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Sigmoid: A Software Infrastructure for Pathway Bioinformatics and Systems Biology
May/June 2005 (vol. 20 no. 3)
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
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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