Find, check, and simulate curated systems-biology models from BioModels.org — with plain Python, AI agents, or YAML workflows.
Built on PraisonAI.
📖 Full documentation: bio.praison.ai
| Required | Optional | |
|---|---|---|
| Python 3.10+ | Yes | |
praisonai-bio package |
Yes | |
import praisonai_bio |
Yes — registers tools for agents/YAML | |
| Internet | Yes — live BioModels.org API | |
OPENAI_API_KEY |
Only for AI agent examples | |
praisonai CLI |
Only for YAML workflows | pip install praisonai |
[simulation] extra |
Only to run ODE simulations (BASICO) | pip install -e "src/praisonai-bio[simulation]" |
git clone https://github.com/MervinPraison/PraisonAIBio.git
cd PraisonAIBio
pip install -e "src/praisonai-bio"
python -c "import praisonai_bio"
Verify:
praisonai-bio validate check
Search BioModels for glycolysis models:
python examples/small/01_search.py
Sample output: JSON list of curated model IDs and names.
→ More small examples
OPENAI_API_KEY)export OPENAI_API_KEY=sk-...
python examples/big/01_find_models.py
Sample output: plain-English answer with recommended model IDs.
→ All agent examples
praisonai CLI + API key)pip install praisonai
export OPENAI_API_KEY=sk-...
python -c "import praisonai_bio"
praisonai workflow run workflows/cookbooks/glycolysis_demo.yaml
Three agents in sequence: find → summarise → simulate BIOMD0000000206.
→ Workflow guide
BIOMD0000000206 — Teusink yeast glycolysis. Used in examples, cookbooks, and docs.
biomodels-readonly (safe), sysbio-full (everything)Details: Tools · Toolsets · Skills · Examples
import praisonai_bio
from praisonai_bio.tools.search_models import search_models
print(search_models.run(query="glycolysis", num_results=5))
pip install -e "src/praisonai-bio[dev,simulation]"
./scripts/test_all.sh
python scripts/validate_repo.py
Build docs locally:
pip install -r docs/requirements.txt && mkdocs serve
→ Development · AGENTS.md
MIT