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Software Engineering for Biological Science (Zero to Hero)

Quote

A journey of a thousand miles begins with a single step.

千里之行，始于足下。

This course is designed for individuals with zero coding experience and provides a focused overview of key software engineering topics relevant to bioinformatics and machine-learning/AI workflows.

It is designed to complement existing bioinformatics courses which have a focus on processing biological datasets, for example using R and Seurat for single-cell sequencing data.

This course is a roadmap and not an exhaustive resource. It highlights the key topics that you need to be familiar with and points you towards further resources for deeper learning.

Course Objectives

This course aims to equip you with a solid foundation in:

  1. Coding practices
  2. Basics of servers and cloud computing
  3. Containerization

so that you can:

  1. Manage your code effectively
  2. Process large datasets
  3. Scale up your computational power
  4. Reproduce every step of your analysis

Why Focus on Python?

While both R and Python offer unique advantages, proficiency in both languages is beneficial. However, this course will focus on Python for the following reasons:

  • Extensive Ecosystem: Python has a robust ecosystem of machine learning and AI software packages.
  • Mature Tooling: Python's language tools are more advanced compared to R.
  • Ease of Production: It's easier to productionize code in Python.
  • Cloud Integration: Python can interact seamlessly with cloud services.
  • Existing Coverage: Many bioinformatics courses already cover R.
  • Support Availability: Python is well-supported by tools like ChatGPT/LLMs due to the abundance of Python code available online.

Feedback

One of the difficulties in creating material for beginners is the curse of knowledge - the inability to remember what it was like to not know something. I would appreciate any feedback on the course material, especially if you are a beginner and find something difficult to understand or there is a gap in the explanations. Let me know and I will improve the material based on your feedback.

Course Author

Dr Shaun Chuah (Shaun.Chuah@glasgow.ac.uk)
Clinical Senior Research Fellow/Honorary Consultant Gastroenterologist
School of Infection and Immunity
University of Glasgow