical, and comparison).
• Input and output operations.

Module 3: Control Structures

• Conditional statements (if-else).
• Loops (for and while).
• Use cases in bioinformatics (e.g., DNA sequence analysis).

Module 4: Functions and Modules

• Writing and calling functions.
• Scope and arguments.
• Importing and using Python modules.

Module 5: Data Structures

• Lists, tuples, and dictionaries.
• Operations and methods on these structures.
• Applications in sequence data storage and manipulation.

Module 6: File Handling

• Reading and writing files.
• Working with FASTA and CSV files.
• Error handling in file operations.

Module 7: Introduction to Libraries

• Overview of useful Python libraries (NumPy, pandas, matplotlib).
• Installing libraries using pip.

Module 8: Data Visualization

• Plotting data using matplotlib.
• Simple bioinformatics visualizations (e.g., GC content graphs).

Module 9: Regular Expressions

• Pattern matching with the re module.
• Extracting motifs from DNA sequences.

Module 10: Debugging and Optimization

• Debugging techniques and tools.
• Optimizing Python code for performance.

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Part 2: Learning BioPython

Module 1: Introduction to BioPython

• Overview of BioPython and its ecosystem.
• Installing BioPython.
• Structure and key modules of BioPython.

Module 2: Working with Sequence Data

• Reading and writing sequence files (FASTA, GenBank).
• Manipulating sequences with Seq and SeqRecord objects.

Module 3: Sequence Alignments

• Pairwise sequence alignments.
• Global and local alignment techniques using Bio.Align.

Module 4: Handling Biological Databases

• Accessing NCBI databases using Bio.Entrez.
• Retrieving sequence data (e.g., protein or gene sequences).

Module 5: Phylogenetics with BioPython

• Parsing phylogenetic trees.
• Visualization and manipulation of trees using Bio.Phylo.

Module 6: Working with Biological Features

• Parsing annotation files (GFF, GenBank).
• Extracting features like genes and promoters.

Module 7: Protein Analysis

• Working with protein sequences.
• Calculating molecular weight and isoelectric point.

Module 8: Parsing and Analyzing Structures

• Working with PDB files.
• Analyzing 3D structures using Bio.PDB.

Module 9: Simulating Sequence Evolution

• Tools for simulating sequence evolution.
• Creating randomized sequences and testing mutations.

Module 10: Advanced Topics and Custom Scripts

• Writing custom scripts for complex workflows.
• Combining BioPython with other libraries for comprehensive analyses.

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Part 3: Project Module

Module 1: Capstone Project

• Choose a project based on personal or academic interest (examples):
  • Building a tool to analyze and visualize GC content across multiple sequences.
  • Automating phylogenetic tree generation from NCBI data.
  • Parsing and analyzing protein structures.
• Presenting the final project with documentation and results.