Biology Reference
In-Depth Information
Fig. 11. Example of externalization of coefficient. The top model has a mass action m1*0.1 on the process p1. The coefficient
of the mass action,
i.e.
, 0.1, can be externalized with an entity e3 and the mass action on the process becomes m1*k1 as in the
bottom model. Once externalized, the parameter can be estimated with the “Pathway Parameter Search Module.”
groundbreaking modeling platforms for Systems Biology. In geophysics, the DA approach is applied
to the prediction of the El Ni no-Southern Oscillation (ENSO) phenomenon [49] that is known as the
strongest climate variation on seasonal to inter-annual timescales. Since this requires high performance
computers to obtain the acceptable performance, we decided not to include this function to the CIO 4.0
module.
As an alternative solution, in CIO 4.0, “Pathway Parameter Search Module” is provided for the normal
computer. This module executes multiple simulations at once with many initial conditions with some
range of values,
e.g.
run six simulations from the initial value zero to ten with every two intervals,
and displays the results with 2D or 3D plots. If user searches ten different conditions for each of three
entities, then in total one thousand simulations (10
3
) should be executed at once. The module cannot work
with acceptable performance without using the technology in “High-performance Simulation Module”.
This module informs how the systems behavior will change according to the changes in initial values.
Additionally, by minor updates of the target model, the module can be applicable to investigate the effect
of the coefficient of reaction speed of process and threshold value of connector. In those cases, the
coefficient (or threshold) itself should be represented by using an entity (what we call externalization
of coefficient or threshold). If the coefficient (or threshold) is once externalized, the instruction to use
“Pathway Parameter Search Module” is the same.
An example to externalize the coefficient of mass
action is shown in Fig. 11.
Pathway Model to Multiple Program Languages Export Module
As an advanced usage, users want to use their CSML models for other applications as simulation
models.
For this purpose, “Pathway Model to Multiple Program Languages Export Module” is pro-
