System News
The Java Post-Genomic Era, Part 2
Computational Biology and Physiome Sciences, Inc.
October 22, 2001,
Volume 44, Issue 4

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. The secure, 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, for its ever-growing and mission-critical database needs.

In Spring of 2002, representatives of both Physiome Sciences and the development team of PatternHunter are expected to speak at the second "Computational Challenges in the Post-Genomic Age" conference, co-sponsored by Pacific Northwest National Laboratory, the San Diego Supercomputer Center, and Sun.

There are illustrations and screen shots available on the web site.

http://java.sun.com/features/2001/10/genome2.html

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