Clarity-Driven Development of Scientific Software

Author

Dr. Franziska Horn

Published

August 3, 2025

Preface

This book is meant to empower researchers to code with confidence and clarity.

If you studied something other than computer science—especially in the natural sciences like physics, chemistry, or biology—it’s likely you were never taught how to properly develop software. Yet, you’re often still expected to write code as part of your daily work. Maybe you’ve taken a programming course like Python for Chemists and can put together functional scripts through trial and error (with a little help from an AI assistant). But chances are, no one ever showed you how to write well-structured, maintainable, and reusable code that could make your life—and collaborating with your colleagues—so much easier.

This book is for you if you want to:

  • Write functional software more quickly
  • Use a structured approach to design better programs
  • Reuse your code in future projects
  • Feel confident about what your scripts are doing
  • Prepare your research code for production
  • Share your work with pride.

Whether you’re just beginning your scientific journey—perhaps working on your first major project like a master’s thesis or your first paper—or you’re contemplating a move from academia to industry, the practical advice in this book can guide you along the way. We will approach software design from first principles and tackle research questions with a product mindset.

While the book contains some example code in Python to illustrate the concepts, the general ideas are independent of any programming language.1

Software development is a craft that’s best learned with the guidance of a senior colleague—someone who can show you the right tools and provide feedback through code reviews. Unfortunately, mentors with industry experience are rare in academia. While a book can’t replace an apprenticeship, I hope this one gives you a head start. It’s the book I wish I could have read at university and the one I always wanted to recommend to the students and junior developers I’ve mentored.

This is still a draft version! Please send me an email, if you have any suggestions for how this book could be improved!
Specifically, I’d really appreciate some feedback on

  • Where you got confused or lost or have an unanswered question
  • Where you disagree, or have different experiences
  • Where you started to get bored and felt like skipping ahead or giving up
  • Anything you find especially interesting or helpful

Thank you so much & enjoy! 😊

Acknowledgments

I would like to thank Marcel Lengert, Sarah Nomura, and Ana Moga for their thoughtful feedback.

The texts in this book were partly edited and refined with the help of ChatGPT, however, all original content is my own.

How to Cite

@book{horn2025cddsci,
  author = {Horn, Franziska},
  title = {Clarity-Driven Development of Scientific Software},
  year = {2025},
  url = {https://franziskahorn.de/rsebook/},
}

  1. Just in case, this tutorial provides a concise overview of the Python concepts used in this book.↩︎