Install

From GitHub (development)

git clone https://github.com/MervinPraison/PraisonAIBio.git
cd PraisonAIBio
pip install -e "src/praisonai-bio"
python -c "import praisonai_bio"

From PyPI (when published)

pip install praisonai-bio
python -c "import praisonai_bio"

Note

PyPI releases track tagged versions on GitHub. Until the first publish, use the GitHub install above.

Required once per session

Always run import praisonai_bio before YAML or CLI toolsets.

---

Optional extras

Simulation (BASICO/COPASI)

pip install -e "src/praisonai-bio[simulation]"
# or: pip install "praisonai-bio[simulation]"

Plotting

pip install -e "src/praisonai-bio[plot]"

Everything

pip install -e "src/praisonai-bio[all,dev]"

---

PraisonAI CLI (workflows)

Install the PraisonAI wrapper for YAML workflows and agents:

pip install praisonai

Scaffold local agent config:

praisonai-bio init   # creates .praisonai/config.yaml + agent templates

---

Verify

praisonai-bio validate check
praisonai-bio tools validate

Expected: 26 tools, toolsets including sysbio-full.

Recipes (PraisonAI wrapper)

Do not use a custom bio recipe CLI. Point the wrapper at this repo:

export PRAISONAI_RECIPE_PATH=recipes/bio
praisonai recipe run biomodels-discovery --policy bio-public

Available recipes: biomodels-discovery, biomodels-research, biomodels-simulate, biomodels-perturb, biomodels-report.

---

Environment

Variable	Purpose
OPENAI_API_KEY	Agent examples (big/)
BIOMODELS_BASE_URL	Default https://www.biomodels.org
PRAISONAI_POLICY_PACK	bio-public or bio-lab — loads policy/packs/*.yaml
PRAISONAI_RECIPE_PATH	Set to recipes/bio for wrapper recipes

---

Documentation site

Live docs: https://bio.praison.ai

Local preview:

pip install -r docs/requirements.txt
mkdocs serve

Next: Get started