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Detailed Python Roadmap Genetics

This document outlines a detailed three-month Python roadmap for PhD students in Genetics and Plant Breeding, covering Python fundamentals, data science, visualization, bioinformatics, and machine learning. It includes specific topics, practices, datasets, and learning resources to enhance skills in data analysis and processing relevant to genetics. The roadmap emphasizes practical applications, such as data cleaning, visualization, and predictive modeling using machine learning techniques.

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13 views3 pages

Detailed Python Roadmap Genetics

This document outlines a detailed three-month Python roadmap for PhD students in Genetics and Plant Breeding, covering Python fundamentals, data science, visualization, bioinformatics, and machine learning. It includes specific topics, practices, datasets, and learning resources to enhance skills in data analysis and processing relevant to genetics. The roadmap emphasizes practical applications, such as data cleaning, visualization, and predictive modeling using machine learning techniques.

Uploaded by

suryapawan50244
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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Detailed Python Roadmap for Genetics & Plant Breeding (PhD Level)

Month 1: Python Fundamentals

1. Python Setup and IDEs:


- Install Python & Anaconda
- Jupyter Notebook, Google Colab

2. Core Python Concepts:


- Variables, Data Types (int, float, string, boolean)
- Lists, Tuples, Dictionaries, Sets

3. Control Flow:
- if-else statements
- for and while loops
- List comprehensions

4. Functions and Modules:


- Writing custom functions
- Importing libraries (math, os, sys)

5. File Handling:
- Reading & writing text/CSV files
- Handling FASTA-like text files

6. Practice:
- Read phenotype CSV file, calculate average yield.
- Parse a small FASTA file to extract sequences.

Month 2: Data Science & Visualization

1. NumPy:
- Arrays, indexing, slicing
- Basic matrix operations

2. Pandas:
- Series & DataFrames
- Importing CSV/Excel files
- Data cleaning (handling NaN values, renaming columns)
- Merging genotype and phenotype data

3. Visualization:
- Matplotlib (line, scatter, histogram)
- Seaborn (heatmap, pairplot, boxplot)
- Customizing plots for publications

4. Basic Statistics in Python:


- Mean, median, mode, variance, std deviation
- Correlation (Pearson, Spearman)
- Linear regression with statsmodels

5. Practice:
- Combine genotype and phenotype CSVs
- Plot yield distribution and correlation heatmap

Month 3: Bioinformatics & Machine Learning

1. Biopython:
- SeqIO module for reading/writing FASTA and GenBank files
- Extracting specific gene sequences
- Running BLAST via Biopython

2. Machine Learning Basics (Scikit-learn):


- Data preprocessing (normalization, encoding)
- Train/test split
- Linear regression, Random Forest (for trait prediction)
- Model evaluation (RMSE, R2 score)

3. Automation:
- Writing scripts to process multiple phenotype/genotype files
- Looping through directories for bulk data processing

4. Pipelines & Integration:


- Using Python to call R scripts (for specialized breeding models)
- Introduction to cloud notebooks (Google Colab for heavy computations)

5. Practice:
- Build a pipeline for reading multiple datasets, cleaning data, and plotting
- Predict trait performance from marker data using ML

Datasets & Resources

Datasets:
- MaizeGDB: https://www.maizegdb.org/
- CIMMYT Wheat Data: https://data.cimmyt.org/
- SoyBase (Soybean): https://www.soybase.org/

Learning Resources:
- Python Basics: https://www.w3schools.com/python/
- Pandas: https://www.kaggle.com/learn/pandas
- Data Visualization: https://seaborn.pydata.org/
- Biopython Tutorial: https://biopython.org/wiki/Tutorial
- Scikit-learn: https://scikit-learn.org/

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