An Aside about Representing Biochemical Reactions

One of the greatest challenges in accurately representing reactions is to partition the available information consistently while preserving the inherent relationships among the different dimensions. Humans strongly mix information about the biochemistry, chemistry, enzymatic mechanism and kinetics of reactions, sliding unnoticed among them. This represents a problem not only in coding data, but in providing mechanisms for both visually zooming and panning (which in this instance is equivalent to mathematically expanding and contracting the graph) among the different dimensions of information. Of course the mathematics is particularly important for quantitative simulations of even the simplest kind. Understanding and testing different ways of partitioning the informational dimensions for reactions has proven particularly challenging.

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