Downloads#

Every script from the book, ready to run. Choose .zip or .tar.gz — the contents are identical.

All scripts#

Python and Perl together, with the setup README.

unzip biobook-all-scripts.zip
# or
tar -xzf biobook-all-scripts.tar.gz

Python only#

39 vanilla + 39 AI scripts (78 total).

Perl only#

49 companion scripts plus the BeginPerlBioinfo.pm module.

How the scripts are paired#

Every Python example exists in two versions:

• chNN_vanilla_NN.py — standard Python and BioPython only. Runs with no API key and no network access.
• chNN_ai_NN.py — the same task with an LLM added to interpret the results.

Reading them side by side is the point of the book.

Start with the vanilla version of any script. Once you understand what it computes, open the AI version and look only at what was added.

Setting up the AI scripts#

Install the client library:

pip install openai

The scripts default to OpenRouter. Set your key:

export OPENAI_API_KEY="sk-..."
python3 ch01_ai_01.py

Three environment variables are honored:

To run against a local model instead:

export OPENAI_BASE_URL="http://localhost:11434/v1"   # Ollama
export OPENAI_MODEL="llama3"
export OPENAI_API_KEY="ollama"

If the openai package is not installed, the AI scripts print a notice and still run their biological analysis — only the AI commentary is replaced with a placeholder. You can study every script without an API key. If the package is installed but the key is missing, the API call itself will error, so set a key before running the AI versions.

Python dependencies#

Most scripts need only the standard library. Some use:

pip install biopython pandas matplotlib numpy

Running the Perl scripts#

The Perl examples need the bundled module, so run them from inside perl/:

cd perl
perl example10-1.pl

From elsewhere, add the directory to the include path:

perl -I/path/to/perl example10-1.pl

Script index#

| 1 | The Language of Life | ch01_vanilla_01-03.py | ch01_ai_01-03.py | 6 | | 2 | Python Basics | ch02_vanilla_01-04.py | ch02_ai_01-04.py | 8 | | 3 | The Central Dogma | ch03_vanilla_01-04.py | ch03_ai_01-04.py | 8 | | 4 | Biological Data | ch04_vanilla_01-03.py | ch04_ai_01-03.py | 6 | | 5 | Sequence Alignment | ch05_vanilla_01-04.py | ch05_ai_01-04.py | 8 | | 6 | Motifs & Restriction Enzymes | ch06_vanilla_01-03.py | ch06_ai_01-03.py | 6 | | 7 | Gene Expression | ch07_vanilla_01-03.py | ch07_ai_01-03.py | 6 | | 8 | Protein Structure | ch08_vanilla_01-02.py | ch08_ai_01-02.py | 4 | | 9 | Genome Analysis | ch09_vanilla_01-02.py | ch09_ai_01-02.py | 4 | | 10 | Metagenomics | ch10_vanilla_01-02.py | ch10_ai_01-02.py | 4 | | 11 | Single-Cell Analysis | ch11_vanilla_01-02.py | ch11_ai_01-02.py | 4 | | 12 | LLM Reasoning | ch12_vanilla_01-02.py | ch12_ai_01-02.py | 4 | | 13 | Pipelines | ch13_vanilla_01-03.py | ch13_ai_01-03.py | 6 | | 14 | Capstone Projects | ch14_vanilla_01-02.py | ch14_ai_01-02.py | 4 |

Totals: 39 vanilla + 39 AI = 78 Python scripts, plus 49 Perl scripts.

Verification#

These archives were checked at packaging time:

• all 78 Python scripts pass python3 -m py_compile — 0 syntax errors
• pyflakes reports 0 unused imports and 0 undefined names
• all 49 Perl scripts pass perl -I. -c
• verified again after extraction from each archive