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Issue No.03 - May/June (2005 vol.20)
pp: 68-75
Jianlin Cheng , University of California, Irvine
Lucas Scharenbroich , University of California, Irvine
Pierre Baldi , University of California, Irvine
Eric Mjolsness , University of California, Irvine
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.
INDEX TERMS
cell modeling, bioinformatics, pathway, systems biology, computer algebra, intelligent middleware, generative software, Sigmoid, Cellerator, UML
CITATION
Jianlin Cheng, Lucas Scharenbroich, Pierre Baldi, Eric Mjolsness, "Sigmoid: A Software Infrastructure for Pathway Bioinformatics and Systems Biology", IEEE Intelligent Systems, vol.20, no. 3, pp. 68-75, May/June 2005, doi:10.1109/MIS.2005.51
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