πBUSS:a parallel BEAST/BEAGLE utility for sequence simulation under complex evolutionary scenarios

Background: Simulated nucleotide or amino acid sequences are frequently used to assess the performance of phylogenetic reconstruction methods. BEAST, a Bayesian statistical framework that focuses on reconstructing time-calibrated molecular evolutionary processes, supports a wide array of evolutionary models, but lacked matching machinery for simulation of character evolution along phylogenies. Results: We present a flexible Monte Carlo simulation tool, called piBUSS, that employs the BEAGLE high performance library for phylogenetic computations within BEAST to rapidly generate large sequence alignments under complex evolutionary models. piBUSS sports a user-friendly graphical user interface (GUI) that allows combining a rich array of models across an arbitrary number of partitions. A command-line interface mirrors the options available through the GUI and facilitates scripting in large-scale simulation studies. Analogous to BEAST model and analysis setup, more advanced simulation options are supported through an extensible markup language (XML) specification, which in addition to generating sequence output, also allows users to combine simulation and analysis in a single BEAST run. Conclusions: piBUSS offers a unique combination of flexibility and ease-of-use for sequence simulation under realistic evolutionary scenarios. Through different interfaces, piBUSS supports simulation studies ranging from modest endeavors for illustrative purposes to complex and large-scale assessments of evolutionary inference procedures. The software aims at implementing new models and data types that are continuously being developed as part of BEAST/BEAGLE.Comment: 13 pages, 2 figures, 1 tabl

The Impact of the User Interface on Simulation Usability and Solution Quality

This research outlines a study that was performed to determine the effects of user interface design variations on the usability and solution quality of complex, multivariate discrete-event simulations. Specifically, this study examined four key research questions: what are the user interface considerations for a given simulation model, what are the current best practices in user interface design for simulations, how is usability best evaluated for simulation interfaces, and specifically what are the measured effects of varying levels of usability of interface elements on simulation operations such as data entry and solution analysis. The overall goal of the study was to show the benefit of applied usability practices in simulation design, supported by experimental evidence from testing two alternative simulation user interfaces designed with varying usability. The study employed directed research in usability and simulation design to support design of an experiment that addressed the core problem of interface effects on simulation. In keeping with the study goal of demonstrating usability practices, the experimental procedures were analogous to the development processes recommended in supporting literature for usability-based design lifecycles. Steps included user and task analysis, concept and use modeling, paper prototypes of user interfaces for initial usability assessment, interface development and assessment, and user-based testing of actual interfaces with an actual simulation model. The experimental tests employed two interfaces designed with selected usability variations, each interacting with the same core simulation model. The experimental steps were followed by an analysis of quantitative and qualitative data gathered, including data entry time, interaction errors, solution quality measures, and user acceptance data. The study resulted in mixed support for the hypotheses that improvements in usability of simulation interface elements will improve data entry, solution quality, and overall simulation interactions. Evidence for data entry was mixed, for solution quality was positive to neutral, and for overall usability was very positive. As a secondary benefit, the study demonstrated application of usability-based interface design best practices and processes that could provide guidelines for increasing usability of future discrete-event simulation interface designs. Examination of the study results also provided suggestions for possible future research on the investigation topics

Calibrated 3D Computational Modeling of Soil-Structure Systems and Liquefaction Scenarios

Three-dimensional (3D) computational simulation is increasingly allowing for insights into the mechanics of seismic soil-structure system response. Calibration is being facilitated by field, full-scale, and centrifuge model laboratory data. Computational algorithms and scenario-specific graphical user-interfaces are gradually permitting the routine adoption of such geometrically realistic simulation environments. This paper presents an overview of salient recent 3D soil-foundation-structure earthquake response simulations. Developments related to graphical user-interfaces (OpenSeesPL, http://cyclic.ucsd.edu/openseespl) are summarized, demonstrating the current and evolving capabilities towards performance-based earthquake engineering (PBEE). From an OpenSeesPL-generated lateral push-over analysis of a large pile-group, it is shown that corner piles may shoulder a significantly higher level of load (axial, shear, and bending). Evolution of large tensile forces in these piles may warrant careful consideration. Modeling of liquefaction response mechanisms are also discussed, highlighting the role of cyclic mobility and influence of permeability in dictating the level of associated ground shear deformations, and related countermeasure performance

An integrated urban systems model with GIS

The purpose of the research is to develop an integrated urban systems model, which will assist in formulating a better land use-transportation policy by simulating the relationships between land use patterns and travel behavior, integrated with geographic information systems (GISs). In order to make an integrated land use-transportation model possible with the assistance of GISs technologies, the following four sub-systems have been developed: (1) an effective traffic analysis zone generation system; (2) an iterative land use and transportation modeling system; (3) efficient interfaces between GIS and land use, and GIS and transportation models; and (4) a user-friendly graphic user interface (GUI) system. By integrating these sub-systems, a variety of alternative land use-transportation policies can be evaluated through the modification of input parameters in each simulation. Eventually, the developed model using a GIS will assist in formulating an effective land use policy by obtaining robust simulation results for both land use-transportation planners and decision makers. The model has been applied to the Urbana-Champaign area as well as to the Seoul region in Korea for a demonstration of the workings of the model.

Efficient utilization of graphics technology for space animation

Efficient utilization of computer graphics technology has become a major investment in the work of aerospace engineers and mission designers. These new tools are having a significant impact in the development and analysis of complex tasks and procedures which must be prepared prior to actual space flight. Design and implementation of useful methods in applying these tools has evolved into a complex interaction of hardware, software, network, video and various user interfaces. Because few people can understand every aspect of this broad mix of technology, many specialists are required to build, train, maintain and adapt these tools to changing user needs. Researchers have set out to create systems where an engineering designer can easily work to achieve goals with a minimum of technological distraction. This was accomplished with high-performance flight simulation visual systems and supercomputer computational horsepower. Control throughout the creative process is judiciously applied while maintaining generality and ease of use to accommodate a wide variety of engineering needs

Decision support system for the long-term city metabolism planning problem

A Decision Support System (DSS) tool for the assessment of intervention strategies (Alternatives) in an Urban Water System (UWS) with an integral simulation model called “WaterMet²” is presented. The DSS permits the user to identify one or more optimal Alternatives over a fixed long-term planning horizon using performance metrics mapped to the TRUST sustainability criteria (Alegre et al., 2012). The DSS exposes lists of in-built intervention options and system performance metrics for the user to compose new Alternatives. The quantitative metrics are calculated by the WaterMet² model and further qualitative or user-defined metrics may be specified by the user or by external tools feeding into the DSS. A Multi-Criteria Decision Analysis (MCDA) approach is employed within the DSS to compare the defined Alternatives and to rank them with respect to a pre-specified weighting scheme for different Scenarios. Two rich, interactive Graphical User Interfaces, one desktop and one web-based, are employed to assist with guiding the end user through the stages of defining the problem, evaluating and ranking Alternatives. This mechanism provides a useful tool for decision makers to compare different strategies for the planning of UWS with respect to multiple Scenarios. The efficacy of the DSS is demonstrated on a northern European case study inspired by a real-life urban water system for a mixture of quantitative and qualitative criteria. The results demonstrate how the DSS, integrated with an UWS modelling approach, can be used to assist planners in meeting their long-term, strategic level sustainability objectives

Decision support system for surface irrigation design

The SADREG decision support system was developed to help decision makers in the process of design and selection of farm surface irrigation systems to respond to requirements of modernization of surface irrigation—furrow, basin, and border irrigation. It includes a database, simulation models, user-friendly interfaces, and multicriteria analysis models. SADREG is comprised of two components: design and selection. The first component applies database information, and through several simulation and computational tools, produces a set of design alternatives in agreement with the user options. These alternatives are characterized by several hydraulic, economic, and environmental indicators that allow appropriate selection and ranking. The selection component bases upon multicriteria analysis using composite programming and ELECTRE II ranking models, which support the decision maker to select the best alternative. The decision maker participates in all decision processes through a user-friendly interface that allows expressing design options and priorities. SADREG was tested with data collected from field experiments. In addition to describing the modeling approach, an application to a sector of the Lower Mondego Irrigation Project, Portugal, is presente

Human motion analysis and simulation tools: a survey

Computational systems to identify objects represented in image sequences and tracking their motion in a fully automatic manner, enabling a detailed analysis of the involved motion and its simulation are extremely relevant in several fields of our society. In particular, the analysis and simulation of the human motion has a wide spectrum of relevant applications with a manifest social and economic impact. In fact, usage of human motion data is fundamental in a broad number of domains (e.g.: sports, rehabilitation, robotics, surveillance, gesture-based user interfaces, etc.). Consequently, many relevant engineering software applications have been developed with the purpose of analyzing and/or simulating the human motion. This chapter presents a detailed, broad and up to date survey on motion simulation and/or analysis software packages that have been developed either by the scientific community or commercial entities. Moreover, a main contribution of this chapter is an effective framework to classify and compare motion simulation and analysis tools

Simulation of vacuum membrane distillation process for desalination with Aspen Plus

YesThis paper presents a simulation study of vacuum membrane distillation (VMD) for desalination. A simulation model was built on Aspen Plus® platform as user defined unit operation for VMD module. A simplified mathematical model was verified and the analysis of process performance based on simulation was also carried out. Temperature and concentration polarization effects are significant in the conditions of higher feed temperature and/or vacuum pressure. The sign of difference of the vapour pressures between at the membrane interfaces, is a pointer of the vacuum pressure threshold. Increasing the vacuum pressure at lower feed temperature is an effective way to increase the permeate flux and reduce the energy consumption simultaneously

A co-simulation approach using powerfactory and matlab/simulink to enable validation of distributed control concepts within future power systems

In power network analysis it is increasingly desirable to implement controller and power systems models within different software environments. This stems from, among other things, an increasing influence of new and distrib-uted control functions within smart grids and a growing influence of market operations. The computation time re-sulting from use of multiple simulation environments can cause significant delays and constrain the number of scenarios considered. This paper introduces and com-pares several techniques for integrating external control system models into power systems models for time do-main simulations. In particular, a new technique is reported in this paper for PowerFactory-MATLAB/Simulink co-simulation interfaces, which offers a significant advantage over alternative methods in terms of the reduction in simulation runtimes and flexi-bility for the end user