Biology Reference
In-Depth Information
(a)
(b)
Fig. 10. Project Manager Dialog. (a) The Project Manager dialog consists of two sections, “User area” (top) and “Library area”
(bottom). (b) Sharing step of a project (here “our shared project”) in the “User area.” Each project can be shared with “Read”,
“Write”, or both permissions.
regulatory network in each cell contains 1,649 elements (the complexity of each script is high) and takes
several hours on a normal machine (12,410 seconds on Intel Core 2 Extreme X9650 3 G Hz) [40,45].
In CIO 4.0 under the SaaS concept, users can activate and use the high-performance simulation module
on demand. The module writes down the CSML model into pure Java native language and compiles it
by using javac, which is freely distributed with Java Development Kit (JDK) [46] (requires JDK 6.0 or
higher). Using this module, the above
C. elegans
model can run within one min,
i.e.
, hundreds times
faster (31 seconds on the same machine). Thus, the High-performance Simulation Module can accept
models with thousands of elements.
Pathway Parameter Search Module
The problem of parameter search for dynamic pathway models is one of the most crucial topics in Sys-
tems Biology. Some challenges have been made for automatic parameter estimation for HFPNe models
by using a technology called data assimilation (DA) which blends simulation models and observational
data rationally [47,48]. This data assimilation method is more suited for a high-performance computing
system with peta FLOPS computing ability. These efforts and developments are anticipated to create
