Cellular-based approaches

In the cellular automata (CA) algorithm, many small cells replace the differential equations by discrete approximations in suitable applications the approximate description that the cellular automata method provides can be every bit as effective as a more abstract equation-based approach. In addition, while differential equations rarely help a novice user to develop an intuitive understanding of a process, the visualization provided by CA can be very informative. 

RNAi and ribozymes represent two additional approaches to gene silencing/down-regulation with therapeutic potential. RNAi is an innate cellular process that achieves silencing of selected genes via an anti-sense mechanism. It shares many characteristics with the antisense-based approach described above, but also some important differences, e.g. in the exact mechanism by which the antisense effect is achieved. 

A considerable improvement over purely graph-based approaches is the analysis of metabolic networks in terms of their stoichiometric matrix. Stoichiometric analysis has a long history in chemical and biochemical sciences [59 62], considerably pre-dating the recent interest in the topology of large-scale cellular networks. In particular, the stoichiometry of a metabolic network is often available, even when detailed information about kinetic parameters or rate equations is lacking. Exploiting the flux balance equation, stoichiometric analysis makes explicit use of the specific structural properties of metabolic networks and allows us to put constraints on the functional capabilities of metabolic networks [61,63 69]. 

Metabolic networks can be quantitatively and qualitatively studied without enzyme kinetic parameters by using a constraints-based approach. Metabolic networks must obey the fundamental physicochemical laws, such as mass, energy, redox balances, diffusion, and thermodynamics. Therefore, when kinetic constants are unavailable, cellular function can still be mathematically constrained based on the mass and energy balance. Flux balance analysis (FBA) is a mathematical modeling framework that can be used to study the steady-state metabolic capabilities of cell-based physicochemical constraints. ... 

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