Biochemical Space Language in Relation to Multiset Rewriting Systems
This work provides a formal connection for modeling biochemical systems, but it is incremental as it builds on existing rewriting frameworks.
The paper relates Biochemical Space Language (BCSL) to Multiset Rewriting Systems (MRS) by constructing an MRS from any BCSL model to represent the same set of runs, enabling the use of MRS regulations in BCSL.
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.