1. A computer implemented process for constructing a scalable phenotypic output network model, comprising the computer implemented steps of: (a) executing commands in a suitably programmed computer to access a database of network gene components comprising an annotated network set of open reading frames (ORFs) of a bioparticle genome; (b) executing commands in the suitably programmed computer to form a data structure associating said network gene components with network reaction components, wherein forming the data structure comprises (i) selecting an ORF of the network gene components, (ii) querying the database to identify network reaction components that are gene products of the selected ORF, (iii) querying the database to identify network gene components or network reaction components that interact with the selected ORF or the identified gene product, (iv) selecting the subset of network gene components and network reaction components identified in steps (b)(ii) and (b)(iii), and (v) associating said network gene components of the subset with said network reaction components of the subset with annotations, said data structure specifying a network model of connectivity and flow of said network reaction components; (c) executing commands in the suitably programmed computer to modify said data structure to enumerate a biochemical demand on said specified network model, and (d) executing commands in the suitably programmed computer to transform said modified data structure into a mathematical description of reactant fluxes defining said network model of connectivity and flow, wherein said enumerated biochemical demand corresponds to an aggregate reactant demand flux defining a phenotypic output of said network model of a bioparticle.