ArticleiScience2020
Mechanistic Modeling of Biochemical Systems without A Priori Parameter Values Using the Design Space Toolbox v.3.0.
Article in iScience, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- UNified FramewOrk for reguLatory Dynamics (UNFOLD): Dissecting robustness, plasticity, evolvability and canalisation of biological function.PLoS computational biology · 2026Article
- Topological Environment in Genetic and Metabolic Networks.bioRxiv : the preprint server for biology · 2026Article
- Using monoids for the integration of genomic and metabolic parameters in the prediction of phenotypes in regulatory cascades.Bio Systems · 2025Article
- Using Monoids for the Integration of Genomic and Metabolic Parameters in the Prediction of Phenotypes in Regulatory Cascades.bioRxiv : the preprint server for biology · 2025Article
- Phenotype Design Space Provides a Mechanistic Framework Relating Molecular Parameters to Phenotype Diversity Available for Selection.Journal of molecular evolution · 2023Article
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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