NEWS BRIEFS: SOFTWARE
Santa Fe, NM, — The National Center for Genome Resources (NCGR) has released a version of ISYStm, an innovative new platform to integrate heterogeneous bioinformatics software tools and databases. The software can be easily downloaded and installed from a Web site, http://www.ncgr.org/research/isys , and offers a significant portion of the functionality planned for the full users’ release in spring 2001.
An initial developer’s release in July 2000 allowed software developers to get a close look at the system architecture and advance their interest in choosing components to integrate into the system. This month’s release offers an expanded set of usable components and refinements to the ISYS platform, in anticipation of the user’s release.
Addressing a Growing Problem in Genomics Research
ISYS addresses a growing problem in the burgeoning field of functional genomics research. Despite wider availability of computer programs and database resources for bioinformatics applications, there has been no efficient way for investigators to combine these unstandardized resources to further their research.
ISYS provides an intuitive environment for scientists to explore data and detect relationships that they might not otherwise see. ISYS, written in JAVA, integrates bioinformatics tools and algorithms developed by specialists in their own areas of expertise. These tools could have been developed completely separately from each other or ISYS, yet ISYS provides a way for them to share data and operate interactively.
“A lot of other integration methods require heavy-duty adaptation of components to fit the system,” explains Damian Gessler, Ph.D., co-project leader for ISYS. “We’ve taken the approach that scientists know best how to develop their own specific area of research. ISYS is a gentle way of tying together disparate components.”
ISYS: Furthering the Development of Genomics and Bioinformatics
The ISYS approach is inspired by complex systems such as cellular automata and Boolean networks, in which the interaction of simple, independent agents results in the emergence of complex properties.
“In many ways, ISYS is just an application of modern component-based software engineering to bioinformatics,” co-project leader Adam Siepel says. “But, what we’ve tried to push a little bit further than what we’ve seen elsewhere is the degree to which the components are insulated from one another. We really wanted to be able to reuse existing and independently evolving software tools, but still to achieve relatively sophisticated integration.”
The problem of integration is crucial to the further development of genomics and bioinformatics. Therefore, a system that can integrate many existing software tools, while allowing independent researchers to develop new tools as they see fit, offers a novel approach to rapid bioinformatics integration. The ISYS platform employs techniques for interoperation among loosely coupled components.
Another advantage of the system is its ability to allow users to customize and modify the environment. Researchers who find a new tool that allow users to bring the best tools to bear on their particular biological problems, without sacrificing integrative behavior. Currently, integrating new components into ISYS requires some programming intervention; the published ISYS API (Application Programming Interface) helps guide the process.
The ISYS project is a dynamic and evolving one; program leaders Gessler and Siepel predict many new features and enhancements to come. Users can access ISYS by visiting http://www.ncgr.org/research/isys . The system will be featured in an upcoming research article in the journal, Bioinformatics.
NCGR ( http://www.ncgr.org ) is an independent, nonprofit life sciences research institute working at the interface of biology, computer science and mathematics (bioinformatics). By conducting and facilitating research, the Center contributes to the improvement of global nutrition, health and environmental well-being.