Tools at a glance¶
What each tool does — no code required to understand.
Discovery (safe, read-only)¶
| Tool | You ask… | You get… |
|---|---|---|
| search_models | “Find p53 models” | List from BioModels.org |
| get_modelinfo | “Details for BIOMD…” | Name, authors, description |
| rank_models | “Best fit for my question?” | Ranked list with scores |
| trust_scorecard | “Is this curated?” | Trust score + reasons |
| compare_models | “How do A and B differ?” | Side-by-side metadata |
| sbml_summarise | “What’s in the model?” | Species, reactions summary |
| sbml_validate | “Is the SBML valid?” | Structure and unit check |
| sedml_parse | “What SED-ML tasks exist?” | Tasks and data generators |
| get_annotation | “What databases link to this?” | MIRIAM annotations |
| query_article | “Which paper?” | DOI / PubMed links |
Simulation (needs pip install praisonai-bio[simulation])¶
| Tool | You ask… | You get… |
|---|---|---|
| load_biomodel | “Load this ID” | SBML on disk |
| simulate_model | “Run for 100 time units” | Time-course preview |
| steady_state | “Steady state?” | Concentrations |
| parameter_scan | “Scan parameter X” | Scan table |
| preview_outcomes | “Quick preview” | Short simulation |
| simulate_perturbation | “Change one parameter” | Perturbed run |
| custom_plotter | “Plot results” | PNG file |
Reporting & reproducibility¶
| Tool | You ask… | You get… |
|---|---|---|
| compare_simulations | “Baseline vs perturbed?” | Comparison summary |
| save_model | “Save SBML” | File on disk |
| repro_export | “Repro bundle” | Folder with SBML + checksums |
| ask_question | “Explain this model” | Metadata for the agent to reason over |
Toolsets (bundles)¶
| Toolset | Who it's for |
|---|---|
| biomodels-readonly | Discovery only — safe |
| sbml_analysis | Load, summarise, validate SBML |
| sysbio-core | Discovery + basic simulation |
| simulation | Running models (BASICO) |
| reporting | Compare models and simulations |
| repro | Reproducibility bundles |
| sysbio-full | All 21 tools |
| sysbio-orchestrator | Multi-step discovery agent |
| sysbio-safe | Read-only, no writes or simulation |
| genomics-bridge | v2 stub — register ClawBio tools at runtime |
Use in agents: toolsets=["biomodels-readonly"]
Full parameter list: Tools reference
Always run import praisonai_bio first.