Sigmoid: A Software Infrastructure for Pathway Bioinformatics and Systems Biology

Sigmoid is 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 and cell model generation and simulation (Cellerator), a pathway-modeling database, Web-services-oriented middleware, and a GUI. Future enhancements will include parameter optimization and other data mining technologies. Key to the infrastructureʹs design 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.