Example — SBML reaction graph¶
Category: Small (no AI) · Script: examples/small/10_sbml_graph.py
Minimal (2 lines): examples/minimal/graph.py
Reaction map for BIOMD0000000206.
How to run¶
pip install -e "src/praisonai-bio"
python examples/small/10_sbml_graph.py
Needs: Internet.
Tested output¶
Live capture from ./scripts/capture_example_outputs.sh.
Click to view full output
{
"model_id": "BIOMD0000000206",
"graph": {
"nodes": [
{
"id": "s1",
"type": "species",
"label": "Glucose"
},
{
"id": "at",
"type": "species",
"label": "ATP"
},
{
"id": "s2",
"type": "species",
"label": "F16P"
},
{
"id": "s3",
"type": "species",
"label": "Triose_Gly3Phos_DHAP"
},
{
"id": "na",
"type": "species",
"label": "NAD"
},
{
"id": "s4",
"type": "species",
"label": "3PG"
},
{
"id": "s5",
"type": "species",
"label": "Pyruvate"
},
{
"id": "s6",
"type": "species",
"label": "Acetaldehyde"
},
{
"id": "s6o",
"type": "species",
"label": "extracellular acetaldehyde"
},
{
"id": "v1",
"type": "reaction",
"label": "v1"
},
{
"id": "v2",
"type": "reaction",
"label": "v2"
},
{
"id": "v3",
"type": "reaction",
"label": "v3"
},
{
"id": "v4",
"type": "reaction",
"label": "v4"
},
{
"id": "v5",
"type": "reaction",
"label": "v5"
},
{
"id": "v7",
"type": "reaction",
"label": "v7"
},
{
"id": "v8",
"type": "reaction",
"label": "v8"
},
{
"id": "v9",
"type": "reaction",
"label": "v9"
},
{
"id": "v10",
"type": "reaction",
"label": "v10"
},
{
"id": "v6",
"type": "reaction",
"label": "v6"
},
{
"id": "v0",
"type": "reaction",
"label": "v0"
},
{
"id": "compartment",
"type": "compartment",
"label": "compartment"
}
],
"edges": [
{
"source": "s1",
"target": "v1",
"type": "reactant"
},
{
"source": "at",
"target": "v1",
"type": "reactant"
},
{
"source": "v1",
"target": "s2",
"type": "product"
},
{
"source": "s2",
"target": "v2",
"type": "reactant"
},
{
"source": "v2",
"target": "s3",
"type": "product"
},
{
"source": "s3",
"target": "v3",
"type": "reactant"
},
{
"source": "na",
"target": "v3",
"type": "reactant"
},
{
"source": "v3",
"target": "s4",
"type": "product"
},
{
"source": "v3",
"target": "at",
"type": "product"
},
{
"source": "s4",
"target": "v4",
"type": "reactant"
},
{
"source": "v4",
"target": "s5",
"type": "product"
},
{
"source": "v4",
"target": "at",
"type": "product"
},
{
"source": "s5",
"target": "v5",
"type": "reactant"
},
{
"source": "v5",
"target": "s6",
"type": "product"
},
{
"source": "at",
"target": "v7",
"type": "reactant"
},
{
"source": "s3",
"target": "v8",
"type": "reactant"
},
{
"source": "v8",
"target": "na",
"type": "product"
},
{
"source": "s6o",
"target": "v9",
"type": "reactant"
},
{
"source": "s6",
"target": "v10",
"type": "reactant"
},
{
"source": "v10",
"target": "s6o",
"type": "product"
},
{
"source": "s6",
"target": "v6",
"type": "reactant"
},
{
"source": "v6",
"target": "na",
"type": "product"
},
{
"source": "v0",
"target": "s1",
"type": "product"
}
],
"meta": {
"species": 9,
"reactions": 11,
"compartments": 1,
"parameters": 18
},
"model_id": "Wolf2000_Glycolytic_Oscillations"
}
}