A scalable and integrative system for pathway bioinformatics and systems biology

• Published in: Advances in experimental medicine and biology Vol. 680; p. 523
• Main Authors: Compani, Behnam, Su, Trent, Chang, Ivan, Cheng, Jianlin, Shah, Kandarp H, Whisenant, Thomas, Dou, Yimeng, Bergmann, Adriel, Cheong, Raymond, Wold, Barbara, Bardwell, Lee, Levchenko, Andre, Baldi, Pierre, Mjolsness, Eric
• Format: Journal Article
• Language: English
• Published: United States 2010
• Subjects: Computational Biology; Computer Communication Networks; Computer Simulation; Databases, Factual; Expert Systems; Internet; Metabolic Networks and Pathways; Models, Biological; Signal Transduction; Software; Systems Biology - statistics & numerical data; User-Computer Interface
• ISSN: 0065-2598
• DOI: 10.1007/978-1-4419-5913-3_58

Progress in systems biology depends on developing scalable informatics tools to predictively model, visualize, and flexibly store information about complex biological systems. Scalability of these tools, as well as their ability to integrate within larger frameworks of evolving tools, is critical to address the multi-scale and size complexity of biological systems. Using current software technology, such as self-generation of database and object code from UML schemas, facilitates rapid updating of a scalable expert assistance system for modeling biological pathways. Distribution of key components along with connectivity to external data sources and analysis tools is achieved via a web service interface. All sigmoid modeling software components and supplementary information are available through: http://www.igb.uci.edu/servers/sb.html.