PathCase-SB architecture and database design

PathCase Systems Biology (PathCase-SB) is built and released. The PathCase-SB database provides data and API for multiple user interfaces and software tools. The current PathCase-SB system provides a database-enabled framework and web-based computational tools towards facilitating the development of kinetic models for biological systems. PathCase-SB aims to integrate data of selected biological data sources on the web (currently, BioModels database and KEGG), and to provide more powerful and/or new capabilities via the new web-based integrative framework. This paper describes architecture and database design issues encountered in PathCase-SB's design and implementation, and presents the current design of PathCase-SB's architecture and database.PathCase-SB architecture and database provide a highly extensible and scalable environment with easy and fast (real-time) access to the data in the database. PathCase-SB itself is already being used by researchers across the world.There are many computer science applications that integrate the data of different data sources, and build new tools that are otherwise difficult or impossible to build. PathCase Systems Biology (PathCase-SB) [1] brings together, under a single database environment, metabolic pathways data and systems biology models, and provides new or expanded browsing, querying, visualization, and simulation capabilities in order to help with systems biology modeling and analysis, all brought about due to the integrated environment. Note that PathCase-SB, which builds on PathCase [2], is not a model- or pathways-data source, and, it does not curate systems biology models. In this paper, we describe architecture and database design issues encountered in PathCase-SB's design and implementation, and present the current design of the PathCase-SB architecture and database. The user interfaces of PathCase-SB are described in detail in another study (Coskun et al: PathCase-SB: Integrating Data Sources and Providing Tools