Model Validation Of Simple-graph Representations Of Metabolism

With the modern biochemistry one has for the first time been able to describe the large scale structure of biochemical reaction systems like the metabolism.


Typically, this is done with graph methods discarding much of the information present in the databases.


How can we make a graph of metabolism encoding as much information as possible?


In this paper, we use a modeling approach to this question, and our conclusion is that the best representations are either to connect all metabolites participating in a reaction to each other, or to connect the vertices reacting to the product of the reaction.


Journal of the Royal Society Interface


Journal of the Royal Society Interface is the Society's cross-disciplinary publication promoting research at the interface between the physical and life sciences. It offers rapidity, visibility and high-quality peer review and is ranked fifth in JCR's multidisciplinary category. The journal also incorporates Interface Focus, a peer-reviewed, themed supplement, each issue of which concentrates on a specific cross-disciplinary subject.


Journal of the Royal Society Interface