From Lab Bench to Command Line

Course Syllabus: CS for Biology

This syllabus provides a week-by-week breakdown of the topics, skills, and projects you will master. The course is designed to build your programming knowledge from the ground up in both C and Python, with a constant focus on real-world scientific applications.

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Module 1: Fundamentals in C & Python

This foundational module gets you writing code from day one. You will learn the core logic of programming in both a low-level compiled language (C) and a high-level interpreted language (Python), understanding the right tool for the right scientific task.

• Week 1: Setup & Basic Commands
  Environment Setup: Installing and configuring a code editor (VS Code), the GCC compiler for C, and the Python interpreter.
  First Programs: Writing "Hello, World!" in both languages to understand the compilation (C) vs. interpretation (Python) workflow.
  Variables & Data Types: C: int, float, char, double. Understanding static typing and memory declaration. Python: int, float, str, bool. Understanding dynamic typing.
  Bio/Chem Application: Storing values like pH, temperature, and molecular weights in variables.
• Week 2: Control Flow & Logic
  Operators: Arithmetic (+, -, *, /), relational (==, >), and logical (&&, ||, !) operators in both languages.
  Conditionals: Using if-else and switch-case (C) / if-elif-else (Python) to make decisions.
  Loops: Iterating with for and while loops to perform repetitive tasks.
  Bio/Chem Application: Writing a script to classify an amino acid as polar or non-polar based on its properties, or iterating through a list of lab results to find values outside a safe range.
• Week 3: Functions & Modularity
  Function Basics: Defining and calling functions in both languages to create reusable and organized code.
  Parameters & Arguments: Understanding how to pass data to functions.
  Scope: Learning about local vs. global variables.
  C Specifics: Introduction to header files (.h) and function prototypes.
  Bio/Chem Application: Creating a single function that calculates the reverse complement of any given DNA sequence.

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Module 2: Data Structures for Scientists

Data is the lifeblood of science. This module teaches you how to structure, store, and manipulate the complex data found in biology and chemistry, from long genetic sequences to tables of experimental results.

• Week 4: Arrays & Lists
  C: Working with fixed-size arrays to store collections of data.
  Python: Using flexible, dynamic lists for easy data manipulation (adding, removing, sorting).
  Bio/Chem Application: Storing a series of absorbance readings from a spectrophotometer in an array/list to calculate the mean and standard deviation.
• Week 5: Handling Strings & Sequences
  C: Manipulating character arrays (char*) and using the <string.h> library.
  Python: Using powerful built-in string methods for searching, slicing, and formatting.
  Bio/Chem Application: The core of bioinformatics—reading DNA, RNA, and protein sequences to search for specific motifs (e.g., a TATA box or a start codon).
• Week 6: Complex Data Types
  C: Defining custom data types with struct to group related information. Introduction to pointers for efficient memory management. Application: Creating an AminoAcid struct to hold its name, 3-letter code, and molecular weight together.
  Python: Using Dictionaries (dict) for key-value mapping and Tuples (tuple) for immutable data. Application: Using a dictionary to store the standard genetic code (mapping codons to amino acids).

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Module 3: Applied Computational Projects

In this final module, you will integrate all your learned skills to build three complete, practical applications from scratch. You can choose to implement them in C, Python, or both to compare the languages.

• Week 7: Project 1 - DNA-to-Protein Translator 🧬
  Objective: Build a program that reads a DNA sequence from a file, transcribes it into mRNA, and translates it into the corresponding amino acid sequence.
  Skills Reinforced: File I/O, string manipulation, loops, and using dictionaries/structs for the genetic code.
• Week 8: Project 2 - Molecular Mass Calculator 🧪
  Objective: Create a tool that accepts a chemical formula (e.g., C6H12O6) or a protein sequence as input and calculates its total molecular weight.
  Skills Reinforced: String parsing, data structures (for atomic weights), and arithmetic calculations.
• Week 9: Project 3 - Reaction Kinetics Simulator ⏱️
  Objective: Write a program that simulates a simple first-order chemical reaction, showing how reactant concentration decreases over time based on a given rate constant.
  Skills Reinforced: Looping, applying mathematical formulas, functions, and logging output data to a file.