Stoichiometrically Minimal Source Pathways via Model Checking

Matthew Fong and Sanjit A. Seshia. Stoichiometrically Minimal Source Pathways via Model Checking. In Proceedings of the 7th International Workshop on Bio-Design Automation (IWBDA), August 2015.
See also the accompanying thesis:here.

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Abstract

We formulate the problem of finding stoichiometrically minimal source pathways (SMSPs) in biochemical metabolic graphs and present a model checking approach to solve it. SMSPs are paths that, when flattened up to the source nodes corresponding to native compounds, use a non-dominated amount of those compounds. Our approach allows one to eliminate inefficient pathways when selecting the best path to a target. We also investigate the impact of the choice of model checking technique on the runtime for our procedure.

BibTeX

@InProceedings{fong-iwbda15,
  author = 	 {Matthew Fong and Sanjit A. Seshia},
  title = 	 {Stoichiometrically Minimal Source Pathways via Model Checking},
  booktitle = 	 {Proceedings of the 7th International Workshop on Bio-Design Automation (IWBDA)},
  month = {August},
  year = 	 {2015},
  abstract = {We formulate the problem of finding stoichiometrically minimal 
source pathways (SMSPs) in biochemical metabolic graphs and 
present a model checking approach to solve it. SMSPs are paths 
that, when flattened up to the source nodes corresponding to native 
compounds, use a non-dominated amount of those compounds. 
Our approach allows one to eliminate inefficient pathways when 
selecting the best path to a target. We also investigate the impact 
of the choice of model checking technique on the runtime for our 
procedure.},
  wwwnote = {See also the accompanying thesis:<a href="http://www.eecs.berkeley.edu/Pubs/TechRpts/2015/EECS-2015-126.html">here</a>.}
}