A Scalable and Integrative System for Pathway Bioinformatics and Systems Biology

  • Behnam Compani
  • Trent Su
  • Ivan Chang
  • Jianlin Cheng
  • Kandarp H. Shah
  • Thomas Whisenant
  • Yimeng Dou
  • Adriel Bergmann
  • Raymond Cheong
  • Barbara Wold
  • Lee Bardwell
  • Andre Levchenko
  • Pierre Baldi
  • Eric Mjolsness
Conference paper
Part of the Advances in Experimental Medicine and Biology book series (AEMB, volume 680)

Abstract

Motivation: 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.

Results: 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.

Availability: All sigmoid modeling software components and supplementary information are available through: http://www.igb.uci.edu/servers/sb.html.

Keywords

Bioinformatics Biosynthetic Database Metabolic Modeling Signal transduction Simulation Systems biology 

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Copyright information

© Springer Science+Business Media, LLC 2010

Authors and Affiliations

  • Behnam Compani
  • Trent Su
  • Ivan Chang
  • Jianlin Cheng
  • Kandarp H. Shah
  • Thomas Whisenant
  • Yimeng Dou
  • Adriel Bergmann
  • Raymond Cheong
  • Barbara Wold
  • Lee Bardwell
  • Andre Levchenko
  • Pierre Baldi
  • Eric Mjolsness
    • 1
    • 2
  1. 1.Institute for Genomics and BioinformaticsUniversity of CaliforniaIrvineUSA
  2. 2.School of Information and Computer SciencesUniversity of CaliforniaIrvineUSA

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