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Minimal examples (2 lines)

Same tools as small examples — fewer lines.

pip install -e "src/praisonai-bio"
python examples/minimal/search.py
Script Tested output
search.py output.txt
info.py same as 02-model-info
trust.py same as 03-trust-score
validate.py same as 04-validate-sbml
graph.py same as 10-sbml-graph
compare_runs.py below

Tested output — compare_runs (offline)

Click to expand 
{
  "baseline_keys": [
    "ATP"
  ],
  "perturbation_keys": [
    "ATP"
  ],
  "parameter_changed": null,
  "metrics": {
    "ATP": {
      "rmse": 0.04082482904638634,
      "peak_time_baseline": 0.0,
      "peak_time_variant": 0.0,
      "auc_baseline": 1.8,
      "auc_variant": 1.725
    }
  },
  "status": "compared"
}
Click to expand 
{
  "query": "glycolysis AND curationstatus:\"Manually curated\"",
  "count": 10,
  "models": [
    {
      "format": "SBML",
      "id": "BIOMD0000000471",
      "lastModified": null,
      "name": "Smallbone2013 - Yeast metabolic model with linlog rate law",
      "submissionDate": "2013-02-14T00:00:00Z",
      "submitter": "Kieran Smallbone",
      "url": "https://www.biomodels.org/BIOMD0000000471"
    },
    {
      "format": "SBML",
      "id": "BIOMD0000000472",
      "lastModified": null,
      "name": "Smallbone2013 - Yeast metabolic model with modular rate law",
      "submissionDate": "2013-02-14T00:00:00Z",
      "submitter": "Kieran Smallbone",
      "url": "https://www.biomodels.org/BIOMD0000000472"
    },
    {
      "format": "SBML",
      "id": "BIOMD0000000473",
      "lastModified": null,
      "name": "Smallbone2013 - Yeast metabolic model with modular rate law, merged with Pritchard 2002",
      "submissionDate": "2013-02-14T00:00:00Z",
      "submitter": "Kieran Smallbone",
      "url": "https://www.biomodels.org/BIOMD0000000473"
    },
    {
      "format": "SBML",
      "id": "BIOMD0000000469",
      "lastModified": null,
      "name": "Smallbone2013 - E.coli metabolic model with linlog rate law",
      "submissionDate": "2013-02-14T00:00:00Z",
      "submitter": "Kieran Smallbone",
      "url": "https://www.biomodels.org/BIOMD0000000469"
    },
    {
      "format": "SBML",
      "id": "BIOMD0000000470",
      "lastModified": null,
      "name": "Smallbone2013 - E.coli metabolic model with modular rate law",
      "submissionDate": "2013-02-14T00:00:00Z",
      "submitter": "Kieran Smallbone",
      "url": "https://www.biomodels.org/BIOMD0000000470"
    },
    {
      "format": "SBML",
      "id": "BIOMD0000000428",
      "lastModified": null,
      "name": "Achcar2012 - Glycolysis in bloodstream form T. brucei",
      "submissionDate": "2012-09-13T00:00:00Z",
      "submitter": "Lukas Endler",
      "url": "https://www.biomodels.org/BIOMD0000000428"
    },
    {
      "format": "SBML",
      "id": "BIOMD0000000513",
      "lastModified": null,
      "name": "Kerkhoven2013 - Glycolysis in T.brucei - MODEL A",
      "submissionDate": "2014-01-31T00:00:00Z",
      "submitter": "Vijayalakshmi Chelliah",
      "url": "https://www.biomodels.org/BIOMD0000000513"
    },
    {
      "format": "SBML",
      "id": "BIOMD0000000503",
      "lastModified": null,
      "name": "Messiha2013 - combined glycolysis and pentose phosphate pathway model",
      "submissionDate": "2013-11-29T00:00:00Z",
      "submitter": "Kieran Smallbone",
      "url": "https://www.biomodels.org/BIOMD0000000503"
    },
    {
      "format": "SBML",
      "id": "BIOMD0000000482",
      "lastModified": null,
      "name": "Noguchi2013 - Insulin dependent glucose metabolism",
      "submissionDate": "2013-01-02T00:00:00Z",
      "submitter": "Rei Noguchi",
      "url": "https://www.biomodels.org/BIOMD0000000482"
    },
    {
      "format": "SBML",
      "id": "BIOMD0000000172",
      "lastModified": null,
      "name": "Pritchard2002_glycolysis",
      "submissionDate": "2008-05-20T00:00:00Z",
      "submitter": "Nicolas Le Nov\u00e8re",
      "url": "https://www.biomodels.org/BIOMD0000000172"
    }
  ]
}

Regenerate all captures: ./scripts/capture_example_outputs.sh

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