Toolsets

Toolsets are named bundles of tools for agents and YAML workflows.

Important

Run python -c "import praisonai_bio" before using toolsets in YAML or CLI.

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Toolsets

Toolset	Use when
biomodels-readonly	Search and metadata only (safe)
sbml_analysis	Load and summarise SBML
sysbio-core	Discovery + basic simulation
simulation	Run models (needs BASICO)
reporting	Compare and report
sysbio-full	All 21 tools
sysbio-orchestrator	Multi-step discovery agent
sysbio-safe	Read-only, no writes or simulation
repro	Reproducibility bundles
genomics-bridge	v2 stub — ClawBio genomics bridge (empty until external tools registered)

---

Python

import praisonai_bio
from praisonaiagents import Agent

agent = Agent(
    name="scout",
    toolsets=["biomodels-readonly"],
    llm="gpt-4o-mini",
)
agent.start("Find curated MAPK models")

---

YAML

agents:
  scout:
    role: BioModels Scout
    toolsets:
      - biomodels-readonly

---

Tools in sysbio-full

T2B (11): search_models, get_modelinfo, load_biomodel, simulate_model, ask_question, steady_state, parameter_scan, custom_plotter, get_annotation, query_article, save_model

Discovery: rank_models, trust_scorecard, compare_models, preview_outcomes, sbml_summarise, sbml_validate, sedml_parse, simulate_perturbation, compare_simulations, repro_export

Details: Tools at a glance · Tools reference