Valderrama-Gómez MÁ, Lomnitz JG, Fasani RA, Savageau MA. Mechanistic Modeling of Biochemical Systems without A Priori Parameter Values Using the Design Space Toolbox v.3.0.
iScience 2020;
23:101200. [PMID:
32531747 PMCID:
PMC7287267 DOI:
10.1016/j.isci.2020.101200]
[Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 05/04/2020] [Accepted: 05/21/2020] [Indexed: 01/24/2023] Open
Abstract
Mechanistic models of biochemical systems provide a rigorous description of biological phenomena. They are indispensable for making predictions and elucidating biological design principles. To date, mathematical analysis and characterization of these models encounter a bottleneck consisting of large numbers of unknown parameter values. Here, we introduce the Design Space Toolbox v.3.0 (DST3), a software implementation of the Design Space formalism enabling mechanistic modeling without requiring previous knowledge of parameter values. This is achieved by using a phenotype-centric modeling approach, in which the system is first decomposed into a series of biochemical phenotypes. Parameter values realizing phenotypes of interest are subsequently predicted. DST3 represents the most generally applicable implementation of the Design Space formalism and offers unique advantages over earlier versions. By expanding the Design Space formalism and streamlining its distribution, DST3 represents a valuable tool for elucidating biological design principles and designing novel synthetic circuits.
DST3 extends the Design Space formalism by identifying additional phenotypes
Additional phenotypes arise from cycles, conservations, and metabolic imbalances
DST3 enables mechanistic modeling without previous knowledge of parameter values
It fully unlocks the potential of the novel phenotype-centric modeling strategy
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