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>.} }