Tools of the Trade: A Survey of Various Agent Based Modeling Platforms

Agent Based Modeling (ABM) toolkits are as diverse as the community of people who use them. With so many toolkits available, the choice of which one is best suited for a project is left to word of mouth, past experiences in using particular toolkits and toolkit publicity. This is especially troublesome for projects that require specialization. Rather than using toolkits that are the most publicized but are designed for general projects, using this paper, one will be able to choose a toolkit that already exists and that may be built especially for one's particular domain and specialized needs. In this paper, we examine the entire continuum of agent based toolkits. We characterize each based on 5 important characteristics users consider when choosing a toolkit, and then we categorize the characteristics into user-friendly taxonomies that aid in rapid indexing and easy reference.Agent Based Modeling, Individual Based Model, Multi Agent Systems

ImageJ2: ImageJ for the next generation of scientific image data

ImageJ is an image analysis program extensively used in the biological sciences and beyond. Due to its ease of use, recordable macro language, and extensible plug-in architecture, ImageJ enjoys contributions from non-programmers, amateur programmers, and professional developers alike. Enabling such a diversity of contributors has resulted in a large community that spans the biological and physical sciences. However, a rapidly growing user base, diverging plugin suites, and technical limitations have revealed a clear need for a concerted software engineering effort to support emerging imaging paradigms, to ensure the software's ability to handle the requirements of modern science. Due to these new and emerging challenges in scientific imaging, ImageJ is at a critical development crossroads. We present ImageJ2, a total redesign of ImageJ offering a host of new functionality. It separates concerns, fully decoupling the data model from the user interface. It emphasizes integration with external applications to maximize interoperability. Its robust new plugin framework allows everything from image formats, to scripting languages, to visualization to be extended by the community. The redesigned data model supports arbitrarily large, N-dimensional datasets, which are increasingly common in modern image acquisition. Despite the scope of these changes, backwards compatibility is maintained such that this new functionality can be seamlessly integrated with the classic ImageJ interface, allowing users and developers to migrate to these new methods at their own pace. ImageJ2 provides a framework engineered for flexibility, intended to support these requirements as well as accommodate future needs

Overview of modern teaching equipment that supports distant learning

Laboratory is a key element of engineering and applied sciences educational systems. With the development of Internet and connecting IT technologies, the appearance of remote laboratories was inevitable. Virtual laboratories are also available; they place the experiment in a simulated environment. However, this writing focuses on remote experiments not virtual ones. From the students’ point of view, it is a great help not only for those enrolling in distant or online courses but also for those studying in a more traditional way. With the spread of smart, portable devices capable of connection to the internet, students can expand or restructure time spent on studying. This is a huge help to them and also allows them to individually divide their time up, to learn how to self-study. This independent approach can prepare them for working environments. It offers flexibility and convenience to the students. From the universities’ point of view, it helps reduce maintenance costs and universities can share experiments which also helps the not so well-resourced educational facilities

Updates in metabolomics tools and resources: 2014-2015

Data processing and interpretation represent the most challenging and time-consuming steps in high-throughput metabolomic experiments, regardless of the analytical platforms (MS or NMR spectroscopy based) used for data acquisition. Improved machinery in metabolomics generates increasingly complex datasets that create the need for more and better processing and analysis software and in silico approaches to understand the resulting data. However, a comprehensive source of information describing the utility of the most recently developed and released metabolomics resources—in the form of tools, software, and databases—is currently lacking. Thus, here we provide an overview of freely-available, and open-source, tools, algorithms, and frameworks to make both upcoming and established metabolomics researchers aware of the recent developments in an attempt to advance and facilitate data processing workflows in their metabolomics research. The major topics include tools and researches for data processing, data annotation, and data visualization in MS and NMR-based metabolomics. Most in this review described tools are dedicated to untargeted metabolomics workflows; however, some more specialist tools are described as well. All tools and resources described including their analytical and computational platform dependencies are summarized in an overview Table

Global Grids and Software Toolkits: A Study of Four Grid Middleware Technologies

Grid is an infrastructure that involves the integrated and collaborative use of computers, networks, databases and scientific instruments owned and managed by multiple organizations. Grid applications often involve large amounts of data and/or computing resources that require secure resource sharing across organizational boundaries. This makes Grid application management and deployment a complex undertaking. Grid middlewares provide users with seamless computing ability and uniform access to resources in the heterogeneous Grid environment. Several software toolkits and systems have been developed, most of which are results of academic research projects, all over the world. This chapter will focus on four of these middlewares--UNICORE, Globus, Legion and Gridbus. It also presents our implementation of a resource broker for UNICORE as this functionality was not supported in it. A comparison of these systems on the basis of the architecture, implementation model and several other features is included.Comment: 19 pages, 10 figure

A Mobile ECG Monitoring System with Context Collection

An objective of a health process is one where patients can stay healthy with the support of expert medical advice when they need it, at any location and any time. An associated aim would be the development of a system which places increased emphasis on preventative measures as a first point of contact with the patient. This research is a step along the road towards this type of preventative healthcare for cardiac patients. It seeks to develop a smart mobile ECG monitoring system that requests and records context information about what is happening around the subject when an arrhythmia event occurs. Context information about the subject’s activities of daily living will, it is hoped, provide an enriched data set for clinicians and so improve clinical decision making. As a first step towards a mobile cardiac wellness guidelines system, the focus of this work is to develop a system that can receive bio-signals wirelessly, analyzing and storing the bio-signal in a handheld device and can collect context information when there are significant changes in bio-signs. For this purpose the author will use a low cost development environment to program a state of the art wireless prototype on a handheld computer that detects and responds to changes in the heart rate as calculated form the interval between successive heart beats. Although the general approach take in this work could be applied to a wide range of bio-signals, the research will focus on ECG signals. The pieces of the system are, A wireless receiver, data collection and storage module An efficient real time ECG beat detection algorithm A rule based (Event-Condition-Action) interactive system A simple user interface, which can request additional information form the user. A selection of real-time ECG detection algorithms have been investigated and one algorithm was implemented in MATLAB [110] and then in Java [142] for this project. In order to collect ECG signals (and in principle any signals) the generalised data collection architecture has also been developed utilizing Java [142] and Bluetooth [5] technology. This architecture uses an implementation of the abstract factory pattern [91] to ensure that the communication channel can be changed conveniently. Another core part of this project is a “wellness” guideline based on Event-Condition-Action (E-C-A) [68] production rule approach that originated in active databases. The work also focuses on design of a guideline based expert system which an E-C-A based implementation will be fully event driven using the Java programming language. Based on the author’s experience and the literature review, some important issues in mobile healthcare along with the corresponding reasons, consequences and possible solutions will be presented