Biology Reference
In-Depth Information
step,
e.g.
, keyword search, user can create a graphical pathway model with an ontology background. The
ontology information is effectively used in some applications. Automatic pathway layouts that consider
cellular locations with this ontology are implemented in CIO4.0. In [40] and [41], semi-automatic
pathway validation and model checking with the ontology information are applied to generate qualified
pathway models from given pathway models. The research outputs of those pathway validations and
models will be available in a future release.
SaaS technology and Cell Illustrator Online
Various types of analysis requests are coming from Systems Biology research and development. Some
of these requests require a huge supercomputer system for tasks such as optimal parameter search,
very expensive/large databases to own, or very specific analysis focused on a specific research topic.
No single software can cover all of these capabilities, and software customization is very expensive or
impossible to cope with. Thus, inevitably, we require Software as a Service (SaaS) technology [42]
for the Systems Biology computational platform. SaaS is a software application delivery model that is
usually associated with software businesses and is considered a low-cost way to obtain the same merits
without the associated complexity and high initial cost as licensing. The technology is introduced in Cell
Illustrator 4.0 and its modules (described in the next section) and is provided by the CIO servers. Users
can select the desired modules from them on their demands. The following six modules including the
beta version, are serviced on the server side:
1. CSMLDB Search Module
2. Project Management Module
3. High-performance Simulation Module
4. Pathway Parameter Search Module
5. Pathway Model to Multiple Program Languages Export Module (Java, FORTRAN, C++, C, Perl,
and Python)
6. CSML to SVG Module and HTML Module (beta)
Moreover, third parties can develop their own modules and deliver them from the server side module
using APIs. To distinguish the Cell Illustrator via Java Web Start (JWS) [3] and the original (standalone)
version, the former one is named Cell Illustrator Online (CIO). After JRE 1.6.0
12, the 64-bit version of
JWS is also supported by Sun Microsystems, Inc. with the technical improvement in 2009. This allows
users to allocate more than 1.4 gigabytes of memory to CIO 4.0, which is very useful since pathways
with more than 3,000 elements with biological annotations sometimes require more memory that cannot
be handled within 32-bit JRE. In our experience, more than 2 terabytes of memory can be allocated and
the limitation will depend on the total memory of the client machine.
With the JWS technology, users can easily publish their CSML model on a website by creating the
URL links with the rules listed in Table 1. If a user creates a link to launch Cell Illustrator Online Player
(CIO Player), the read-only version of CIO that can launch without user registration, the linked CSML
model can be freely accessed by any user with a Java 6.0 installed on a machine. If the linked CSML
file is generated with logging information of simulation called CIL file, CIO Player can also replay the
simulation by using the logged information (Fig. 7). Thus, without using CIO itself, the overview of
the pathway structure, the kinetics of reactions, and the simulation behavior of the CSML model are
available via the Internet.
