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The relentless advance of biochemistry has enabled us to take apart biological systems with ever more fine-grained and precise instruments. The fruits of this dissection are millions of measurements of base pairs and biochemical con- centrations. Yet to make sense of these numbers, we need to reverse our dissection by putting the system back together on the computer. This first step in this process is reconstructing molecular anatomy through static modeling, the determination of which pieces (DNA, RNA, protein, and metabolite) is present, and how they are related (e.g., regulator, target, inhibitor, cofactor). Given this broad outline of com- ponent connectivity, we may then attempt to reconstruct molecular physiology via dynamic modeling, computer simulations that model when cellular events occur (ODE), where they occur (PDE), and how frequently they recur (SDE). In this review we discuss techniques for both of these modeling paradigms, illustrating each by reference to important recent papers. |
