KIDDS Summer 2025 – Software Engineering Seminar

📒 The slide is available in the docs/ directory. Download PDF version here.

Welcome to the lab session! This hands-on exercise simulates evolving real-world code through a series of progressive changes.

Getting Started

1. Clone this repository to your local machine.

   git clone https://github.com/seoklab/kidds-lab && cd kidds-lab

2. Edit src/main.py as you progress through each stage of the lab.

   • Each stage introduces a new goal or modification, much like real-world software evolution.

   • Updated requirements will be presented live during the seminar.

   • You can test your code by running it with the provided PDB file:

     python src/main.py data/protein.pdb

     The file data/protein.pdb is provided for testing¹. Expected outputs for each stage will be shared during the session.

If You're Stuck

If you miss a stage or want to align with the current one, use the prepare-stage.sh script.

• It applies naive reference solutions for all previous stages and prepares your working directory for the stage you specify.

  ./prepare-stage.sh <stage>

  Replace <stage> with a number from 1 to 5. For example:

  ./prepare-stage.sh 3

  This will apply solutions for stages 0 through 2 and leave stage 3 ready for you to implement.

• The script is reentrant, so you can run it again or switch between stages as needed.

⚠️ Important: This script will overwrite your working files. To keep your current progress, commit your changes first. The git history is preserved, so you can always roll back if needed.

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Footnotes

1. It is PDB entry 3CYE, a very unusual file with both multiple models and alternate locations, and differing residue ids across models. It highlights the complexity of real-world PDB data. ↩