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Tools reference

All 21 tools with parameters agents can use. Provide every option explicitly in prompts or YAML — agents do not read env vars or config files.

Tip

Run python -c "import praisonai_bio" before calling tools from agents or workflows.

Discovery (read-only)

Tool Parameters Returns
search_models query (str), num_results (int, default 10), offset (int, default 0), curated_only (bool, default true) JSON list of matching models
get_modelinfo model_id (str, e.g. BIOMD0000000206) Name, authors, description
rank_models query (str), num_results (int, default 10), research_question (str, optional) Ranked models with scores
trust_scorecard model_id (str) Curation score and reasons
compare_models model_id_a (str), model_id_b (str) Side-by-side metadata
get_annotation model_id (str) MIRIAM / RDF annotations
query_article model_id (str) DOI, PubMed, citation links
ask_question model_id (str), question (str) Metadata-grounded answer text
sbml_summarise model_id (str) Species, compartments, reactions summary
sbml_validate model_id (str, optional), sbml_path (str, optional) — one required Validation report (structure, units)
sedml_parse model_id (str), filename (str, optional SED-ML file in bundle) SED-ML tasks and data generators

Simulation (needs pip install praisonai-bio[simulation])

Tool Parameters Returns
load_biomodel model_id (str), save_path (str, optional) Path to downloaded SBML
simulate_model model_id (str, optional), sbml_path (str, optional), duration (float, default 100), step (float, default 0.1) Time-course JSON preview
steady_state model_id (str, optional), sbml_path (str, optional) Steady-state concentrations
parameter_scan model_id (str), parameter (str), start (float), end (float), steps (int, default 10) Scan table JSON
preview_outcomes model_id (str), duration (float, default 50) Short baseline simulation
simulate_perturbation model_id (str), parameter (str), value (float), duration (float, default 100) Perturbed time-course JSON
custom_plotter data_json (str), x_column (str), y_column (str), title (str, default "Simulation plot"), output_path (str, default plot.png) PNG path (needs [plot])

Reporting & reproducibility

Tool Parameters Returns
compare_simulations baseline_json (str), perturbation_json (str) Comparison summary JSON
save_model model_id (str), output_path (str) Saved SBML path
repro_export model_id (str), output_dir (str), run_id (str, optional) Bundle dir with SBML, metadata, commands.sh, checksums

Python example

import praisonai_bio
from praisonai_bio.tools.search_models import search_models
from praisonai_bio.tools.sbml_validate import sbml_validate

print(search_models.run(query="glycolysis", num_results=5))
print(sbml_validate.run(model_id="BIOMD0000000206"))

See also