During the past several years, biology has witnessed a transition from being a
low-throughput to what-is-now a high-throughput science. From a typical
data-gathering and data-poor era scientists have moved to a more
data-interpretation and data-rich era. This has enabled develop a holistic view
of the cell and an organism, by extension. The paradigm shift has given birth to
a new field called Systems Biology. Systems Biology deals with the way cell uses
its entire inventory of nucleic acids, proteins and other molecules to support
its physiology. The fundamental unit of Systems Biology is an in-silico model
that is built up from the raw material of cell-parts and their language of
communication. Systems Biology offers a unique opportunity of weaving molecules
and their messages into an in-silico fabric that can be tested against a wide
range of conditions and combinations.
To create an in-silico model, researchers use a tool that not only encapsulates
the topology of the network but also understands the expression among its
constituent components. In order to capture diverse interactions among objects,
various mathematical representations and modeling platforms are required. In an
ideal setting, the modeling community needs a computational tool that integrates
and graphically models biological information of varying complexity, conducts
large-scale simulations with heavy number crunching capability, is user friendly
(especially for the non-specialists) and offers services over the web.
Furthermore, as the complexity of the model grows, the modeling platform may
move from serial to a distributed computing environment. To address this niche
requirement, Cellware - a grid based modeling and simulation tool, is being
developed by the Systems Biology
Group at the Bioinformatics Institute, Singapore.
Cellware has not only been designed to conduct modeling and simulation of gene
regulatory and metabolic pathways but also offer an integrated environment for
diverse mathematical representations, parameter estimation and optimization. In
addition, a user-friendly graphical display and capability to run large and
complex models would be provided by default. A very special feature of Cellware
is that it would be the first grid based modeling and simulation tool in the
field of Systems Biology, to our best knowledge.