Sigmoid: Towards an Intelligent, Scalable, Software Infrastructure for Pathway Bioinformatics and Systems Biology

We describe a generative, scalable software infrastructure for pathway bioinformatics and systems biology. The Sigmoid modeling system is a three-tier architecture comprising distributed modules that implement pathway/cell model generation and simulation (Cellerator), a pathway modeling database (Sigmoid proper), a Web service-oriented middleware, a graphical user interface, and in the future, parameter optimization and other datamining technologies. Key to the design of the infrastructure is its scalability ensured by leveraging symbolic computer algebra and self-generation of database and other code from high-level representations such as UML schema. All Sigmoid modeling software components are available through: http://www.igb.uci.edu/servers/sb.html.