Biology Reference
In-Depth Information
Fig. 9. Importing models from CSMLDB. When a canvas has a model p53 + Mdm p53:Mdm and to the canvas, a model for
p53 MDM2 (activation of transcription of MDM2 by p53) is imported with the combination of checkbox options: “Merge”,
“Auto-Layout” and “Create New Canvas” (in a total of six patterns). If “Merge” is checked, the entities with the same ID on a
canvas are merged into one entity. If “Auto-Layout” is checked, automatic layout is applied to the whole elements on the canvas.
If “Create New Canvas” is checked, the newly inserted model (without “Merge” option) or merged model (with “Merge” option)
is inserted on the new canvas.
complex math engine is used. The selected mode is shown in the status bar at the bottom as Optimize
on or off (“on” means use of the simple math engine).
The simulation performance of the simple math engine is ten times better than the complex math engine
on average and both engines are acceptable with 100 reactions (200 to 300 as total elements) on a normal
machine. Most of the simulation models are categorized into this range of reactions and acceptable
for most users while sometimes the size of a simulation model is getting more than thousand reactions
(3,000 to 4,000 as total elements, depend on the complexity of scripts). For example, a Caenorhabditis
elegans vulval development model that modeled cell-cell regulations of six cells and signal transduction
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