With the mapping complete of the human genom (genomics), along with the
companion study of proteomics (the mapping and understanding
of the coded proteins in a given genome), research goals are
expanding computationally. These enormous computational tasks can
present scalability problems for many of the previously established
genomic research facilities.
network-aware, cross-platform power of Java technology is
increasingly proving indispensable to this ongoing Herculean task.
Physiome Sciences, Inc.'s computer-based biological simulation
technologies is an example of the growing acceptance of Java
technology in bioinformatics and computational biology.
Physiome Sciences is a privately held company focused on helping
pharmaceutical firms to better develop drugs through the use of
computer-based biological simulations.
Biological simulations have become crucial in an era of more precise,
sophisticated, and targeted drugs, leading to elevated costs in the
development process, as well as danger in the human testing phases.
"The industry is built on failure," says Jeremy Levin, CEO of Physiome
Sciences. Clearly, a means of speeding drug development, as well as
making it safer, is needed. Physiome Sciences accomplishes this mission
by "in-silico" (computer) simulations.
Computational biology is often challenged by the use of
diverse computer languages, hardware systems, and data formats, making
it difficult for scientists from around the world to effectively share
information, findings, and computational facilities. It is for this
reason that Physiome Sciences' technology solutions are built almost
entirely using Java technology.
"We made use of Java technology's native ability to run on all of these
different platforms, as well as its facility to communicate across
networks," says Dr. Scott Lett, Distinguished Computational Scientist
for Physiome Sciences. "And we used XML to define the mathematical
models, so that we could translate them on any platform. As a result,
we were able to get real, working systems up and running in less than a
year's time. We would still be programming if we were trying to write
this in any other language."
Physiome Sciences' Java technology based solutions include tools,
application frameworks, and complex databases, all of which are
licensed to pharmaceutical drug developers. Underlying the company's
product offerings, is the core technology of In Silico Cell
architecture, which supports the hierarchical modeling of biological
systems, and the creation of more complex models from simpler ones.
The XML-based technologies provide a complete vocabulary
for describing "virtual" biological systems--from the subcellular to
the organism level.
Together, the component driven design of the Physiome Sciences platform
allows for the development of predictive models--beginning at the level
of biochemical pathways, to cells, to tissues, and on up to living
systems. And by being network enabled, multiple users, in different
locations, can share data and more effectively work together.
Researchers are able to view and edit underlying mathematical
equations, create and merge complex pathway maps, access in-house
bioinformatics data, and link to external databases via the
Internet--thus speeding understanding, and drug discovery.
Meanwhile, Java DataBase ConnectivityTM (JDBCTM) technology
allows the company to hide differences
between databases from scientists who use the software. And the
availability of XML parsing technology for Java technology based
programs has allowed Physiome Sciences to create a structure by which
users can define the mathematical model of a cell without knowing any
programming, and have that definition be portable to different
environments--and even to other programming languages.
Physiome Sciences considers Sun as the preferred vendor for its bio
databases, having chosen Sun EnterpriseTM 3500 and 4500 Servers,
running SolarisTM Operating Environment (Solaris OE), and Oracle,
ever-growing and mission-critical database needs.
In Spring of 2002, representatives of both Physiome Sciences 