Scientist workflow¶

Industry six-stage model development (Gadkar et al.) mapped to PraisonAI YAML + bio tools.

flowchart LR
  S1[Scope] --> S2[Define]
  S2 --> S3[Represent]
  S3 --> S4[Calibrate]
  S4 --> S5[Explore]
  S5 --> S6[Publish]

Stage	Workflow	Tools
1 Scope	`gadkar_stage1_scope.yaml`	`query_article`, `search_models`
2 Define	`gadkar_stage2_define.yaml`	`trust_scorecard`, HITL
3 Represent	`gadkar_stage3_represent.yaml`	`sbml_to_graph`, `get_annotation`
4 Calibrate	`gadkar_stage4_calibrate.yaml`	`sedml_simulate`, `simulate_model`
5 Explore	`gadkar_stage5_variability.yaml`	`parameter_scan`, `compare_simulations`
6 Publish	`gadkar_stage6_clinical_design.yaml`	`repro_export`

Full chain:

praisonai workflow run workflows/lifecycle/scientist_full_pipeline.yaml

Talk2BioModels cookbooks: workflows/cookbooks/t2b_*.yaml