Type Disciplines for Analysing Biologically Relevant Properties

Aman, Bogdan; Dezani‐Ciancaglini, Mariangiola; Troina, Angelo

doi:10.1016/j.entcs.2008.12.106

Cited by 13 publications

(12 citation statements)

References 12 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Vice versa simulations could be the base for new hypotheses and experiments. As a future extension of the modelling technique, we plan to follow the direction taken in [14,5] for SCLS and to define a type systems to guarantee that an SCWC term satisfies certain biological properties (enforced by a set of typing rules), and also investigate how type systems could enrich the study of quantitative systems.…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Modelling Ammonium Transporters in Arbuscular Mycorrhiza Symbiosis

Coppo

Damiani

Drocco

et al. 2011

Lecture Notes in Computer Science

Self Cite

View full text Add to dashboard Cite

Abstract. The Stochastic Calculus of Wrapped Compartments (SCWC)is a recently proposed variant of the Stochastic Calculus of Looping Sequences (SCLS), a language for the representation and simulation of biological systems. In this work we apply SCWC to model a newly discovered ammonium transporter. This transporter is believed to play a fundamental role for plant mineral acquisition, which takes place in the arbuscular mycorrhiza, the most wide-spread plant-fungus symbiosis on earth. Investigating this kind of symbiosis is considered one of the most promising ways to develop methods to nurture plants in more natural manners, avoiding the complex chemical productions used nowadays to produce artificial fertilizers. In our experiments the passage of N H3 / N H + 4 from the fungus to the plant has been dissected in known and hypothetical mechanisms; with the model so far we have been able to simulate the behavior of the system under different conditions. Our simulations confirmed some of the latest experimental results about the LjAMT2;2 transporter. Moreover, by comparing the behaviour of LjAMT2;2 with the behaviour of another ammonium transporter which exists in plants, viz. LjAMT1;1, our simulations support an hypothesis about why LjAMT2;2 is so selectively expressed in arbusculated cells.

show abstract

Section: Discussionmentioning

confidence: 99%

“…We refer to [12] for more details and explanation. 5 In particular, the function O is analogous to the one defined for SCLS in [7].…”

Section: The Stochastic Calculus Of Wrapped Compartmentsmentioning

confidence: 99%

Modelling Ammonium Transporters in Arbuscular Mycorrhiza Symbiosis

Coppo

Damiani

Drocco

et al. 2011

Lecture Notes in Computer Science

Self Cite

View full text Add to dashboard Cite

show abstract

“…The Calculus of Looping Sequences has been extended with type systems in [6,31,32,8,16]. As an application to ecology, stochastic CLS (see [7]) is used in [12] to model population dynamics.…”

Section: Related Workmentioning

confidence: 99%

“…The linearity condition, in biological terms, corresponds to excluding that a transformation can depend on the presence of two (or more) identical (and generic) components in different compartments (see also[52]). 6 The implicit (distinguished) variable X matches with all the remaining part of the compartment content.…”

mentioning

confidence: 99%

Modelling Ecological Systems with the Calculus of Wrapped Compartments

Ramón

Troina

2013

Membrane Computing

Self Cite

View full text Add to dashboard Cite

Abstract. The Calculus of Wrapped Compartments is a framework based on stochastic multiset rewriting in a compartmentalised setting originally developed for the modelling and analysis of biological interactions. In this paper, we propose to use this calculus for the description of ecological systems and we provide the modelling guidelines to encode within the calculus some of the main interactions leading ecosystems evolution. As a case study, we model the distribution of height of Croton wagneri, a shrub constituting the endemic predominant species of the dry ecosystem in southern Ecuador. In particular, we consider the plant at different altitude gradients (i.e. at different temperature conditions), to study how it adapts under the effects of global climate change.

show abstract

“…The model has been extended with several features such as bisimulations [4,7], combining the simplicity of notation of rewrite systems with the advantage of a form of compositionality. In [1,2] a type system was defined to ensure the well-formedness of links between protein sites within the Linked Calculus of Looping Sequences (see [3]). In [13] we defined a type system to guarantee the soundness of reduction rules with respect to the requirement of certain elements, and the repellency of others.…”

Section: Introductionmentioning

confidence: 99%

A Calculus of Looping Sequences with Local Rules

Bioglio

Dezani‐Ciancaglini

Giannini

et al. 2012

Electron. Proc. Theor. Comput. Sci.

Self Cite

View full text Add to dashboard Cite

In this paper we present a variant of the Calculus of Looping Sequences (CLS for short) with global and local rewrite rules. While global rules, as in CLS, are applied anywhere in a given term, local rules can only be applied in the compartment on which they are defined. Local rules are dynamic: they can be added, moved and erased. We enrich the new calculus with a parallel semantics where a reduction step is lead by any number of global and local rules that could be performed in parallel. A type system is developed to enforce the property that a compartment must contain only local rules with specific features. As a running example we model some interactions happening in a cell starting from its nucleus and moving towards its mitochondria.

show abstract

Type Disciplines for Analysing Biologically Relevant Properties

Abstract: The calculus of looping sequences is a formalism for describing evolution of biological systems by means of term rewriting rules. We propose to enrich this calculus with type disciplines to guarantee the soundness of reduction rules with respect to interesting biological properties.

Cited by 13 publications

References 12 publications

Modelling Ammonium Transporters in Arbuscular Mycorrhiza Symbiosis

Modelling Ammonium Transporters in Arbuscular Mycorrhiza Symbiosis

Modelling Ecological Systems with the Calculus of Wrapped Compartments

A Calculus of Looping Sequences with Local Rules

Contact Info

Product

Resources

About