This conversion requires three main steps. 1. The first step involves the mathematical representation by a stoichiometric matrix, S, of the network reaction list. The columns of S correspond to the network reactions, while the rows represent the network metabolites. The substrates in a reaction are defined to have a negative coefficient, while products have a positive value. The metabolites participating in a reaction have non-zero entry in the S matrix. 2. Now that the reconstruction is in a computer-readable format, the systems boundaries need to be defined. In particular, this means that for all metabolites that can be consumed or secreted by the target cell a so-called exchange reaction needs to be added to the reconstruction. The exchange reactions can be employed in later simulation to define for example environmental conditions (e.g., carbon source). 3. As a last step, constraints will be added to the reconstruction, thus rendering it to a condition-specific model. Mass conservation is a basic physical law. All steady-states can be thus described by S.v = 0 where v is a vector of reaction fluxes. Adding further constraints such as thermodynamics (reaction directionality), enzyme capacity or regulation (i.e., presence or absence of an enzyme) to the model will lead to a smaller, more confined set of feasible steady-states flux solutions.

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