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Geovisualization of dynamics, movement and change: key issues and developing approaches in visualization research
GUBS, a Behavior-based Language for Open System Dedicated to Synthetic Biology
In this article, we propose a domain specific language, GUBS (Genomic Unified
Behavior Specification), dedicated to the behavioral specification of synthetic
biological devices, viewed as discrete open dynamical systems. GUBS is a
rule-based declarative language. By contrast to a closed system, a program is
always a partial description of the behavior of the system. The semantics of
the language accounts the existence of some hidden non-specified actions
possibly altering the behavior of the programmed device. The compilation
framework follows a scheme similar to automatic theorem proving, aiming at
improving synthetic biological design safety.Comment: In Proceedings MeCBIC 2012, arXiv:1211.347
Approaches for advancing scientific understanding of macrosystems
The emergence of macrosystems ecology (MSE), which focuses on regional- to continental-scale ecological patterns and processes, builds upon a history of long-term and broad-scale studies in ecology. Scientists face the difficulty of integrating the many elements that make up macrosystems, which consist of hierarchical processes at interacting spatial and temporal scales. Researchers must also identify the most relevant scales and variables to be considered, the required data resources, and the appropriate study design to provide the proper inferences. The large volumes of multi-thematic data often associated with macrosystem studies typically require validation, standardization, and assimilation. Finally, analytical approaches need to describe how cross-scale and hierarchical dynamics and interactions relate to macroscale phenomena. Here, we elaborate on some key methodological challenges of MSE research and discuss existing and novel approaches to meet them
The physics of spreading processes in multilayer networks
The study of networks plays a crucial role in investigating the structure,
dynamics, and function of a wide variety of complex systems in myriad
disciplines. Despite the success of traditional network analysis, standard
networks provide a limited representation of complex systems, which often
include different types of relationships (i.e., "multiplexity") among their
constituent components and/or multiple interacting subsystems. Such structural
complexity has a significant effect on both dynamics and function. Throwing
away or aggregating available structural information can generate misleading
results and be a major obstacle towards attempts to understand complex systems.
The recent "multilayer" approach for modeling networked systems explicitly
allows the incorporation of multiplexity and other features of realistic
systems. On one hand, it allows one to couple different structural
relationships by encoding them in a convenient mathematical object. On the
other hand, it also allows one to couple different dynamical processes on top
of such interconnected structures. The resulting framework plays a crucial role
in helping achieve a thorough, accurate understanding of complex systems. The
study of multilayer networks has also revealed new physical phenomena that
remain hidden when using ordinary graphs, the traditional network
representation. Here we survey progress towards attaining a deeper
understanding of spreading processes on multilayer networks, and we highlight
some of the physical phenomena related to spreading processes that emerge from
multilayer structure.Comment: 25 pages, 4 figure
Principles and Concepts of Agent-Based Modelling for Developing Geospatial Simulations
The aim of this paper is to outline fundamental concepts and principles of the Agent-Based Modelling (ABM) paradigm, with particular reference to the development of geospatial simulations. The paper begins with a brief definition of modelling, followed by a classification of model types, and a comment regarding a shift (in certain circumstances) towards modelling systems at the individual-level. In particular, automata approaches (e.g. Cellular Automata, CA, and ABM) have been particularly popular, with ABM moving to the fore. A definition of agents and agent-based models is given; identifying their advantages and disadvantages, especially in relation to geospatial modelling. The potential use of agent-based models is discussed, and how-to instructions for developing an agent-based model are provided. Types of simulation / modelling systems available for ABM are defined, supplemented with criteria to consider before choosing a particular system for a modelling endeavour. Information pertaining to a selection of simulation / modelling systems (Swarm, MASON, Repast, StarLogo, NetLogo, OBEUS, AgentSheets and AnyLogic) is provided, categorised by their licensing policy (open source, shareware / freeware and proprietary systems). The evaluation (i.e. verification, calibration, validation and analysis) of agent-based models and their output is examined, and noteworthy applications are discussed.Geographical Information Systems (GIS) are a particularly useful medium for representing model input and output of a geospatial nature. However, GIS are not well suited to dynamic modelling (e.g. ABM). In particular, problems of representing time and change within GIS are highlighted. Consequently, this paper explores the opportunity of linking (through coupling or integration / embedding) a GIS with a simulation / modelling system purposely built, and therefore better suited to supporting the requirements of ABM. This paper concludes with a synthesis of the discussion that has proceeded. The aim of this paper is to outline fundamental concepts and principles of the Agent-Based Modelling (ABM) paradigm, with particular reference to the development of geospatial simulations. The paper begins with a brief definition of modelling, followed by a classification of model types, and a comment regarding a shift (in certain circumstances) towards modelling systems at the individual-level. In particular, automata approaches (e.g. Cellular Automata, CA, and ABM) have been particularly popular, with ABM moving to the fore. A definition of agents and agent-based models is given; identifying their advantages and disadvantages, especially in relation to geospatial modelling. The potential use of agent-based models is discussed, and how-to instructions for developing an agent-based model are provided. Types of simulation / modelling systems available for ABM are defined, supplemented with criteria to consider before choosing a particular system for a modelling endeavour. Information pertaining to a selection of simulation / modelling systems (Swarm, MASON, Repast, StarLogo, NetLogo, OBEUS, AgentSheets and AnyLogic) is provided, categorised by their licensing policy (open source, shareware / freeware and proprietary systems). The evaluation (i.e. verification, calibration, validation and analysis) of agent-based models and their output is examined, and noteworthy applications are discussed.Geographical Information Systems (GIS) are a particularly useful medium for representing model input and output of a geospatial nature. However, GIS are not well suited to dynamic modelling (e.g. ABM). In particular, problems of representing time and change within GIS are highlighted. Consequently, this paper explores the opportunity of linking (through coupling or integration / embedding) a GIS with a simulation / modelling system purposely built, and therefore better suited to supporting the requirements of ABM. This paper concludes with a synthesis of the discussion that has proceeded
Gemini Spectroscopic Survey of Young Star Clusters in Merging/Interacting Galaxies. IV. Stephan's Quintet
We present a spectroscopic survey of 21 young massive clusters and complexes
and one tidal dwarf galaxy candidate (TDG) in Stephan's Quintet, an interacting
compact group of galaxies. All of the selected targets lie outside the main
galaxies of the system and are associated with tidal debris. We find clusters
with ages between a few and 125 Myr and confirm the ages estimated through HST
photometry by Fedotov et al. (2011), as well as their modelled interaction
history of the Quintet. Many of the clusters are found to be relatively
long-lived, given their spectrosopically derived ages, while their high masses
suggest that they will likely evolve to eventually become intergalactic
clusters. One cluster, T118, is particularly interesting, given its age (\sim
125 Myr), high mass (\sim 2\times10^6 M\odot) and position in the extreme outer
end of the young tidal tail. This cluster appears to be quite extended (Reff
\sim 12 - 15 pc) compared to clusters observed in galaxy disks (Reff \sim 3 - 4
pc), which confirms an effect we previously found in the tidal tails of NGC
3256, where clusters are similarly extended. We find that star and cluster
formation can proceed at a continuous pace for at least \sim 150 Myr within the
tidal debris of interacting galaxies. The spectrum of the TDG candidate is
dominated by a young population (\sim 7 Myr), and assuming a single age for the
entire region, has a mass of at least 10^6 M\odot.Comment: 37 pages, 10 Figures, 7 Tabl
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