Database Software for Complex Cell Biological Pathways

Integrative Bioinformatics, Inc., Los Altos CA

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Abstract

[unreadable] DESCRIPTION (provided by applicant): [unreadable] Database technology is widely recognized as essential for managing and analyzing large-scale experimental datasets. The innovative idea of this SBIR project is to apply database technology to the corresponding problem of managing large-scale cell biological theories or models. This is significant because computational cell biology/systems biology is playing an increasingly important role in helping molecular cell biologists extract mechanistic, cause-and-effect information from time course experimental data. With Phase I SBIR support, Integrative Biolnformatics, Inc. has developed a prototype and successfully demonstrated feasibility for ProcessDB, a fast, flexible and scalable software product whose long term objective is faster, more efficient testing of complex cell biological theories involving hundreds or even thousands of interacting molecules. This Phase II SBIR project has two specific aims: 1) to expand the ProcessDB prototype into a commercial version that successfully integrates database technology with kinetic modeling in a way that will be embraced by a broad range of molecular cell biologists in academic research, biotechnology companies, and pharmaceutical R&D; and 2) to successfully apply the ProcessDB software product in multiple research environments covering a wide range of current cell biological problems. To achieve these aims, new features will be added to expand the functionality and the usability of the already powerful ProcessDB prototype: 1) a flexible standards-based visual user interface allowing users the option to draw rather than use forms to enter their hypotheses; 2) standards-based interoperability with more than 30 systems biology software tools and full native interfaces with two key solver applications; 3) inclusion of tested and verified ProcessDB versions of published models; and 4) interoperability with public domain pathway and signaling databases. This work will be carried out using methods that we successfully tested in Phase I: 1) a modern computer assisted software engineering (CASE*Method) approach to the analysis, design, building, testing, documentation, and production of ProcessDB; and 2) extensive consulting, collaboration, and client relationships with expert cell biologists who provide us with continuous feedback on each software release and knowledgeable requests for new features that will help ProcessDB become an essential tool for integrative work in modern molecular cell biology and ultimately in other disciplines as well. [unreadable] [unreadable] [unreadable]