The biodegradation network, a new scenario for computational systems biology research

  • Authors:

  • Florencio Pazos;David Guijas;Manuel J. Gomez;Almudena Trigo;Victor de Lorenzo;Alfonso Valencia

  • Affiliations:

  • bioALMA;bioALMA;Protein Design Group, National Center for Biotechnology, CNB-CSIC, Cantoblanco, Madrid;Protein Design Group, National Center for Biotechnology, CNB-CSIC, Cantoblanco, Madrid;Bacterial Biotechnology Department. National Center for Biotechnology, CNB-CSIC;Protein Design Group, National Center for Biotechnology, CNB-CSIC, Cantoblanco, Madrid

  • Venue:
  • CMSB'04 Proceedings of the 20 international conference on Computational Methods in Systems Biology
  • Year:
  • 2004

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Abstract

The study of the global properties of complex metabolic networks in organisms such as E. coli and Yeast has become a priority in the new area of Computational Systems Biology, leading to the first models about the organization and evolution of these networks. Here we propose the analysis of biodegradation networks as an alternative to this, now classical, studies of metabolic networks. The biodegradation reactions carried out by communities of bacteria in contaminated environments offer interesting computational and biological advantages and challenges. Here we first describe our preliminary results on the analysis of the systems properties of the biodegradation network and the comparison with the other metabolic networks, and second describe the computational developments necessary for the analysis of the information. In particular we introduce the MetaRouter system, as an integrated information system for Biodegradation. Furthermore we describe the current work for improving the system with an alternative enzyme-centric view and new rule-based systems for the prediction of the capacity of biological systems to degrade new chemical compounds.