The Archive
2021—2025

A granular documentation of Mus Ab Ali's academic evolution. This repository tracks the transition from foundational engineering physics to advanced AI-integrated biotechnological research.

01

Foundational Engineering

Mechanics, Innovative Design, and Cell Architecture.

02

Biological Architecture

Genetics, Microbiology, and Algorithmic Thinking in Python.

Semesters 1 & 2

Structural Foundations

Innovative Design (MEC125)

  • Design Thinking Methodology: Empathize, Define, Ideate, Prototype, Test.
  • Hands-on fabrication: Transforming conceptual sketches into physical models.
  • Collaborative engineering: Solving real-world problems through interdisciplinary team dynamics.

Cell & Molecular Biology

  • Understanding the "Central Dogma": DNA → RNA → Protein.
  • Organelle function: Mastering the metabolic pathways of the Mitochondria and Golgi.
  • Cell Signaling: Study of G-protein coupled receptors and secondary messengers.

Engineering Sciences

  • Physics: Maxwell's equations and wave mechanics applied to biological imaging.
  • Chemistry: Thermodynamics and kinetics of enzyme-substrate interactions.
  • Digital Fabrication: Introduction to CAD and 3D printing workflows (MEC124).
Semesters 3 & 4

Mechanisms of Life

Python & MATLAB (BTE201/BTY177)

  • Python: Writing scripts for DNA sequence parsing and data visualization.
  • Object-Oriented Programming (OOP): Building classes for biological entities.
  • MATLAB: Numerical simulations of population growth and enzyme kinetics.

Microbiology & Genetics

  • Microbial Techniques: Gram staining, agar plating, and serial dilutions.
  • Mendelian & Non-Mendelian Genetics: Analysis of inheritance patterns and pedigrees.
  • Population Genetics: Study of Hardy-Weinberg equilibrium and genetic drift.

Immunology (BTY213)

  • Immune System Anatomy: T-cells, B-cells, and the complement system.
  • Antibody Engineering: Structure and function of different Immunoglobulins (IgG, IgM).
  • Vaccinology: Understanding the mechanics of mRNA and attenuated vaccines.
Semesters 5 & 6

Computational Systems

Bioinformatics & Genomic Data

  • Database Mining: Navigating NCBI, PDB, and UniProt.
  • Alignment Algorithms: Mastering BLAST, FASTA, and ClustalW.
  • Phylogeny: Building evolutionary trees using UPGMA and Neighbor-Joining.
  • Structural Biology: Protein folding prediction and secondary structure analysis.
  • Biopython: Automating large-scale genomic file processing (.pdb, .fasta).

Bioprocess Engineering

  • Bioreactor Design: Batch, Fed-batch, and Continuous cultures.
  • Scale-up Strategy: Oxygen transfer rates (OTR) and heat transfer in large tanks.
  • Downstream Processing: Centrifugation, filtration, and chromatography.

Emerging Technologies (ICT202B)

Exploration of AI and Machine Learning in Biotechnology. This course marked the pivot toward data-driven biology, focusing on neural networks for protein structure prediction.

Machine Learning AI Ethics Data Mining Predictive Analytics
Semester 7 & Specialization

Professional Mastery

Cheminformatics & Drug Design

Analyzing chemical structures using computational methods to predict drug-likeness (Lipinski's Rule of Five) and performing molecular docking to visualize ligand-receptor affinity.

QSAR Modeling
Virtual Screening

Regulatory Affairs & IPR

Understanding the legal landscape of biotechnology. Mastery of patent filing (IPR), clinical trial phases, FDA/ISO regulations, and the ethics of genetic engineering.

GMP/GLP
Patent Law

The Skill Matrix (Recap)

Wet Lab

Genetic Engineering (rDNA)

Microbial Fermentation

Immunology (ELISA)

Plant Tissue Culture

Software

Python / Biopython

MATLAB / Simulink

R-Programming

PyMol / AutoDock

Industry

Bioprocess Scale-up

Regulatory Compliance

Quality Control (QC)

Waste Management

Academic

Scientific Writing

Experimental Design

Statistical Analysis

Bioethics