For researchers

Start here: Interactive guide — pick your path, self-checks, and troubleshooting (click to expand).

PraisonAIBio helps you find, check, and simulate models from BioModels.org — without browsing thousands of entries by hand.

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The problem it solves

Manual work	With PraisonAIBio
Weeks browsing BioModels	Minutes: search + ranked shortlist
Reading papers for assumptions	Agent summary + trust score
Setting up COPASI by hand	Optional one-command simulation

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Two ways to work

A — Direct tools (small examples)

You run a short script. No chat.

→ Best for: quick lookup, one model ID, validation.

→ Folder: examples/small/

B — AI agent (big examples)

You ask in English. The agent picks tools.

→ Best for: open questions, comparing models, reports.

→ Folder: examples/big/

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Typical study flow

graph TD
    A[Research question] --> B[Search BioModels]
    B --> C[Rank & trust score]
    C --> D[Assumption review]
    D --> E{Happy?}
    E -->|Yes| F[Simulate]
    E -->|No| B
    F --> G[Compare & report]

YAML workflows in workflows/discovery/ automate this team.

Workflow file	What it does
biomodels_discovery_pipeline.yaml	Question → shortlist
biomodels_assumption_review.yaml	Check assumptions (human approval step)
biomodels_baseline_simulation.yaml	Run baseline simulation
biomodels_full_research_workflow.yaml	All phases together
cookbooks/full_platform_pipeline.yaml	Eight-step end-to-end demo

Run any workflow:

praisonai workflow run workflows/discovery/biomodels_discovery_pipeline.yaml

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Demo model to try

BIOMD0000000206 — yeast glycolysis (Teusink et al.)

Used in cookbooks, examples, and benchmarks.

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Need help choosing?

If you…	Use
Know the model ID	examples/small/02_model_info.py
Have a pathway name only	examples/big/01_find_models.py
Want a full pipeline	workflows/cookbooks/glycolysis_demo.yaml

See Tools at a glance and Tools reference for the full tool list and parameters.