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Table 5 Benchmarking the newly developed plug-and-play modeling tool against commonly used and established tools

From: A new flexible plug and play scheme for modeling, simulating, and predicting gastric emptying

No.

Requirements

Proposed tool

COPASI/SimBiology

PhysioDesigner

1

Organ level modeling, and simulation

Models and simulates at organ level

Models and simulates at cellular level

Models and simulates at organ level

2

Lesser programing effort for:

Programing effort for:

Programing effort for:

Uses ISML (standard programing language)

    

and thus requires programing effort.

 

1. Structural description

1. Structural description: No

1. Structural description: No

 
 

2. Functional description

2. Functional description:

2. Functional description:

 
  

single time effort, and reusable

No (COPASI, but not reusable); single time effort and reusable (SimBiology)

 
 

3. Experimental data

3. Experimental data: No

3. Experimental data: No

 

3

User interface for model structural description

Textual thus machine readable and adaptable

Graphical

Graphical

 

(components and interconnections)

   

4

Dynamic* model construction * Adaptive to experimental data collected, and structural change requests in time

Dynamic model construction is possible

Dynamic model construction is not possible

Dynamic model construction is not possible

5

Experimental data suppliable at the level of

Possible without any additional interface

Not possible without additional interface

Not possible without additional interface

 

physiological entities constituting the model

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