Biochemical Space Language in Relation to Multiset Rewriting Systems

TL;DR

This paper establishes a formal relationship between Biochemical Space Language (BCSL) and Multiset Rewriting Systems (MRS), enabling the transfer of properties and regulations from MRS to BCSL models.

Contribution

It demonstrates how BCSL models can be represented as MRS, allowing for the application of MRS properties and regulations to biochemical modeling.

Findings

BCSL transition systems can be related to sets of runs in MRS.

For every BCSL model, an equivalent MRS can be constructed.

Regulations from MRS can be applied to BCSL models.

Abstract

This technical report relates Biochemical Space Language (BCSL) to Multiset rewriting systems (MRS). 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.