Module: Microbial Systematics Course

Module: Computational Microbiology in the Microbial Systematics Course

Welcome to Computational Microbiology, a core component of the Microbial Systematics course. This module was developed to give students practical experience in analyzing microbial diversity and understanding the principles of taxonomy and classification using real-world data.

This project was created during my time as a lab assistant in the Microbial Systematics course at Institut Teknologi Sepuluh Nopember (ITS) Surabaya.

Module Objectives

Students will explore microbial samples from various environments, ranging from soil and water to more specialized ecosystems—and apply computational tools in R to:

• Understand microbial taxonomy and classification
• Retrieve and align genetic sequences
• Construct and interpret phylogenetic trees

What You’ll Learn

1. Dataset Preparation
   Select diverse microbial species from various ecological niches for phylogenetic analysis.

2. Genetic Data Retrieval
   Access and retrieve DNA sequence data from GenBank for selected microbial taxa.

3. Sequence Alignment
   Perform multiple sequence alignment using bioinformatics tools to identify conserved regions and ensure accurate comparisons.

4. Phylogenetic Tree Construction
   Build evolutionary trees using methods like neighbor-joining or maximum likelihood, and learn how different approaches impact the resulting topology.

Note: This module is currently available in Bahasa Indonesia.

Explore the Module

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Want to Collaborate?

I’m always open to discussing education projects, bioinformatics modules, or teaching collaborations. Feel free to get in touch!