kPWorkbench: A software suit for membrane systems

YesMembrane computing is a new natural computing paradigm inspired by the functioning and structure of biological cells, and has been successfully applied to many different areas, from biology to engineering. In this paper, we present kPWorkbench, a software framework developed to support membrane computing and its applications. kPWorkbench offers unique features, including modelling, simulation, agent-based high performance simulation and verification, which allow modelling and computational analysis of membrane systems. The kPWorkbench formal verification component provides the opportunity to analyse the behaviour of a model and validate that important system requirements are met and certain behaviours are observed. The platform also features a property language based on natural language statements to facilitate property specification.EPSR

Kernel P Systems - Version 1

A basic P system, called kernel P system4 (kP system for short), combining features of di erent P systems introduced and studied so far is de ned and discussed. The structure of such systems is de ned as a dynamic graph, similar to tissue-like P systems, the objects are organised as multisets, and the rules in each compartment, rewriting and communication together with system structure changing rules, are applied in accordance with a speci c execution strategy. The de nition of kP systems is introduced and some examples illustrate this concept. Two classes of P systems, namely neural-like and generalised communicating P systems are simulated by kP systems. Some case studies prove the expressive power of these systems.Ministerio de Economía y Competitividad TIN2012-37434Junta de Andalucía P08-TIC-0420

3-Col problem modelling using simple kernel P systems

This paper presents the newly introduced class of (simple) kernel P systems ((s)kP systems) and investigates through a 3-colouring problem case study the expressive power and efficiency of kernel P systems. It describes two skP systems that model the problem and analyses them in terms of efficiency and complexity. The skP models prove to be more succinct (in terms of number of rules, objects, number of cells and execution steps) than the corresponding tissue P system, available in the literature, that solves the same problem, at the expense of a greater length of the rules.Ministerio de Ciencia e Innovación TIN2009–13192Junta de Andalucía P08-TIC-0420

Toward full-stack in silico synthetic biology: integrating model specification, simulation, verification, and biological compilation

YesWe present the Infobiotics Workbench (IBW), a user-friendly, scalable, and integrated computational environment for the computer-aided design of synthetic biological systems. It supports an iterative workflow that begins with specification of the desired synthetic system, followed by simulation and verification of the system in high- performance environments and ending with the eventual compilation of the system specification into suitable genetic constructs. IBW integrates modelling, simulation, verification and bicompilation features into a single software suite. This integration is achieved through a new domain-specific biological programming language, the Infobiotics Language (IBL), which tightly combines these different aspects of in silico synthetic biology into a full-stack integrated development environment. Unlike existing synthetic biology modelling or specification languages, IBL uniquely blends modelling, verification and biocompilation statements into a single file. This allows biologists to incorporate design constraints within the specification file rather than using decoupled and independent formalisms for different in silico analyses. This novel approach offers seamless interoperability across different tools as well as compatibility with SBOL and SBML frameworks and removes the burden of doing manual translations for standalone applications. We demonstrate the features, usability, and effectiveness of IBW and IBL using well-established synthetic biological circuits.The work of S.K. is supported by EPSRC (EP/R043787/1). N.K., A.W., and B.B. acknowledge a Royal Academy of Engineering Chair in Emerging Technologies award and an EPSRC programme grant (EP/N031962/1)

Some climate parameters evolution within Danube Delta Biosphere Reserve territory for 1961-2013 period

This study aims to study the climate change knowing the climate parameters as an important step to determine the changes and their meaning. Knowing that the meaning of the changes is valuable information for future actions to adapt to climate change. For a consistent study, ROCADA dataset was used for the evolution of climatic parameters in the Danube Delta Biosphere Reserve territory. This is a set of daily gridded data for the entire Romanian territory, covering data from 1961 to 2013 with values for weather variables. From the mentioned dataset there were extracted information for the Danube Delta Biosphere Reserve and a 20 km buffer zone. From the extracted data, it was taken into account a set of 16 points widely distributed in a manner to cover all the area in order to provide weather information as much as possible close to the reality from the field. Inside the expanded study area there were materialized the selected points (centred cell) in order to be relatively evenly distributed across it’s the entire surface. In the point selection process there were taken into account the S-N and V-E directions. From the data the assessment of rainfall evolution for most points shows very little decrease which can be interpreted as a very slight increase of the dryness for the studied period. This very slight decrease in rainfall is supported by the low or very low negative correlation coefficients along the passing of the years. The area under research shows, in terms of climate, a trend toward aridity

Study of some morphometric aspects of Cama and Dinu islets using remote sensing

Cama and Dinu are two islets on the Danube course near the Giurgiu City. These kinds of islets are on all long stretch of the Romanian Danube. Some of these kinds of islets are younger and some of them are older. Till the year 1960, when the damming action started, the Danube water regime was almost natural. The islets shapes and dimensions have changed due the alteration of the natural regime of the Danube water. The main processes that model the two islets are the alluvial depositing and erosion

The harmoniation of cultural heritage and architectural conseration needs with socio-economic requirements of rural habitat in Danube Delta

The paper present a study of cultural heritage of rural landscape in Danube Delta Biosphere Reserve focuses on cultural landscapes that reflect traditional lifestyle of the locals, activities of deltas’ resource sustainable exploitation, creating visual elements in the rural landscape, especially on traditional buildings, fishermens’ temporary shelters from fishing areas and other traditional activities. In order to highlight the necessity of cultural heritage harmonization and architectural conservation with the socio-economic requirements of rural habitat in Danube Delta were made some field activities through different methods of field investigation, like structured and semistructured interviews, questionnaires, focus groups. In Danube Delta villages, the changes imposed by the touristic function of most of existing or new construction have produced important changes in the architectural landscape of existing settlements impending danger of destroying traditional architectural values which demonstrates on the one hand the personality and inovation spirit of local people in their constructions, particularly in the use of local materials, and on the other hand gives a specific area feature that blends perfectly with the natural landscape. Danube Delta, the space of complex features in terms of cultural values, characterized as open gate of cultural interference, is the area that can provide options to balance cohabitation and cultural heritage

The analyse of the geographical DDBR’s landscape dynamic using Land and Ecosystem Accounting (LEAC) methodology

The paper presents an evaluation of the main indices regarding the functionality of the land use systems and an exposure of Land Ecosystem Accounting methodology developed by the European Agency (EA), starting from the existing Corine land Cover information. The purpose of LEAC analyze is to reflect the changes survenite in the land cover categories in DDBR, having in consideration the forth level of the Work Flow Analyze – functional accounts

kPWorkbench: a software framework for Kernel P systems

NoP systems are the computational models introduced in the context of membrane computing, a computational paradigm within the more general area of unconventional computing. Kernel P (kP) systems are defined to unify the specification of different variants of P systems, motivated by challenging theoretical aspects and the need to model different problems. In this paper, we present kPWorkbench, a software framework developed to support kP systems. kPWorkbench integrates several simulation and verification tools and methods, and provides a software suit for the modelling and analysis of membrane systems

Mathematical model of the Danube Delta Hydrographical Network Morphological Dynamics

This paper presents an innovative technology used to investigate the Danube Delta Biosphere Reserve hydrographical network from the morphologic changes point of view, as result of fluvial processes, erosion and alluvial sedimentation. Field measurements and data processing are performed on water flow, sediment transport andbathymetry. Geospatial databases resulted help for constructing the mathematical /hydraulic model to simulate the hydro-morphological dynamics. There is used as workbench the Delft3D software – a product of DELTARES - Delft Hydraulic Institute, The Netherlands. The model results serve as practical tool for end users to scientifically justify the management decisions made on hydrographic network rehabilitation / reconstruction in order to improve the water flow regime