## Towards a causal semantics for Brane Calculi (2007)

Venue: | What is it About Government that Americans Dislike |

Citations: | 2 - 1 self |

### BibTeX

@INPROCEEDINGS{Busi07towardsa,

author = {Nadia Busi},

title = {Towards a causal semantics for Brane Calculi},

booktitle = {What is it About Government that Americans Dislike},

year = {2007},

pages = {1945--1965},

publisher = {University Press}

}

### OpenURL

### Abstract

Summary. Brane Calculi are a family of biologically inspired process calculi, proposed in [6] to model the interactions of dynamically nested membranes. We propose a semantics that describes the causal dependencies occurring between the reactions of a system described in Brane Calculi. We investigate the basic properties that are satisfied by such a semantics. The notion of causality turns out to be quite relevant for biological systems, as it permits to point out which events occurring in a biological pathway are necessary for another event to happen. 1

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Citation Context ...could be of precious help, e.g., for limiting the search space in the case some unpredicted event occurs. The study of a causal semantics for process algebras dates back to the early nineties for CCS =-=[17]-=- (see, e.g., [10, 9, 15]), and to the mid nineties for the πcalculus [18] (see, e.g., [1, 3, 11, 12]). To the best of our knowledge, the only other work that deals with causality in bio-inspired calcu... |

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Citation Context ...e some unpredicted event occurs. The study of a causal semantics for process algebras dates back to the early nineties for CCS [17] (see, e.g., [10, 9, 15]), and to the mid nineties for the πcalculus =-=[18]-=- (see, e.g., [1, 3, 11, 12]). To the best of our knowledge, the only other work that deals with causality in bio-inspired calculi is [14], where a causal semantics for Beta Binders [21, 22] – based on... |

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Citation Context ...nguage theory, with the definition of P systems. In a process algebraic setting, the notions of membranes and compartments are explicitly represented in BioAmbients [23], a variant of Mobile Ambients =-=[8]-=- based on a set of biologically inspired primitives of interaction. Brane calculi represent an evolution of BioAmbients: the main difference w.r.t. previous approaches consists in the fact that the ac... |

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Citation Context ...e current step, then it must be performed) for MBD. It is also the common approach used in the definition of the maximal parallelism semantics for Membrane Systems with evolving membranes (see, e.g., =-=[19, 20]-=-). In the present paper, we consider the opposite approach: in the above system, we consider the drip operation independent from the mate operation, as the drip operation can be executed regardless of... |

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Citation Context ...the field of automata and formal language theory, with the definition of P systems. In a process algebraic setting, the notions of membranes and compartments are explicitly represented in BioAmbients =-=[23]-=-, a variant of Mobile Ambients [8] based on a set of biologically inspired primitives of interaction. Brane calculi represent an evolution of BioAmbients: the main difference w.r.t. previous approache... |

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Citation Context ...Scienze dell’Informazione, Università di Bologna, Mura A. Zamboni 7, I-40127 Bologna, Italy. busi@cs.unibo.it Summary. Brane Calculi are a family of biologically inspired process calculi, proposed in =-=[6]-=- to model the interactions of dynamically nested membranes. We propose a semantics that describes the causal dependencies occurring between the reactions of a system described in Brane Calculi. We inv... |

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Citation Context ...ous help, e.g., for limiting the search space in the case some unpredicted event occurs. The study of a causal semantics for process algebras dates back to the early nineties for CCS [17] (see, e.g., =-=[10, 9, 15]-=-), and to the mid nineties for the πcalculus [18] (see, e.g., [1, 3, 11, 12]). To the best of our knowledge, the only other work that deals with causality in bio-inspired calculi is [14], where a caus... |

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Citation Context ... the πcalculus [18] (see, e.g., [1, 3, 11, 12]). To the best of our knowledge, the only other work that deals with causality in bio-inspired calculi is [14], where a causal semantics for Beta Binders =-=[21, 22]-=- – based on the π-calculus semantics and on the enhanced operational semantics approach of [12] – is defined. One of the main differences between Beta Binders and Brane Calculi is that the membrane st... |

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Citation Context ...d event occurs. The study of a causal semantics for process algebras dates back to the early nineties for CCS [17] (see, e.g., [10, 9, 15]), and to the mid nineties for the πcalculus [18] (see, e.g., =-=[1, 3, 11, 12]-=-). To the best of our knowledge, the only other work that deals with causality in bio-inspired calculi is [14], where a causal semantics for Beta Binders [21, 22] – based on the π-calculus semantics a... |

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Citation Context ...d event occurs. The study of a causal semantics for process algebras dates back to the early nineties for CCS [17] (see, e.g., [10, 9, 15]), and to the mid nineties for the πcalculus [18] (see, e.g., =-=[1, 3, 11, 12]-=-). To the best of our knowledge, the only other work that deals with causality in bio-inspired calculi is [14], where a causal semantics for Beta Binders [21, 22] – based on the π-calculus semantics a... |

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Citation Context ...ous help, e.g., for limiting the search space in the case some unpredicted event occurs. The study of a causal semantics for process algebras dates back to the early nineties for CCS [17] (see, e.g., =-=[10, 9, 15]-=-), and to the mid nineties for the πcalculus [18] (see, e.g., [1, 3, 11, 12]). To the best of our knowledge, the only other work that deals with causality in bio-inspired calculi is [14], where a caus... |

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Citation Context ...d event occurs. The study of a causal semantics for process algebras dates back to the early nineties for CCS [17] (see, e.g., [10, 9, 15]), and to the mid nineties for the πcalculus [18] (see, e.g., =-=[1, 3, 11, 12]-=-). To the best of our knowledge, the only other work that deals with causality in bio-inspired calculi is [14], where a causal semantics for Beta Binders [21, 22] – based on the π-calculus semantics a... |

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Citation Context ...[14] in the definition of a causal semantics for Beta-binders [21, 22] , a bio-inspired process calculus roughly consisting of unnested compartments enclosing π-calculus processes. It is also used in =-=[2]-=- for the definition of a maximal parallelism semantics (i.e., step semantics with maximal progress: if an action can be performed in the current step, then it must be performed) for MBD. It is also th... |

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Citation Context ... the πcalculus [18] (see, e.g., [1, 3, 11, 12]). To the best of our knowledge, the only other work that deals with causality in bio-inspired calculi is [14], where a causal semantics for Beta Binders =-=[21, 22]-=- – based on the π-calculus semantics and on the enhanced operational semantics approach of [12] – is defined. One of the main differences between Beta Binders and Brane Calculi is that the membrane st... |

3 |
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Citation Context ...estigating the causal dependencies arising in biological pathways involving membranes, such as, e.g., the LDL Cholesterol Degradation Pathway [16], that has been modeled in the full Brane Calculus in =-=[5]-=-. We also plan to perform a thorough investigation of the properties that are enjoyed by the causal semantics, and possibly to refine the definition of the causal semantics in order to fulfill some of... |

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Citation Context ... e.g., [10, 9, 15]), and to the mid nineties for the πcalculus [18] (see, e.g., [1, 3, 11, 12]). To the best of our knowledge, the only other work that deals with causality in bio-inspired calculi is =-=[14]-=-, where a causal semantics for Beta Binders [21, 22] – based on the π-calculus semantics and on the enhanced operational semantics approach of [12] – is defined. One of the main differences between Be... |

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Citation Context ...ous help, e.g., for limiting the search space in the case some unpredicted event occurs. The study of a causal semantics for process algebras dates back to the early nineties for CCS [17] (see, e.g., =-=[10, 9, 15]-=-), and to the mid nineties for the πcalculus [18] (see, e.g., [1, 3, 11, 12]). To the best of our knowledge, the only other work that deals with causality in bio-inspired calculi is [14], where a caus... |

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Comparing truly concurrent semantics for contextual place/transition nets with inhibitor and read arcs
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Citation Context ...actions: the occurrence of the bud action prevents the mate action to happen, but the vice versa does not hold. A similar phenomenon takes place, e.g., in Petri nets with read and inhibitor arcs (see =-=[4]-=- for a discussion on this topic). A possible way to capture this kind of asymmetric conflict is based on the following idea: if a mate synchronization with causal label k is performed, we decorate the... |