Formal Cellular Machinery

Damgaard, Troels C.; Højsgaard, Espen; Krivine, Jean

doi:10.1016/j.entcs.2012.05.015

Cited by 10 publications

(8 citation statements)

References 9 publications

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“…However, such a machine would not scale well, as in general the COW strategy may be not very useful; thus, we can restrict our attentions to smaller subsets of BRSs, specifically designed to some application domain. For biological applications, the bigraphic reactive systems considered in [1,7] might be a more reasonable target.…”

Section: Discussionmentioning

confidence: 99%

Implementing the Stochastics Brane Calculus in a Generic Stochastic Abstract Machine

Miculan

Sambarino

2012

Electron. Proc. Theor. Comput. Sci.

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In this paper, we deal with the problem of implementing an abstract machine for a stochastic version of the Brane Calculus. Instead of defining an ad hoc abstract machine, we consider the generic stochastic abstract machine introduced by Lakin, Paulevé and Phillips. The nested structure of membranes is flattened into a set of species where the hierarchical structure is represented by means of names. In order to reduce the overhead introduced by this encoding, we modify the machine by adding a copy-on-write optimization strategy. We prove that this implementation is adequate with respect to the stochastic structural operational semantics recently given for the Brane Calculus. These techniques can be ported also to other stochastic calculi dealing with nested structures

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Section: Discussionmentioning

confidence: 99%

Implementing the Stochastics Brane Calculus in a Generic Stochastic Abstract Machine

Miculan

Sambarino

2012

Electron. Proc. Theor. Comput. Sci.

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“…The resulting expression e[v2/x] is further evaluated to v. (6) describes that if the expressions that denote the attributes and the subsolution of a species can be evaluated to values, they are replaced by these values. (7) shows how expressions that evaluate to solutions can be composed to describe the composition of solutions.…”

Section: Semantics Of Ml-rulesmentioning

confidence: 99%

“…In the context of rule-based approaches, compartmental dynamics like merging of two compartments or endocytosis are supported inherently, e.g., by ML-Rules [21], CSMMR [25], ML-Space [2], and Bigraphs [20] and have also been suggested as extensions of other rule-based languages, e.g., for Kappa [6]. Endocytosis is a process by which cells absorb molecules by engulfing them; it might be used to transport larger molecules into the cell or to recycle receptors.…”

Section: Compartments and Dynamic Nesting Structuresmentioning

confidence: 99%

“…Thus, one quadruple represents a reaction template, which contains all information to execute the corresponding reaction. Within loop (6), all quadruples are computed for each rule and the given solution sol by following the (INST) rule of the stochastic semantics in Figure 6. Within loop (7), all quadruples for each species of the given solution sol are computed recursively according to the recursion within the (SUB) and (SUM) rule of the stochastic semantics.…”

Section: Simulator Implementationmentioning

confidence: 99%

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Syntax and Semantics of a Multi-Level Modeling Language

Warnke

Helms

Uhrmacher

2015

Proceedings of the 3rd ACM SIGSIM Conference on Principles of Advanced Discrete Simulation

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The domain specific modeling and simulation language ML-Rules makes it possible to describe cell biological systems at different levels of organization. A model is formed by attributed and dynamically nested species, with reactions that are constrained by functions on attributes. In this paper, we extend ML-Rules to also support constraints using functions on multi-sets of species, i.e., solutions. Further, we present the formal syntax and semantics of ML-Rules, we define its stochastic simulator and we illustrate its expressiveness based on a model of the cell cycle and proliferation.

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“…These are used to keep track and separate each flux on the bases of the points handle. The constraint families 7and (8) define the outgoing and ingoing flux of host points and handles respectively. The former has to send exactly one unit considering every edge they are involved with and the latter receive one unit for each of their point regardless if this unit comes from the point directly or from a handle of the guest.…”

Section: Directed Link Graphsmentioning

confidence: 99%

Computing Embeddings of Directed Bigraphs

Chiapperini

Miculan

Peressotti

2020

Graph Transformation

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Directed bigraphs are a meta-model which generalises Milner's bigraphs by taking into account the request flow between controls and names. A key problem about these bigraphs is that of bigraph embedding, i.e., finding the embeddings of a bigraph inside a larger one. We present an algorithm for computing embeddings of directed bigraphs, via a reduction to a constraint satisfaction problem. We prove soundness and completeness of this algorithm, and provide an implementation in jLibBig, a general Java library for manipulating bigraphical reactive systems, together with some experimental results.

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Formal Cellular Machinery

Cited by 10 publications

References 9 publications

Implementing the Stochastics Brane Calculus in a Generic Stochastic Abstract Machine

Implementing the Stochastics Brane Calculus in a Generic Stochastic Abstract Machine

Syntax and Semantics of a Multi-Level Modeling Language

Computing Embeddings of Directed Bigraphs

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