diff --git a/temp/modelTemplate.html b/temp/modelTemplate.html index e661e4e..f3350a6 100644 --- a/temp/modelTemplate.html +++ b/temp/modelTemplate.html @@ -1,56 +1,77 @@ + + - + + + Model Details - ModelBricks + + + +
- {{#each data.vcml.BioModel}} {{#each this.Version}} - Dashboard + {{#each data.vcml.BioModel}} + {{#each this.Version}} + + + + Dashboard + + +

Name - {{this.$.Name}}

BioModel ID - {{this.$.KeyValue}}

- {{/each}} {{/each}} + + {{/each}} + {{/each}}
+

Reaction Diagram

- {{#each data.vcml.BioModel}} {{#each this.Version}} + + {{#each data.vcml.BioModel}} + {{#each this.Version}} + reactionDiagram - {{/each}} {{/each}} + + {{/each}} + {{/each}}
+

Physiology

- {{!-- reactions table --}} + +
+ @@ -59,490 +80,66 @@

Physiology

+ - {{#each data.vcml.BioModel}} {{#each this.Model}} {{#each - this.SimpleReaction}} + {{#each data.vcml.BioModel}} + {{#each this.Model}} + {{#each this.SimpleReaction}} + - - - - - - - - {{#each this.Kinetics}} {{#each this.Parameter}} - - {{/each}} {{/each}} - - {{/each}} {{/each}} {{/each}} - -
Reactions - See in - Dashboard + + + See in Dashboard + +
Reaction Kinetics
- {{#each this.Reactant}} {{this.$.LocalizedCompoundRef}} + {{#each this.Reactant}} + {{this.$.LocalizedCompoundRef}} {{/each}} - --> - {{#each this.Product}} {{this.$.LocalizedCompoundRef}} {{/each}} - {{this.$.Name}}{{this.$.Structure}} - {{#each this.Kinetics}} {{this.$.KineticsType}} {{/each}} -
-
- {{!-- universal ID's --}} -
-

Universal ID's:

-
-
- 		-
- {{!-- annotation --}} -
-

Text Annotations:

-
-
- 		-
- {{!-- Kinetics --}} -
-

- Reaction rate: {{this._}} - [{{this.$.Unit}}] -

-
-
-
-
-
+ + --> - {{!-- Structures table --}} -
-
- - - - - - - - - - - {{#each data.vcml.BioModel}} {{#each this.Model}} {{#each - this.Membrane}} - - - - - - - - - - {{/each}} {{/each}} {{/each}} {{#each data.vcml.BioModel}} {{#each - this.Model}} {{#each this.Feature}} - - - - - - - - - - {{/each}} {{/each}} {{/each}} - -
- Structures - See in - Dashboard -
NameTypeElectrical (Membrane Polarity)
{{this.$.Name}}Membrane - {{this.$.PositiveFeature}}(+)   - {{this.$.NegativeFeature}}(-) -
-
- {{!-- universal ID's --}} -
-

Universal ID's:

-
-
- 		-
- {{!-- annotation --}} -
-

Text Annotations:

-
-
-
{{this.$.Name}}Compartment - {{this.$.PositiveFeature}}(+)   - {{this.$.NegativeFeature}}(-) -
-
- {{!-- universal ID's --}} -
-

Universal ID's:

-
-
- 		-
- {{!-- annotation --}} -
-

Text Annotations:

-
-
+ {{#each this.Product}} + {{this.$.LocalizedCompoundRef}} + {{/each}}
-
-
- {{!-- Species table --}} -
-
- - - - - - - - - - {{#each data.vcml.BioModel}} {{#each this.Model}} {{#each - this.LocalizedCompound}} - - - - - - - {{/each}} {{/each}} {{/each}} - -
- Species - See in - Dashboard -
NameStructure
{{this.$.Name}} {{this.$.Structure}}
-
- {{!-- universal ID's --}} -
-

Universal ID's:

-
-
- 		-
- {{!-- annotation --}} -
-

Text Annotations:

-
-
-
-
-
- - {{!-- Molecules table --}} -
-
- - - - - - - - - - {{#each data.vcml.BioModel}} {{#each this.Model}} {{#each - this.RbmModelContainer}} {{#each this.MolecularTypeList}} {{#each - this.MolecularType}} - - - - - - - - - - - {{/each}} {{/each}} {{/each}} {{/each}} {{/each}} - -
- Molecules - See in - Dashboard -
NameDescription
{{this.$.Name}} - {{#each this.MolecularComponent}} {{this.$.Name}} {{#if - this.AllowableState}} {{#each this.AllowableState}} - ~{{this.$.Name}} {{/each}} {{/if}} . {{/each}} -
-
- {{!-- universal ID's --}} -
-

Universal ID's:

-
-
- 		-
- {{!-- annotation --}} -
-

Text Annotations:

-
-
-
-
-
- - {{!-- Observables table --}} -
-
- - - - - - - - - - - - {{#each data.vcml.BioModel}} {{#each this.Model}} {{#each - this.RbmModelContainer}} {{#each this.RbmObservableList}} {{#each - this.Observable}} - - - - - {{#each this.SpeciesPattern}} {{#each this.MolecularTypePattern}} - {{#each this.MolecularType}} - - {{/each}} {{/each}} {{/each}} - - - - - - {{/each}} {{/each}} {{/each}} {{/each}} {{/each}} - -
- Observables - See in - Dashboard -
NameTypeBioNetGen DefinationCount
{{this.$.Name}}{{this.$.ObservableType}}{{this.$.Name}}{{this.$.Sequence}}
-
- {{!-- universal ID's --}} -
-

Universal ID's:

-
-
- 		-
- {{!-- annotation --}} -
-

Text Annotations:

-
-
+ 		+ {{#each this.Kinetics}} + {{this.$.KineticsType}} + {{/each}}
-
-
- -
- -

Applications

- {{!-- Applications table --}} -
-
- - - - - - - - - - - {{#each data.vcml.BioModel}} {{#each this.SimulationSpec as |value - key|}} - - - - - - - {{/each}} {{/each}} - -
- Applications -
NameMath TypeAnnotation
{{value.$.Name}}{{value.Annotation}}
-
-
- - {{!-- for each application --}} {{#each data.vcml.BioModel}} {{#each - this.SimulationSpec as |value key|}} -

{{key}} - {{value.$.Name}}

- - {{!-- specifications table --}} -
-
- - - - - - - - - - - {{#each value.ReactionContext}} {{#each this.LocalizedCompoundSpec}} - - - - - - {{/each}} {{/each}} + {{/each}} + {{/each}} + {{/each}}
- Specifications(Species) - {{value.$.Name}} -
SpeciesInitial ConditionDiffusion Constant
{{this.$.LocalizedCompoundRef}} - {{this.InitialConcentration}} - {{this.Diffusion}}
- {{!-- specifications table --}} +
- - - - - - - - - {{#each value.ReactionContext}} {{#each this.ReactionSpec}} - - - - - {{/each}} {{/each}} - -
- Specifications(Reaction) - {{value.$.Name}} -
NameReaction Mapping
{{this.$.ReactionStepRef}}{{this.$.ReactionMapping}}
-
-
+ Observables - {{!-- Simulations table --}} -
-
- - - - - - - - {{#each value.Simulation}} - - - {{#each this.SolverTaskDescription}} {{#each this.TimeBound}} - - {{/each}} {{#each this.OutputOptions}} - - {{/each}} {{/each}} - - {{/each}} - -
- Simulations - {{value.$.Name}} -
NameEnd TimeOutput Options
{{ this.$.Name}}{{ this.$.EndTime}} - every {{ this.$.OutputTimeStep}} -
-
-
- {{/each}} {{/each}} + Type -
-

Global Parameters

+ + BioNetGen Definition - {{!-- Global Parameters table --}} -
-
- - - - - - + - - {{#each data.vcml.BioModel}} {{#each this.Model}} {{#each - this.ModelParameters}} {{#each this.Parameter}} - - - - - - - - - {{/each}} {{/each}} {{/each}} {{/each}} -
- Global Parameters - See in - Dashboard -
NameExpressionCount
{{ this.$.Name}}{{this._}}
-
- {{!-- universal ID's --}} -
-

Universal ID's:

-
-
- 		-
- {{!-- annotation --}} -
-

Text Annotations:

-
-
-
-
- - +