Causal static analysis for Brane Calculi

We present here a static analysis, based on Abstract Interpretation, obtained by defining an abstract version of the causal semantics for the Mate/Bud/Drip (MBD) version of Brane Calculi, proposed by Busi. Our analysis statically approximates the dynamic behaviour of MBD systems. More precisely, the analysis is able to describe the essential behaviour of the represented membranes, in terms of their possible interactions. Furthermore, our analysis is able to statically capture the possible causal dependencies among interactions, whose determination can be exploited to better understand the modelled biological phenomena. Finally, we apply our analysis to an abstract specification of the receptor-mediated endocytosis mechanism

Toward Accessible Multilevel Modeling in Systems Biology: A Rule-based Language Concept

Promoted by advanced experimental techniques for obtaining high-quality data and the steadily accumulating knowledge about the complexity of life, modeling biological systems at multiple interrelated levels of organization attracts more and more attention recently. Current approaches for modeling multilevel systems typically lack an accessible formal modeling language or have major limitations with respect to expressiveness. The aim of this thesis is to provide a comprehensive discussion on associated problems and needs and to propose a concrete solution addressing them

Studying the effects of adding spatiality to a process algebra model

We use NetLogo to create simulations of two models of disease transmission originally expressed in WSCCS. This allows us to introduce spatiality into the models and explore the consequences of having different contact structures among the agents. In previous work, mean field equations were derived from the WSCCS models, giving a description of the aggregate behaviour of the overall population of agents. These results turned out to differ from results obtained by another team using cellular automata models, which differ from process algebra by being inherently spatial. By using NetLogo we are able to explore whether spatiality, and resulting differences in the contact structures in the two kinds of models, are the reason for this different results. Our tentative conclusions, based at this point on informal observations of simulation results, are that space does indeed make a big difference. If space is ignored and individuals are allowed to mix randomly, then the simulations yield results that closely match the mean field equations, and consequently also match the associated global transmission terms (explained below). At the opposite extreme, if individuals can only contact their immediate neighbours, the simulation results are very different from the mean field equations (and also do not match the global transmission terms). These results are not surprising, and are consistent with other cellular automata-based approaches. We found that it was easy and convenient to implement and simulate the WSCCS models within NetLogo, and we recommend this approach to anyone wishing to explore the effects of introducing spatiality into a process algebra model

Rule-based Methodologies for the Specification and Analysis of Complex Computing Systems

Desde los orígenes del hardware y el software hasta la época actual, la complejidad de los sistemas de cálculo ha supuesto un problema al cual informáticos, ingenieros y programadores han tenido que enfrentarse. Como resultado de este esfuerzo han surgido y madurado importantes áreas de investigación. En esta disertación abordamos algunas de las líneas de investigación actuales relacionada con el análisis y la verificación de sistemas de computación complejos utilizando métodos formales y lenguajes de dominio específico. En esta tesis nos centramos en los sistemas distribuidos, con un especial interés por los sistemas Web y los sistemas biológicos. La primera parte de la tesis está dedicada a aspectos de seguridad y técnicas relacionadas, concretamente la certificación del software. En primer lugar estudiamos sistemas de control de acceso a recursos y proponemos un lenguaje para especificar políticas de control de acceso que están fuertemente asociadas a bases de conocimiento y que proporcionan una descripción sensible a la semántica de los recursos o elementos a los que se accede. También hemos desarrollado un marco novedoso de trabajo para la Code-Carrying Theory, una metodología para la certificación del software cuyo objetivo es asegurar el envío seguro de código en un entorno distribuido. Nuestro marco de trabajo está basado en un sistema de transformación de teorías de reescritura mediante operaciones de plegado/desplegado. La segunda parte de esta tesis se concentra en el análisis y la verificación de sistemas Web y sistemas biológicos. Proponemos un lenguaje para el filtrado de información que permite la recuperación de informaciones en grandes almacenes de datos. Dicho lenguaje utiliza información semántica obtenida a partir de ontologías remotas para re nar el proceso de filtrado. También estudiamos métodos de validación para comprobar la consistencia de contenidos web con respecto a propiedades sintácticas y semánticas. Otra de nuestras contribuciones es la propuesta de un lenguaje que permite definir y comprobar automáticamente restricciones semánticas y sintácticas en el contenido estático de un sistema Web. Finalmente, también consideramos los sistemas biológicos y nos centramos en un formalismo basado en lógica de reescritura para el modelado y el análisis de aspectos cuantitativos de los procesos biológicos. Para evaluar la efectividad de todas las metodologías propuestas, hemos prestado especial atención al desarrollo de prototipos que se han implementado utilizando lenguajes basados en reglas.Baggi ., M. (2010). Rule-based Methodologies for the Specification and Analysis of Complex Computing Systems [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/8964Palanci

Reversible Computation: Extending Horizons of Computing

This open access State-of-the-Art Survey presents the main recent scientific outcomes in the area of reversible computation, focusing on those that have emerged during COST Action IC1405 "Reversible Computation - Extending Horizons of Computing", a European research network that operated from May 2015 to April 2019. Reversible computation is a new paradigm that extends the traditional forwards-only mode of computation with the ability to execute in reverse, so that computation can run backwards as easily and naturally as forwards. It aims to deliver novel computing devices and software, and to enhance existing systems by equipping them with reversibility. There are many potential applications of reversible computation, including languages and software tools for reliable and recovery-oriented distributed systems and revolutionary reversible logic gates and circuits, but they can only be realized and have lasting effect if conceptual and firm theoretical foundations are established first