395 research outputs found
On Designing Multicore-aware Simulators for Biological Systems
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.Comment: 19 pages + cover pag
A new P-Lingua toolkit for agile development in membrane computing
Membrane computing is a massively parallel and non-deterministic bioinspired computing paradigm whose models are called P systems. Validating and testing such models is a challenge which is being overcome by developing simulators. Regardless of their heterogeneity, such simulators require to read and interpret the models to be simulated. To this end, P-Lingua is a high-level P system definition language which has been widely used in the last decade. The P-Lingua ecosystem includes not only the language, but also libraries and software tools for parsing and simulating membrane computing models. Each version of P-Lingua supported new types or variants of P systems. This leads to a shortcoming: Only a predefined list of variants can be used, thus making it difficult for researchers to study custom ones. Moreover, derivation modes cannot be user-defined, i.e, the way in which P system computations should be generated is determined by the simulation algorithm in the source code.
The main contribution of this paper is a completely new design of the P-Lingua language, called P-Lingua 5, in which the user can define custom variants and derivation modes, among other improvements such as including procedural programming and simulation directives. It is worth mentioning that it has backward-compatibility with previous versions of the language. A completely new set of command-line tools is provided for parsing and simulating P-Lingua 5 files. Finally, several examples are included in this paper covering the most common P system types.Agencia Estatal de Investigación TIN2017-89842-
CHR Grammars
A grammar formalism based upon CHR is proposed analogously to the way
Definite Clause Grammars are defined and implemented on top of Prolog. These
grammars execute as robust bottom-up parsers with an inherent treatment of
ambiguity and a high flexibility to model various linguistic phenomena. The
formalism extends previous logic programming based grammars with a form of
context-sensitive rules and the possibility to include extra-grammatical
hypotheses in both head and body of grammar rules. Among the applications are
straightforward implementations of Assumption Grammars and abduction under
integrity constraints for language analysis. CHR grammars appear as a powerful
tool for specification and implementation of language processors and may be
proposed as a new standard for bottom-up grammars in logic programming.
To appear in Theory and Practice of Logic Programming (TPLP), 2005Comment: 36 pp. To appear in TPLP, 200
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