Example

SBML specification - L3V2

Some examples of Arrow’s schemas and Neo4j views coming from the (SBML specification) chapter 7.

1 - A simple example application of SBML

Arrow schema (JSON)
Model (XML.zip)

Arrows

_images/L3V2.7-1.svg

Neo4j

_images/L3V2.7-11.svg

2 - A simple example using the conversionFactor attribute

Arrow schema (JSON)
Model (XML.zip)

Arrows

_images/L3V2.7-2.svg

Neo4j

_images/L3V2.7-21.svg

3 - An alternative formulation of the conversionFactor example

Arrow schema (JSON)
Model (XML.zip)

Arrows

_images/L3V2.7-3.svg

Neo4j

_images/L3V2.7-31.svg

4 - Example of a discrete version of a simple dimerization reaction

Arrow schema (JSON)
Model (XML.zip)

Arrows

_images/L3V2.7-4.svg

Neo4j

_images/L3V2.7-41.svg

5 - Example involving assignment rules

Arrow schema (JSON)
Model (XML.zip)

Arrows

_images/L3V2.7-5.svg

Neo4j

_images/L3V2.7-51.svg

6 - Example involving algebraic rules

Arrow schema (JSON)
Model (XML.zip)

Arrows

_images/L3V2.7-6.svg

Neo4j

_images/L3V2.7-61.svg

7 - Example with combinations of boundaryCondition and constant values on Species with RateRule objects

Arrow schema (JSON)
Model (XML.zip)

Arrows

_images/L3V2.7-7.svg

Neo4j

_images/L3V2.7-71.svg

8 - Example of translation from a multi-compartmental model to ODEs

Arrow schema (JSON)
Model (XML.zip)

Arrows

_images/L3V2.7-8.svg

Neo4j

_images/L3V2.7-81.svg

9 - Example involving function definitions

Arrow schema (JSON)
Model (XML.zip)

Arrows

_images/L3V2.7-9.svg

Neo4j

_images/L3V2.7-91.svg

10 - Example involving delay functions

Arrow schema (JSON)
Model (XML.zip)

Arrows

_images/L3V2.7-10.svg

Neo4j

_images/L3V2.7-101.svg

11 - Example involving events

Arrow schema (JSON)
Model (XML.zip)

Arrows

_images/L3V2.7-111.svg

Neo4j

_images/L3V2.7-112.svg

12 - Example involving two-dimensional compartments

Arrow schema (JSON)
Model (XML.zip)

Arrows

_images/L3V2.7-12.svg

Neo4j

_images/L3V2.7-121.svg

13 - Example of a reaction located at a membrane

Arrow schema (JSON)
Model (XML.zip)

Arrows

_images/L3V2.7-13.svg

Neo4j

_images/L3V2.7-131.svg

14 - Example using an event with a non-persistent trigger and a delay

Arrow schema (JSON)
Model (XML.zip)

Arrows

_images/L3V2.7-14.svg

Neo4j

_images/L3V2.7-141.svg

SBML plugins

Some plugins can be used by Neo4jSbml: * Flux Balance Constraints (specification) * Groups (specification) * Layout (specification) * Qualitative Models (specification)

1 - Flux Balance Constraints

Arrow schema (JSON)
Model (XML.zip)

Arrows

_images/L3V1.fbc.V2R1.4-1.svg

Neo4j

_images/L3V1.fbc.V2R1.4-11.svg

2 - Groups

Arrow schema (JSON)
Model (XML.zip)

Arrows

_images/L3V1.groups.V1R1.5-2.svg

Neo4j

_images/L3V1.groups.V1R1.5-21.svg

3 - Layout

Arrow schema (JSON)
Model (XML.zip)

Arrows

_images/L3V1.layout.V1R1.4-5.svg

Neo4j

_images/L3V1.layout.V1R1.4-51.svg

4 - Qualitative Models

Arrow schema (JSON)
Model (XML.zip)

Arrows

_images/L3V1.qual.V1R1.4-2.svg

Neo4j

_images/L3V1.qual.V1R1.4-21.svg

SBML specification - L2V5

Some examples of Arrow’s schemas and Neo4j views coming from the (SBML specification) chapter 7.

1 - A simple example application of SBML

Arrow schema (JSON)
Model (XML.zip)

Arrows

_images/L2V5.7-1.svg

Neo4j

_images/L2V5.7-11.svg

2 - Example involving units

Arrow schema (JSON)
Model (XML.zip)

Arrows

_images/L2V5.7-2.svg

Neo4j

_images/L2V5.7-21.svg

3 - Example of a discrete version of a simple dimerization reaction

Arrow schema (JSON)
Model (XML.zip)

Arrows

_images/L2V5.7-3.svg

Neo4j

_images/L2V5.7-31.svg

4 - Example involving assignment rules

Arrow schema (JSON)
Model (XML.zip)

Arrows

_images/L2V5.7-4.svg

Neo4j

_images/L2V5.7-41.svg

5 - Example involving algebraic rules

Arrow schema (JSON)
Model (XML.zip)

Arrows

_images/L2V5.7-5.svg

Neo4j

_images/L2V5.7-51.svg

6 - Example with combinations of boundaryCondition and constant values on Species with RateRule objects

Arrow schema (JSON)
Model (XML.zip)

Arrows

_images/L2V5.7-6.svg

Neo4j

_images/L2V5.7-61.svg

7 - Example of translation from a multi-compartmental model to ODEs

Arrow schema (JSON)
Model (XML.zip)

Arrows

_images/L2V5.7-7.svg

Neo4j

_images/L2V5.7-71.svg

8 - Example involving function definitions

Arrow schema (JSON)
Model (XML.zip)

Arrows

_images/L2V5.7-8.svg

Neo4j

_images/L2V5.7-81.svg

9 - Example involving delay functions

Arrow schema (JSON)
Model (XML.zip)

Arrows

_images/L2V5.7-9.svg

Neo4j

_images/L2V5.7-91.svg

10 - Example involving events

Arrow schema (JSON)
Model (XML.zip)

Arrows

_images/L2V5.7-10.svg

Neo4j

_images/L2V5.7-101.svg

11 - Example involving two-dimensional compartments

Arrow schema (JSON)
Model (XML.zip)

Arrows

_images/L2V5.7-111.svg

Neo4j

_images/L2V5.7-112.svg