Examples¶

Runnable scripts with recorded sample output (captured from live runs against BioModels.org).

Minimal — 2 lines

Shortest possible scripts. Same tools, fewer lines.

Minimal examples
Small — no AI

10 direct tool calls. No API key. Fastest learning path.

Small examples
Agent — with AI

PraisonAI agents using gpt-4o-mini and BioModels toolsets.

Agent examples
Notebooks

Five Jupyter notebooks for interactive workflows.

Notebooks

Before you run¶

cd PraisonAIBio
pip install -e "src/praisonai-bio"
python -c "import praisonai_bio"

Agent examples also need:

export OPENAI_API_KEY=sk-...
pip install -e "src/praisonai-bio[simulation]"   # optional — for BASICO simulation

Regenerate all saved outputs:

./scripts/capture_example_outputs.sh

Not sure which to run? → Interactive guide

Example	Script	Docs
Search models	`examples/small/01_search.py`	01 — Search
Model metadata	`examples/small/02_model_info.py`	02 — Model info
Trust score	`examples/small/03_trust_score.py`	03 — Trust score
Validate SBML	`examples/small/04_validate_sbml.py`	04 — Validate SBML
Simulate	`examples/small/05_simulate.py`	05 — Simulate
Perturb	`examples/small/06_perturb.py`	06 — Perturb
Compare models	`examples/small/07_compare_models.py`	07 — Compare models
Compare sims	`examples/small/08_compare_sims.py`	08 — Compare sims
Repro export	`examples/small/09_repro_export.py`	09 — Repro export
SBML graph	`examples/small/10_sbml_graph.py`	10 — SBML graph

Example	Script	Docs
Find models	`examples/big/01_find_models.py`	01 — Find models
Summarise model	`examples/big/02_summarise_model.py`	02 — Summarise
Discovery study	`examples/big/03_discovery_study.py`	03 — Discovery
Glycolysis demo	`examples/big/04_glycolysis_demo.py`	04 — Glycolysis

Agent output varies

LLM replies differ slightly each run. Saved output.txt files show a real capture.

praisonai workflow run workflows/cookbooks/glycolysis_demo.yaml