Tools and Environments

This page describes a recommended setup for course work and a checklist for getting started.

Recommended software

• Miniconda or Mamba for package management.
  • https://docs.conda.io/en/latest/miniconda.html
  • https://mamba.readthedocs.io/en/latest/installation.html
• Python 3.11+
  • Core language for notebooks and scripting.
• Jupyter (Lab or Notebook)
  • https://jupyter.org/
• Git + GitHub
  • https://git-scm.com/
  • https://github.com/
• BLAST
  • https://blast.ncbi.nlm.nih.gov/Blast.cgi
• Biopython
  • https://biopython.org/

Suggested environment checklist

• Install Python and a package manager.
• Create a new environment for this course.
• Install core libraries: biopython, pandas, numpy, matplotlib.
• Open a notebook and run a short test script.

Example conda workflow

conda create -n bioinfo python=3.11
conda activate bioinfo
conda install biopython pandas numpy matplotlib
pip install jupyterlab

Reproducibility tips

• Keep environment files (e.g., environment.yml).
• Record software versions in reports.
• Use clear file naming and folder structure.

Suggested class activity

• Set up a new environment and run a short sequence parsing script.