Modeling Biological Systems in Stochastic Concurrent Constraint Programming

Bortolussi, Luca; Policriti, Alberto

doi:10.1007/s10601-007-9034-8

Cited by 51 publications

(65 citation statements)

References 32 publications

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“…In such case, the thesis follows from the fact that δ∈TD(q,x) p(δ) = 1. For the inductive step, observe that by condition (10), each sequence α ∈ T(q,x) is of the form δ ·T(e 2 [δ],r δ (x)) for some δ ∈ TD(q,x). This means that sequences in T(q,x) are longer than those in T(e 2 [δ],r δ (x)), hence by induction p(T(e 2 [δ],r δ (x))) = 1.…”

Section: Definition 42mentioning

confidence: 99%

“…Note that all agents in D, 8 are sequential, 7 The notion of entailment of CCP (see [37]) takes here a very simple form: a guard g(X) is entailed by a configuration c, c g(X), if g(c) is true. 8 In the following, with a slight abuse of notation, we sometimes write Remark 5.1 sCCP has been used as a modelling language for biological systems in [9], where models of biochemical and genetic networks have been addressed. The modelling style is predominantly reaction-centric: agents represent reactions and store variables maintain the numerousness of the different reactants.…”

Section: Stochastic Concurrent Constraint Programmingmentioning

confidence: 99%

“…Hence, genes are usually described in sCCP as multi state agents, see Example 5.1 below. For a more detailed discussion on modelling styles, we refer the reader to [9]. For biochemical and genetic networks, the simplified language presented here suffices.…”

Section: Stochastic Concurrent Constraint Programmingmentioning

confidence: 99%

“…The pros and cons of using sCCP as a modelling language for biological systems are discussed in detail in [9]. Basically, sCCP combines on one side the logical simplicity of process algebras and on the other side the computational power of constraints.…”

Section: Remark 52mentioning

confidence: 99%

“…Operational semantics: the operational semantics of sCCP is given by a transition relation that generates a labelled transition system (LTS), from which a Continuous Time Markov Chain (CTMC [35]) can be inferred, see [6], [9] for further details. We sketch briefly the mechanism:…”

Section: Remark 52mentioning

confidence: 99%

See 4 more Smart Citations

(Hybrid) automata and (stochastic) programs * The hybrid automata lattice of a stochastic program

Bortolussi¹,

Policriti²

2011

Journal of Logic and Computation

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We define a semantics for stochastic Concurrent Constraint Programming (sCCP), a stochastic process algebra, in terms of stochastic hybrid automata with piecewise deterministic continuous dynamics. To each program we associate a lattice of hybrid models, parameterized with respect to the degree of discreteness left. We study some properties of this lattice, presenting also an alternative semantics in which the degree of discreteness can be dynamically changed.

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Section: Definition 42mentioning

confidence: 99%

Section: Stochastic Concurrent Constraint Programmingmentioning

confidence: 99%

Section: Stochastic Concurrent Constraint Programmingmentioning

confidence: 99%

Section: Remark 52mentioning

confidence: 99%

Section: Remark 52mentioning

confidence: 99%

See 3 more Smart Citations

(Hybrid) automata and (stochastic) programs * The hybrid automata lattice of a stochastic program

Bortolussi¹,

Policriti²

2011

Journal of Logic and Computation

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A Declarative View of Signaling Pathways

Chiarugi

Falaschi

Olarte

et al. 2015

Programming Languages With Applications to Biology and Security

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Due to the inherent limitations of wet-lab techniques, the experimental data regarding cellular signaling pathways often consider single pathways or a small subset of them. We propose a methodology for composing signaling pathways data in a coherent framework. Our method consists in specifying the signaling pathway as a computationally executable model. We rely on the timed concurrent constraint language ntcc to represent the system in hand as a set of stoichiometric-like equations resembling the essential features of molecular interactions. The main advantages of our approach stem from the use of constraints (formulas in logic) and from modeling of discrete time clocks in ntcc. We can deal with partial information, representing the fact that several features of the biological system may be undetermined. We can explicitly represent the time needed for a reaction to occur. We model and simulate some well known cross-talking networks, such as the TNFα, the EGF and the insulin signaling pathways as well as their interactions

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Slicing Concurrent Constraint Programs

Falaschi

Gabbrielli

Olarte

et al. 2017

Lecture Notes in Computer Science

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Concurrent Constraint Programming (CCP) is a declarative model for concurrency where agents interact by telling and asking constraints (pieces of information) in a shared store. Some previous works have developed (approximated) declarative debuggers for CCP languages. However, the task of debugging concurrent programs remains difficult. In this paper we define a dynamic slicer for CCP and we show it to be a useful companion tool for the existing debugging techniques. We start with a partial computation (a trace) that shows the presence of bugs. Often, the quantity of information in such a trace is overwhelming, and the user gets easily lost, since she cannot focus on the sources of the bugs. Our slicer allows for marking part of the state of the computation and assists the user to eliminate most of the redundant information in order to highlight the errors. We show that this technique can be tailored to timed variants of CCP. We also develop a prototypical implementation freely available for making experiments.

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Modeling Biological Systems in Stochastic Concurrent Constraint Programming

Cited by 51 publications

References 32 publications

(Hybrid) automata and (stochastic) programs * The hybrid automata lattice of a stochastic program

(Hybrid) automata and (stochastic) programs * The hybrid automata lattice of a stochastic program

A Declarative View of Signaling Pathways

Slicing Concurrent Constraint Programs

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