Parameter Synthesis and Robustness Analysis of Rule-Based Models

Troják, Matej; Šafránek, David; Mertová, Lukrécia; Brim, Luboš

doi:10.1007/978-3-030-55754-6_3

Cited by 3 publications

(1 citation statement)

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“…Additional knowledge about the described biological system can further reduce possible model behaviour scenarios. These are usually introduced by defining quantitative properties [2]. However, these properties are not always easy to define, and alternative mechanisms are needed.…”

Section: Regulationsmentioning

confidence: 99%

Biochemical Space Language in Relation to Multiset Rewriting Systems

Troják¹,

Šafránek²,

Brim³

2022

Preprint

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This technical report relates Biochemical Space Language (BCSL) [4] to Multiset rewriting systems (MRS) [3]. For a BCSL model, the semantics are defined in terms of transition systems, while for an MRS, they are defined in terms of a set of runs. In this report, we relate BCSL to MRS by first showing how the transition system is related to a set of runs and consequently showing how for every BCSL model, an MRS can be constructed such that both represent the same set of runs. The motivation of this step is to establish BCSL in the context of a more general rewriting system and benefit from properties shown for them. Finally, we show that regulations defined for MRS can be consequently used in the BCSL model. Multiset rewriting systemsThis section recalls some definitions and known results about multisets and rewriting systems over them. Intuitively, a multiset is a set of elements with allowed repetitions. A multiset rewriting rule describes how a particular multiset is transformed into another one. A multiset rewriting system consists of a set of rewriting rules, defining how the system can evolve, and an initial multiset, representing the starting point for the rewriting.

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Section: Regulationsmentioning

confidence: 99%