The JWS online simulation database

Summary: JWS Online is a web-based platform for construction, simulation and exchange of models in standard formats. We have extended the platform with a database for curated simulation experiments that can be accessed directly via a URL, allowing one-click reproduction of published results. Users can modify the simulation experiments and export them in standard formats. The Simulation database thus lowers the bar on exploring computational models, helps users create valid simulation descriptions and improves the reproducibility of published simulation experiments. Availability and Implementation: The Simulation Database is available on line at https://jjj.bio.vu. nl/models/experiments/

A Web-based Repository of Reproducible Simulation Experiments for Systems Biology.

Systems Biology requires increasingly complex simulation models. Effectively interpreting and building upon previous simulation results is both difficult and time consuming. Thus, simulation results often cannot be reproduced exactly; making it difficult for other modellers to validate results and take the next step in a simulation study. The Simulation Experiment Description Mark-up Language~(SED-ML), a subset of the Minimum Information About a Simulation Experiment~(MIASE) guidelines, promises to solve this problem by prescribing the form and content of the information required to reproduce simulation experiments. SED-ML is detailed enough to enable automatic rerunning of simulation experiments. Here, we present a web-based simulation-experiment repository that lets modellers develop SED-ML compliant simulation-experiment descriptions The system encourages modellers to annotate their experiments with text and images, experimental data and domain meta-information. These informal annotations aid organisation and classification of the simulations and provide rich search criteria. They complement SED-ML's formal precision to produce simulation-experiment descriptions that can be understood by both men and machines. The system combines both human-readable and formal machine-readable content, thus ensuring exact reproducibility of the simulation results of a modelling study. </p

A Semantic Grid Service for Experimentation with an Agent-Based Model of Land-Use Change

Agent-based models, perhaps more than other models, feature large numbers of parameters and potentially generate vast quantities of results data. This paper shows through the FEARLUS-G project (an ESRC e-Social Science Initiative Pilot Demonstrator Project) how deploying an agent-based model on the Semantic Grid facilitates international collaboration on investigations using such a model, and contributes to establishing rigorous working practices with agent-based models as part of good science in social simulation. The experimental workflow is described explicitly using an ontology, and a Semantic Grid service with a web interface implements the workflow. Users are able to compare their parameter settings and results, and relate their work with the model to wider scientific debate.Agent-Based Social Simulation, Experiments, Ontologies, Replication, Semantic Grid

A Reliable and Cost-Efficient Auto-Scaling System for Web Applications Using Heterogeneous Spot Instances

Cloud providers sell their idle capacity on markets through an auction-like mechanism to increase their return on investment. The instances sold in this way are called spot instances. In spite that spot instances are usually 90% cheaper than on-demand instances, they can be terminated by provider when their bidding prices are lower than market prices. Thus, they are largely used to provision fault-tolerant applications only. In this paper, we explore how to utilize spot instances to provision web applications, which are usually considered availability-critical. The idea is to take advantage of differences in price among various types of spot instances to reach both high availability and significant cost saving. We first propose a fault-tolerant model for web applications provisioned by spot instances. Based on that, we devise novel auto-scaling polices for hourly billed cloud markets. We implemented the proposed model and policies both on a simulation testbed for repeatable validation and Amazon EC2. The experiments on the simulation testbed and the real platform against the benchmarks show that the proposed approach can greatly reduce resource cost and still achieve satisfactory Quality of Service (QoS) in terms of response time and availability

A proposal for the evaluation of adaptive information retrieval systems using simulated interaction

The Centre for Next Generation Localisation (CNGL) is involved in building interactive adaptive systems which combine Information Retrieval (IR), Adaptive Hypermedia (AH) and adaptive web techniques and technologies. The complex functionality of these systems coupled with the variety of potential users means that the experiments necessary to evaluate such systems are difficult to plan, implement and execute. This evaluation requires both component-level scientific evaluation and user-based evaluation. Automated replication of experiments and simulation of user interaction would be hugely beneficial in the evaluation of adaptive information retrieval systems (AIRS). This paper proposes a methodology for the evaluation of AIRS which leverages simulated interaction. The hybrid approach detailed combines: (i) user-centred methods for simulating interaction and personalisation; (ii) evaluation metrics that combine Human Computer Interaction (HCI), AH and IR techniques; and (iii) the use of qualitative and quantitative evaluations. The benefits and limitations of evaluations based on user simulations are also discussed

The Resistance of Ship Web Girders in Collision and Grounding

Ship web girders play an important role in ship structure performance during collision and grounding accidents. The behavior of web girders subjected to in-plane concentrated load is investigated by numerical simulation and theoretical analysis in this paper. A numerical simulation based on previous experiment is conducted to give insight to the deformation mechanism of crushing web girders. Some new important deformation characteristics are observed through the simulation results. A new theoretical deformation model is proposed featured with these deformation characteristics, and a simplified analytical method for predicting the instantaneous and mean resistances of crushing web girders is proposed. The proposed method is verified by two previous experiments and a series of numerical simulations. The agreement between the solutions by the proposed method and the experiment results is good. The comparison results between the proposed analytical method and numerical simulation results are satisfactory for most cases. The proposed analytical method will contribute to the establishment of an efficient method for fast and reliable assessment of the outcome of ship accidental collisions and grounding events

A Web-Based High Performance Simulation System for Transport and Retention of Dissolved Contaminants in Soils

Groundwater, the major source of human drinking water, is susceptible to contamination from industrial and agricultural activities. This research develops a web-based simulation system of remote high performance computing model for contaminant transport and retention in soils. A three-dimensional advection-dispersion-reaction MRTM model, based on previous experimental and theoretical studies, is proposed to analyze the transport and retention of chemical contaminants in groundwater flowing through soils. Since three-dimensional experiments are difficult to implement and verify, this simulation system provides scientists an alternative to trace the contaminant movement in soils outside laboratories. The alternating direction implicit (ADI) algorithm is used in this study to reduce the computational complexity. Although the ADI method is very efficient to solve the governing advection-dispersionsorption equations in the three-dimensional MRTM model, achieving higher order accuracy with different boundary conditions remains a difficult research topic. This research develops a new numerical scheme to achieve second-order accuracy with the Neumann-type boundary conditions. Furthermore, parallel computing is used to achieve high performance using powerful multiprocessor computers. A web-based simulation system provides users a friendly interface for remote access to the system through Internet browsers, so as to utilize remote computing resources transparently and efficiently. In the client-side computing one-dimensional MRTM simulation system, the legacy code written in FORTRAN and C are wrapped and reused with Java code, which provides the web-based graphic user interface (GUI). The server-side computing three-dimensional MRTM simulation system integrates the remote high performance computing resources, database management systems, online visualization functionality, and web-based userriendly GUIs. Given access to the Internet, users can execute and manage remote high performance computing jobs anywhere anytime, even through a web browser from a laptop personal computer

Simulation and Visualization Enhanced Engineering Education- Development and Implementation of Virtual Experiments in a Laboratory Course

This paper presents results from a National Science Foundation grant titled Simulation and Visualization Enhanced Engineering Education , funded by the EEC division. Although the scope of the project is quite broad, embracing a wide range of courses in three engineering disciplines, the present work describes the results obtained from application of simulation and visualization for development and implementation of web-based virtual engineering laboratories. The present work leverages the advancement in hardware and software technologies to map physical experiments into web-based virtual experiments that can be used to enrich student\u27s laboratory experience. Four physical experiments in the thermo-fluids laboratory course have been mapped into virtual experiments, and the newly created virtual experiments have been used by students to conduct pre-lab practice sessions prior to performing corresponding physical experiment sessions. By performing virtual experiments, students learn in more detail about the objectives, procedure and expected outcomes ahead of scheduled physical experiments. Use of virtual experiments in the supplementation mode makes students better learners, and the assessment results show that students are better prepared and get more out of physical laboratory sessions. To test the efficacy of the proposed pre-lab practice session pedagogy, assessment instruments and statistical experimental designs have been developed and implemented to objectively determine whether implemented virtual experiments, used in supplementation mode, enhance student learning compared to the pre-implementation setting (without virtual experiments) and to test if the learning gains are statistically significant or not. The pedagogy of supplementation of physical experiments with pre-lab practice sessions with virtual experiments shows promise, based on results obtained in this project. Impact of various demographic factors such as gender, age, ethnicity, student level etc. on student learning was also analyzed