examples/sbtab/layout_model.yml
Compartment:
- __id: 0
__type: Compartment
comment: ''
description: ''
i_d: Compartment_1
identifiers: ''
identifiers_sbo_go: ''
miriam_annotations: ''
name: Compartment_1
outer_compartment: ''
outer_compartment_s_b_m_l_compartment_id: ''
position_x: .nan
position_y: .nan
reference_d_o_i: ''
reference_name: ''
reference_pub_med: ''
s_b_m_l_compartment_id: ''
s_b_o_term: ''
size: .nan
symbol: ''
type: ''
unit: ''
Compound:
- __id: 1
__type: Compound
charge: null
comment: ''
compound_sum_formula: ''
description: ''
enzyme_role: ''
has_only_substance_units: false
i_d: Species_1
identifiers: ''
identifiers_kegg_compound: ''
identifiers_obo_chebi: ''
identifiers_sbo_kegg: ''
initial_concentration: .nan
initial_value: .nan
is_constant: false
location: Compartment_1
mass: .nan
miriam_annotations: ''
name: ''
name_for_plots: ''
position_x: .nan
position_y: .nan
reference_d_o_i: ''
reference_name: ''
reference_pub_med: ''
regulator_role: ''
s_b_m_l_fbc_charge: .nan
s_b_m_l_fbc_chemical_formula: ''
s_b_m_l_species_id: ''
s_b_m_l_speciestype_id: ''
s_b_o_term: ''
state: ''
structure_formula: ''
symbol: ''
type: ''
unit: ''
- __id: 2
__type: Compound
charge: null
comment: ''
compound_sum_formula: ''
description: ''
enzyme_role: ''
has_only_substance_units: false
i_d: Species_2
identifiers: ''
identifiers_kegg_compound: ''
identifiers_obo_chebi: ''
identifiers_sbo_kegg: ''
initial_concentration: .nan
initial_value: .nan
is_constant: false
location: Compartment_1
mass: .nan
miriam_annotations: ''
name: ''
name_for_plots: ''
position_x: .nan
position_y: .nan
reference_d_o_i: ''
reference_name: ''
reference_pub_med: ''
regulator_role: ''
s_b_m_l_fbc_charge: .nan
s_b_m_l_fbc_chemical_formula: ''
s_b_m_l_species_id: ''
s_b_m_l_speciestype_id: ''
s_b_o_term: ''
state: ''
structure_formula: ''
symbol: ''
type: ''
unit: ''
Definition: []
Enzyme: []
FbcObjective: []
Gene: []
Layout:
- __id: 3
__type: Layout
i_d: Layout_1
name: ''
s_b_m_l_layout_compartment_id: ''
s_b_m_l_layout_curve_segment: ''
s_b_m_l_layout_height: 220.0
s_b_m_l_layout_model_entity: LayoutCanvas
s_b_m_l_layout_reaction_id: ''
s_b_m_l_layout_species_id: ''
s_b_m_l_layout_species_role: ''
s_b_m_l_layout_text: ''
s_b_m_l_layout_width: 400.0
s_b_m_l_layout_x: .nan
s_b_m_l_layout_y: .nan
- __id: 4
__type: Layout
i_d: CompartmentGlyph_1
name: ''
s_b_m_l_layout_compartment_id: Compartment_1
s_b_m_l_layout_curve_segment: ''
s_b_m_l_layout_height: 210.0
s_b_m_l_layout_model_entity: Compartment
s_b_m_l_layout_reaction_id: ''
s_b_m_l_layout_species_id: ''
s_b_m_l_layout_species_role: ''
s_b_m_l_layout_text: ''
s_b_m_l_layout_width: 390.0
s_b_m_l_layout_x: 5.0
s_b_m_l_layout_y: 5.0
- __id: 5
__type: Layout
i_d: SpeciesGlyph_1
name: ''
s_b_m_l_layout_compartment_id: ''
s_b_m_l_layout_curve_segment: ''
s_b_m_l_layout_height: 24.0
s_b_m_l_layout_model_entity: Species
s_b_m_l_layout_reaction_id: ''
s_b_m_l_layout_species_id: Species_1
s_b_m_l_layout_species_role: ''
s_b_m_l_layout_text: ''
s_b_m_l_layout_width: 240.0
s_b_m_l_layout_x: 80.0
s_b_m_l_layout_y: 26.0
- __id: 6
__type: Layout
i_d: TextGlyph_01
name: ''
s_b_m_l_layout_compartment_id: ''
s_b_m_l_layout_curve_segment: ''
s_b_m_l_layout_height: 24.0
s_b_m_l_layout_model_entity: SpeciesText
s_b_m_l_layout_reaction_id: ''
s_b_m_l_layout_species_id: Species_1
s_b_m_l_layout_species_role: ''
s_b_m_l_layout_text: ''
s_b_m_l_layout_width: 228.0
s_b_m_l_layout_x: 92.0
s_b_m_l_layout_y: 26.0
- __id: 7
__type: Layout
i_d: SpeciesGlyph_2
name: ''
s_b_m_l_layout_compartment_id: ''
s_b_m_l_layout_curve_segment: ''
s_b_m_l_layout_height: 24.0
s_b_m_l_layout_model_entity: Species
s_b_m_l_layout_reaction_id: ''
s_b_m_l_layout_species_id: Species_2
s_b_m_l_layout_species_role: ''
s_b_m_l_layout_text: ''
s_b_m_l_layout_width: 240.0
s_b_m_l_layout_x: 80.0
s_b_m_l_layout_y: 170.0
- __id: 8
__type: Layout
i_d: TextGlyph_02
name: ''
s_b_m_l_layout_compartment_id: ''
s_b_m_l_layout_curve_segment: ''
s_b_m_l_layout_height: 24.0
s_b_m_l_layout_model_entity: SpeciesText
s_b_m_l_layout_reaction_id: ''
s_b_m_l_layout_species_id: Species_2
s_b_m_l_layout_species_role: ''
s_b_m_l_layout_text: ''
s_b_m_l_layout_width: 228.0
s_b_m_l_layout_x: 92.0
s_b_m_l_layout_y: 170.0
- __id: 9
__type: Layout
i_d: ReactionGlyph_1
name: ''
s_b_m_l_layout_compartment_id: ''
s_b_m_l_layout_curve_segment: Start
s_b_m_l_layout_height: .nan
s_b_m_l_layout_model_entity: ReactionCurve
s_b_m_l_layout_reaction_id: Reaction_1
s_b_m_l_layout_species_id: ''
s_b_m_l_layout_species_role: ''
s_b_m_l_layout_text: ''
s_b_m_l_layout_width: .nan
s_b_m_l_layout_x: 165.0
s_b_m_l_layout_y: 105.0
- __id: 10
__type: Layout
i_d: ReactionGlyph_1
name: ''
s_b_m_l_layout_compartment_id: ''
s_b_m_l_layout_curve_segment: End
s_b_m_l_layout_height: .nan
s_b_m_l_layout_model_entity: ReactionCurve
s_b_m_l_layout_reaction_id: Reaction_1
s_b_m_l_layout_species_id: ''
s_b_m_l_layout_species_role: ''
s_b_m_l_layout_text: ''
s_b_m_l_layout_width: .nan
s_b_m_l_layout_x: 165.0
s_b_m_l_layout_y: 115.0
- __id: 11
__type: Layout
i_d: SpeciesReferenceGlyph_1
name: ''
s_b_m_l_layout_compartment_id: ''
s_b_m_l_layout_curve_segment: Start
s_b_m_l_layout_height: .nan
s_b_m_l_layout_model_entity: SpeciesReferenceCurve
s_b_m_l_layout_reaction_id: Reaction_1
s_b_m_l_layout_species_id: SpeciesGlyph_1
s_b_m_l_layout_species_role: ''
s_b_m_l_layout_text: ''
s_b_m_l_layout_width: .nan
s_b_m_l_layout_x: 165.0
s_b_m_l_layout_y: 105.0
- __id: 12
__type: Layout
i_d: SpeciesReferenceGlyph_1
name: ''
s_b_m_l_layout_compartment_id: ''
s_b_m_l_layout_curve_segment: End
s_b_m_l_layout_height: .nan
s_b_m_l_layout_model_entity: SpeciesReferenceCurve
s_b_m_l_layout_reaction_id: Reaction_1
s_b_m_l_layout_species_id: SpeciesGlyph_1
s_b_m_l_layout_species_role: ''
s_b_m_l_layout_text: ''
s_b_m_l_layout_width: .nan
s_b_m_l_layout_x: 195.0
s_b_m_l_layout_y: 60.0
- __id: 13
__type: Layout
i_d: SpeciesReferenceGlyph_1
name: ''
s_b_m_l_layout_compartment_id: ''
s_b_m_l_layout_curve_segment: BasePoint1
s_b_m_l_layout_height: .nan
s_b_m_l_layout_model_entity: SpeciesReferenceCurve
s_b_m_l_layout_reaction_id: Reaction_1
s_b_m_l_layout_species_id: SpeciesGlyph_1
s_b_m_l_layout_species_role: ''
s_b_m_l_layout_text: ''
s_b_m_l_layout_width: .nan
s_b_m_l_layout_x: 165.0
s_b_m_l_layout_y: 90.0
- __id: 14
__type: Layout
i_d: SpeciesReferenceGlyph_1
name: ''
s_b_m_l_layout_compartment_id: ''
s_b_m_l_layout_curve_segment: BasePoint2
s_b_m_l_layout_height: .nan
s_b_m_l_layout_model_entity: SpeciesReferenceCurve
s_b_m_l_layout_reaction_id: Reaction_1
s_b_m_l_layout_species_id: SpeciesGlyph_1
s_b_m_l_layout_species_role: ''
s_b_m_l_layout_text: ''
s_b_m_l_layout_width: .nan
s_b_m_l_layout_x: 165.0
s_b_m_l_layout_y: 90.0
- __id: 15
__type: Layout
i_d: SpeciesReferenceGlyph_2
name: ''
s_b_m_l_layout_compartment_id: ''
s_b_m_l_layout_curve_segment: Start
s_b_m_l_layout_height: .nan
s_b_m_l_layout_model_entity: SpeciesReferenceCurve
s_b_m_l_layout_reaction_id: Reaction_1
s_b_m_l_layout_species_id: SpeciesGlyph_2
s_b_m_l_layout_species_role: ''
s_b_m_l_layout_text: ''
s_b_m_l_layout_width: .nan
s_b_m_l_layout_x: 165.0
s_b_m_l_layout_y: 115.0
- __id: 16
__type: Layout
i_d: SpeciesReferenceGlyph_2
name: ''
s_b_m_l_layout_compartment_id: ''
s_b_m_l_layout_curve_segment: End
s_b_m_l_layout_height: .nan
s_b_m_l_layout_model_entity: SpeciesReferenceCurve
s_b_m_l_layout_reaction_id: Reaction_1
s_b_m_l_layout_species_id: SpeciesGlyph_2
s_b_m_l_layout_species_role: ''
s_b_m_l_layout_text: ''
s_b_m_l_layout_width: .nan
s_b_m_l_layout_x: 195.0
s_b_m_l_layout_y: 160.0
- __id: 17
__type: Layout
i_d: SpeciesReferenceGlyph_2
name: ''
s_b_m_l_layout_compartment_id: ''
s_b_m_l_layout_curve_segment: BasePoint1
s_b_m_l_layout_height: .nan
s_b_m_l_layout_model_entity: SpeciesReferenceCurve
s_b_m_l_layout_reaction_id: Reaction_1
s_b_m_l_layout_species_id: SpeciesGlyph_2
s_b_m_l_layout_species_role: ''
s_b_m_l_layout_text: ''
s_b_m_l_layout_width: .nan
s_b_m_l_layout_x: 165.0
s_b_m_l_layout_y: 130.0
- __id: 18
__type: Layout
i_d: SpeciesReferenceGlyph_2
name: ''
s_b_m_l_layout_compartment_id: ''
s_b_m_l_layout_curve_segment: BasePoint2
s_b_m_l_layout_height: .nan
s_b_m_l_layout_model_entity: SpeciesReferenceCurve
s_b_m_l_layout_reaction_id: Reaction_1
s_b_m_l_layout_species_id: SpeciesGlyph_2
s_b_m_l_layout_species_role: ''
s_b_m_l_layout_text: ''
s_b_m_l_layout_width: .nan
s_b_m_l_layout_x: 165.0
s_b_m_l_layout_y: 130.0
- __id: 19
__type: Layout
i_d: ReactionGlyph_2
name: ''
s_b_m_l_layout_compartment_id: ''
s_b_m_l_layout_curve_segment: Start
s_b_m_l_layout_height: .nan
s_b_m_l_layout_model_entity: ReactionCurve
s_b_m_l_layout_reaction_id: Reaction_2
s_b_m_l_layout_species_id: ''
s_b_m_l_layout_species_role: ''
s_b_m_l_layout_text: ''
s_b_m_l_layout_width: .nan
s_b_m_l_layout_x: 235.0
s_b_m_l_layout_y: 105.0
- __id: 20
__type: Layout
i_d: ReactionGlyph_2
name: ''
s_b_m_l_layout_compartment_id: ''
s_b_m_l_layout_curve_segment: End
s_b_m_l_layout_height: .nan
s_b_m_l_layout_model_entity: ReactionCurve
s_b_m_l_layout_reaction_id: Reaction_2
s_b_m_l_layout_species_id: ''
s_b_m_l_layout_species_role: ''
s_b_m_l_layout_text: ''
s_b_m_l_layout_width: .nan
s_b_m_l_layout_x: 235.0
s_b_m_l_layout_y: 115.0
- __id: 21
__type: Layout
i_d: SpeciesReferenceGlyph_3
name: ''
s_b_m_l_layout_compartment_id: ''
s_b_m_l_layout_curve_segment: Start
s_b_m_l_layout_height: .nan
s_b_m_l_layout_model_entity: SpeciesReferenceCurve
s_b_m_l_layout_reaction_id: Reaction_2
s_b_m_l_layout_species_id: SpeciesGlyph_2
s_b_m_l_layout_species_role: ''
s_b_m_l_layout_text: ''
s_b_m_l_layout_width: .nan
s_b_m_l_layout_x: 235.0
s_b_m_l_layout_y: 115.0
- __id: 22
__type: Layout
i_d: SpeciesReferenceGlyph_3
name: ''
s_b_m_l_layout_compartment_id: ''
s_b_m_l_layout_curve_segment: End
s_b_m_l_layout_height: .nan
s_b_m_l_layout_model_entity: SpeciesReferenceCurve
s_b_m_l_layout_reaction_id: Reaction_2
s_b_m_l_layout_species_id: SpeciesGlyph_2
s_b_m_l_layout_species_role: ''
s_b_m_l_layout_text: ''
s_b_m_l_layout_width: .nan
s_b_m_l_layout_x: 205.0
s_b_m_l_layout_y: 160.0
- __id: 23
__type: Layout
i_d: SpeciesReferenceGlyph_3
name: ''
s_b_m_l_layout_compartment_id: ''
s_b_m_l_layout_curve_segment: BasePoint1
s_b_m_l_layout_height: .nan
s_b_m_l_layout_model_entity: SpeciesReferenceCurve
s_b_m_l_layout_reaction_id: Reaction_2
s_b_m_l_layout_species_id: SpeciesGlyph_2
s_b_m_l_layout_species_role: ''
s_b_m_l_layout_text: ''
s_b_m_l_layout_width: .nan
s_b_m_l_layout_x: 235.0
s_b_m_l_layout_y: 130.0
- __id: 24
__type: Layout
i_d: SpeciesReferenceGlyph_3
name: ''
s_b_m_l_layout_compartment_id: ''
s_b_m_l_layout_curve_segment: BasePoint2
s_b_m_l_layout_height: .nan
s_b_m_l_layout_model_entity: SpeciesReferenceCurve
s_b_m_l_layout_reaction_id: Reaction_2
s_b_m_l_layout_species_id: SpeciesGlyph_2
s_b_m_l_layout_species_role: ''
s_b_m_l_layout_text: ''
s_b_m_l_layout_width: .nan
s_b_m_l_layout_x: 235.0
s_b_m_l_layout_y: 130.0
- __id: 25
__type: Layout
i_d: SpeciesReferenceGlyph_4
name: ''
s_b_m_l_layout_compartment_id: ''
s_b_m_l_layout_curve_segment: Start
s_b_m_l_layout_height: .nan
s_b_m_l_layout_model_entity: SpeciesReferenceCurve
s_b_m_l_layout_reaction_id: Reaction_2
s_b_m_l_layout_species_id: SpeciesGlyph_1
s_b_m_l_layout_species_role: ''
s_b_m_l_layout_text: ''
s_b_m_l_layout_width: .nan
s_b_m_l_layout_x: 235.0
s_b_m_l_layout_y: 105.0
- __id: 26
__type: Layout
i_d: SpeciesReferenceGlyph_4
name: ''
s_b_m_l_layout_compartment_id: ''
s_b_m_l_layout_curve_segment: End
s_b_m_l_layout_height: .nan
s_b_m_l_layout_model_entity: SpeciesReferenceCurve
s_b_m_l_layout_reaction_id: Reaction_2
s_b_m_l_layout_species_id: SpeciesGlyph_1
s_b_m_l_layout_species_role: ''
s_b_m_l_layout_text: ''
s_b_m_l_layout_width: .nan
s_b_m_l_layout_x: 205.0
s_b_m_l_layout_y: 60.0
- __id: 27
__type: Layout
i_d: SpeciesReferenceGlyph_4
name: ''
s_b_m_l_layout_compartment_id: ''
s_b_m_l_layout_curve_segment: BasePoint1
s_b_m_l_layout_height: .nan
s_b_m_l_layout_model_entity: SpeciesReferenceCurve
s_b_m_l_layout_reaction_id: Reaction_2
s_b_m_l_layout_species_id: SpeciesGlyph_1
s_b_m_l_layout_species_role: ''
s_b_m_l_layout_text: ''
s_b_m_l_layout_width: .nan
s_b_m_l_layout_x: 235.0
s_b_m_l_layout_y: 90.0
- __id: 28
__type: Layout
i_d: SpeciesReferenceGlyph_4
name: ''
s_b_m_l_layout_compartment_id: ''
s_b_m_l_layout_curve_segment: BasePoint2
s_b_m_l_layout_height: .nan
s_b_m_l_layout_model_entity: SpeciesReferenceCurve
s_b_m_l_layout_reaction_id: Reaction_2
s_b_m_l_layout_species_id: SpeciesGlyph_1
s_b_m_l_layout_species_role: ''
s_b_m_l_layout_text: ''
s_b_m_l_layout_width: .nan
s_b_m_l_layout_x: 235.0
s_b_m_l_layout_y: 90.0
Measurement: []
PbConfig: []
Position: []
Protein: []
Quantity: []
QuantityInfo: []
QuantityMatrix: []
Reaction:
- __id: 29
__type: Reaction
build_enzyme: false
build_enzyme_production: false
build_reaction: false
comment: ''
description: ''
enzyme: ''
enzyme_s_b_m_l_parameter_id: ''
enzyme_s_b_m_l_species_id: ''
flux: .nan
gene: ''
gene_symbol: ''
i_d: Reaction_1
identifiers: ''
identifiers_ec_code: ''
identifiers_kegg_reaction: ''
identifiers_obo_sbo: ''
is_complete: false
is_exchange_reaction: false
is_in_equilibrium: false
is_non_enzymatic: false
is_reversible: false
kinetic_law: ''
kinetic_law_formula: ''
kinetic_law_name: ''
location: ''
miriam_annotations: ''
model: ''
modifier: ''
name: ''
name_for_plots: ''
operon: ''
pathway: ''
position_x: .nan
position_y: .nan
reaction_formula: '1 Species_1 <=> 1 Species_2 <=> '
reference_d_o_i: ''
reference_name: ''
reference_pub_med: ''
regulator: ''
s_b_m_l_fbc_gene_association: ''
s_b_m_l_fbc_lower_bound: ''
s_b_m_l_fbc_upper_bound: ''
s_b_m_l_reaction_id: ''
s_b_o_term: ''
subreaction_of: ''
symbol: ''
type: ''
- __id: 30
__type: Reaction
build_enzyme: false
build_enzyme_production: false
build_reaction: false
comment: ''
description: ''
enzyme: ''
enzyme_s_b_m_l_parameter_id: ''
enzyme_s_b_m_l_species_id: ''
flux: .nan
gene: ''
gene_symbol: ''
i_d: Reaction_2
identifiers: ''
identifiers_ec_code: ''
identifiers_kegg_reaction: ''
identifiers_obo_sbo: ''
is_complete: false
is_exchange_reaction: false
is_in_equilibrium: false
is_non_enzymatic: false
is_reversible: false
kinetic_law: ''
kinetic_law_formula: ''
kinetic_law_name: ''
location: ''
miriam_annotations: ''
model: ''
modifier: ''
name: ''
name_for_plots: ''
operon: ''
pathway: ''
position_x: .nan
position_y: .nan
reaction_formula: '1 Species_2 <=> 1 Species_1 <=> '
reference_d_o_i: ''
reference_name: ''
reference_pub_med: ''
regulator: ''
s_b_m_l_fbc_gene_association: ''
s_b_m_l_fbc_lower_bound: ''
s_b_m_l_fbc_upper_bound: ''
s_b_m_l_reaction_id: ''
s_b_o_term: ''
subreaction_of: ''
symbol: ''
type: ''
ReactionStoichiometry: []
Regulator: []
Relation: []
Relationship: []
SparseMatrix: []
SparseMatrixColumn: []
SparseMatrixOrdered: []
SparseMatrixRow: []
StoichiometricMatrix: []
_classMetadata:
Compartment:
class: Compartment
document: TestModel layout
name: Compartment
Compound:
class: Compound
document: TestModel layout
name: Compound
Definition:
class: Definition
name: Definition
Enzyme:
class: Enzyme
name: Enzyme
FbcObjective:
class: FbcObjective
name: FbcObjective
Gene:
class: Gene
name: Gene
Layout:
class: Layout
description: SBML Layout
document: TestModel layout
name: Layout
Measurement:
class: Measurement
name: Measurement
PbConfig:
class: PbConfig
name: PbConfig
Position:
class: Position
name: Position
Protein:
class: Protein
name: Protein
Quantity:
class: Quantity
name: Quantity
QuantityInfo:
class: QuantityInfo
name: QuantityInfo
QuantityMatrix:
class: QuantityMatrix
name: QuantityMatrix
Reaction:
class: Reaction
document: TestModel layout
name: Reaction
ReactionStoichiometry:
class: ReactionStoichiometry
name: ReactionStoichiometry
Regulator:
class: Regulator
name: Regulator
Relation:
class: Relation
name: Relation
Relationship:
class: Relationship
name: Relationship
SparseMatrix:
class: SparseMatrix
name: SparseMatrix
SparseMatrixColumn:
class: SparseMatrixColumn
name: SparseMatrixColumn
SparseMatrixOrdered:
class: SparseMatrixOrdered
name: SparseMatrixOrdered
SparseMatrixRow:
class: SparseMatrixRow
name: SparseMatrixRow
StoichiometricMatrix:
class: StoichiometricMatrix
name: StoichiometricMatrix
rxnconContingencyList:
class: rxnconContingencyList
name: rxnconContingencyList
rxnconReactionList:
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