Gap Detection for Genome-Scale Constraint-Based Models.pdfVIP

Hindawi Publishing Corporation Advances in Bioinformatics Volume 2012, Article ID 323472, 10 pages doi:10.1155/2012/323472 Research Article Gap Detection for Genome-Scale Constraint-Based Models J. Paul Brooks,1, 2 William P. Burns,1 Stephen S. Fong,1, 3 Chris M. Gowen,1, 3 and Seth B. Roberts1, 3 1 Center for the Study of Biological Complexity, Virginia Commonwealth University, P.O. Box 843083, Richmond, VA 23284, USA 2 Department of Statistical Sciences and Operations Research, Virginia Commonwealth University, P.O. Box 843083, Richmond, VA 23284, USA 3 Department of Chemical and Life Science Engineering, Virginia Commonwealth University, P.O. Box 843083, Richmond, VA 23284, USA Correspondence should be addressed to J. Paul Brooks, jpbrooks@ Received 23 April 2012; Accepted 16 July 2012 Academic Editor: T. Akutsu Copyright © 2012 J. Paul Brooks et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Constraint-based metabolic models are currently the most comprehensive system-wide models of cellular metabolism. Several challenges arise when building an in silico constraint-based model of an organism that need to be addressed before flux balance analysis (FBA) can be applied for simulations. An algorithm called FBA-Gap is presented here that aids the construction of a working model based on plausible modifications to a given list of reactions that are known to occur in the organism. When applied to a working model, the algorithm gives a hypothesis concerning a minimal medium for sustaining the cell in culture. The utility of the algorithm is demonstrated in creating a new model organ