Biology Reference
In-Depth Information
Table 2
Total number of entries in CSMLDB 7.4 and CSMLDB 8.4
Database
Element type
Number of entries
CSMLDB 7.4
Entity
89,469
Process
140,868
CSMLDB 8.4
Entity
117,967
Process
182,383
drag-and-drop (D&D) to the main canvas by merging to the current model of the active canvas or by
insertion onto a new canvas with or without applying automatic graph layout (Fig. 9). It should be noted
that the source CSML models of CSMLDB Academic and Professional are simulatable models since
entity and process elements are stored in the CSMLDB. In other words, no content is stored in the Fact
tab of that dialog in the current version. Facts,
e.g.
, indirect reactions, that do not have any effect on
simulation models will be prepared as fact elements in a future release.
The module allows users to simplify the modeling step into two steps: (i) search the genes and proteins
of interest from the known 100,000 reactions, and (ii) D&D the matched result by filtering. Moreover
the created model will be a template ready for simulation.
Project Management and CSML Pathway Library Modules
As already mentioned, CIO 4.0 is launched with JWS technology after user authentication. With this
feature, the CIO 4.0 server can identify each user and can provide services in each user level.
The “Project Management Module” (the top rectangle region in Fig. 10a) allows users to create their
own projects on the server side and stores the CSML models and any files related with those projects,
e.g.
, pdf, ppt, doc, xls, and txt. With this module, users can launch CIO 4.0 on any computer and can
access his/her projects on the server side. With D&D operation of a CSML model into the main canvas,
the CSML model is automatically opened in the main canvas. Moreover, users can share the contents
with other users for project level with read or read-write permissions (Fig. 10b).
The “CSML Pathway Library Module” (the bottom rectangle region in Fig. 10a) provides the CSML
pathway libraries in public domains (public library) or commercial (commercial library). The public
library contains all CSML models in
http://www.csml.org/
with three categories, signal transduction
pathways, gene regulatory networks and metabolic pathways. The library also contains all CSML models
in the text book [13]. The commercial library registers more than 1,000 well-established biopathways
that originated from TRANSPATH [43] in BIOBASE with the Transpath2CSML application [31]. All
of those CSML models can be loaded, edited, saved, and simulated with CIO 4.0.
Those modules ease users to access and share their CSML models and reuse of CSML libraries in
public or commercial domains.
High-performance Simulation Module
The native simulation engine in CIO 4.0 is tightly integrated with one of the script engines, named
Pnuts [44], which can be compiled into Java byte code. The native simulation engine has two modes:
simple math engine and complex math engine. The two modes are automatically switched depending
on the complexity of the reactions of the pathway model. In more detail, if the reaction rules consist of
simple math,
e.g.
four arithmetic operations, simple math engine is used. If other reaction rules that can
be described with Pnuts script language -
e.g.
“if
...
then
...
”, pow, log, and Java method itself - then
