Sigmoid: A Software Infrastructure for Pathway Bioinformatics and Systems Biology

Authors:
Jianlin Cheng;Lucas Scharenbroich;Pierre Baldi;Eric Mjolsness
Affiliations:
University of California, Irvine;University of California, Irvine;University of California, Irvine;University of California, Irvine
Venue:
IEEE Intelligent Systems
Year:
2005

Citing 2
Cited 0

The Unified Modeling Language user guide

The Unified Modeling Language user guide
An enzyme mechanism language for the mathematical modeling of metabolic pathways

Bioinformatics

Quantified Score

Hi-index	0.00

Visualization

Abstract

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 infrastructure's 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.