Stochastic Calculus of Looping Sequences for the Modelling and Simulation of Cellular Pathways

Lecture Notes in Computer Science

Drocco

et al. 2011

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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.

Section: Abstract the Stochastic Calculus Of Wrapped Compartments (Smentioning

confidence: 99%

Section: The Stochastic Calculus Of Wrapped Compartmentsmentioning

confidence: 99%

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Modelling Ammonium Transporters in Arbuscular Mycorrhiza Symbiosis

Lecture Notes in Computer Science

Drocco

et al. 2011

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“…To define the "canonical" function that represents the law of mass action the application rate of a reduction rule should depend on the kinetic constant of the reaction and the number of possible reactants in the considered compartment in which the reaction will take place. Following an approach similar to that of [4,18], this can be obtained counting the number of different ways in which the rule representing a reaction can be applied in the considered context producing the same outcome. In our setting, however, we can formalize the canonical function in a simpler way.…”

Section: Definition 43 (Stochastic Reduction)mentioning

confidence: 99%

Stochastic Calculus of Wrapped Compartments

Electron. Proc. Theor. Comput. Sci.

Drocco

et al. 2010

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The Calculus of Wrapped Compartments (CWC) is a variant of the Calculus of Looping Sequences (CLS). While keeping the same expressiveness, CWC strongly simplifies the development of automatic tools for the analysis of biological systems. The main simplification consists in the removal of the sequencing operator, thus lightening the formal treatment of the patterns to be matched in a term (whose complexity in CLS is strongly affected by the variables matching in the sequences). We define a stochastic semantics for this new calculus. As an application we model the interaction between macrophages and apoptotic neutrophils and a mechanism of gene regulation in E.Coli

“…Quantitative simulations of biological models represented with these kinds of frameworks (e.g. [2], [6], [7]) are usually developed via a stochastic method derived by Gillespie's algorithm [8].…”

Section: Introductionmentioning

confidence: 99%

On Designing Multicore-Aware Simulators for Biological Systems

Aldinucci

2011 19th International Euromicro Conference on Parallel, Distributed and Network-Based Processing

et al. 2011

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Abstract-The stochastic simulation of biological systems is an increasingly popular technique in bioinformatics. It often is an enlightening technique, which may however result in being computational expensive. We discuss the main opportunities to speed it up on multi-core platforms, which pose new challenges for parallelisation techniques. These opportunities are developed in two general families of solutions involving both the single simulation and a bulk of independent simulations (either replicas of derived from parameter sweep). Proposed solutions are tested on the parallelisation of the CWC simulator (Calculus of Wrapped Compartments) that is carried out according to proposed solutions by way of the FastFlow programming framework making possible fast development and efficient execution on multi-cores.