You've Got to Start Somewhere

Our current work is focused on a single question: can we trace the path of the atoms through each compound in a biochemical pathway? This question is a logical abstract of in vivo metabolic tracer experiments, and requires representations of the compounds' structures (the objects) , the chemistry of the reactions (the processes) , and the specificities of the enzymes (the constraints) . Since these are ultimately questions about the fates of molecules, we have named the project Moirai.

Because we need to reason with all three dimensions of information, we are implementing a symmetric representation of each within a declarative framework. We have been experimenting with alternative representations in Prolog , and we test them by comparing the results of our predictions to the known experimental biochemistry. Our biological example is glycolysis .

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