DGD Gallery: Storage, sharing, and publication of digital research data

We describe a project, called the "Discretization in Geometry and Dynamics Gallery", or DGD Gallery for short, whose goal is to store geometric data and to make it publicly available. The DGD Gallery offers an online web service for the storage, sharing, and publication of digital research data.Comment: 19 pages, 8 figures, to appear in "Advances in Discrete Differential Geometry", ed. A. I. Bobenko, Springer, 201

ranacapa: An R package and Shiny web app to explore environmental DNA data with exploratory statistics and interactive visualizations.

Environmental DNA (eDNA) metabarcoding is becoming a core tool in ecology and conservation biology, and is being used in a growing number of education, biodiversity monitoring, and public outreach programs in which professional research scientists engage community partners in primary research. Results from eDNA analyses can engage and educate natural resource managers, students, community scientists, and naturalists, but without significant training in bioinformatics, it can be difficult for this diverse audience to interact with eDNA results. Here we present the R package ranacapa, at the core of which is a Shiny web app that helps perform exploratory biodiversity analyses and visualizations of eDNA results. The app requires a taxonomy-by-sample matrix and a simple metadata file with descriptive information about each sample. The app enables users to explore the data with interactive figures and presents results from simple community ecology analyses. We demonstrate the value of ranacapa to two groups of community partners engaging with eDNA metabarcoding results

Global-Scale Resource Survey and Performance Monitoring of Public OGC Web Map Services

One of the most widely-implemented service standards provided by the Open Geospatial Consortium (OGC) to the user community is the Web Map Service (WMS). WMS is widely employed globally, but there is limited knowledge of the global distribution, adoption status or the service quality of these online WMS resources. To fill this void, we investigated global WMSs resources and performed distributed performance monitoring of these services. This paper explicates a distributed monitoring framework that was used to monitor 46,296 WMSs continuously for over one year and a crawling method to discover these WMSs. We analyzed server locations, provider types, themes, the spatiotemporal coverage of map layers and the service versions for 41,703 valid WMSs. Furthermore, we appraised the stability and performance of basic operations for 1210 selected WMSs (i.e., GetCapabilities and GetMap). We discuss the major reasons for request errors and performance issues, as well as the relationship between service response times and the spatiotemporal distribution of client monitoring sites. This paper will help service providers, end users and developers of standards to grasp the status of global WMS resources, as well as to understand the adoption status of OGC standards. The conclusions drawn in this paper can benefit geospatial resource discovery, service performance evaluation and guide service performance improvements.Comment: 24 pages; 15 figure

Adaptive transfer functions: improved multiresolution visualization of medical models

The final publication is available at Springer via http://dx.doi.org/10.1007/s00371-016-1253-9Medical datasets are continuously increasing in size. Although larger models may be available for certain research purposes, in the common clinical practice the models are usually of up to 512x512x2000 voxels. These resolutions exceed the capabilities of conventional GPUs, the ones usually found in the medical doctors’ desktop PCs. Commercial solutions typically reduce the data by downsampling the dataset iteratively until it fits the available target specifications. The data loss reduces the visualization quality and this is not commonly compensated with other actions that might alleviate its effects. In this paper, we propose adaptive transfer functions, an algorithm that improves the transfer function in downsampled multiresolution models so that the quality of renderings is highly improved. The technique is simple and lightweight, and it is suitable, not only to visualize huge models that would not fit in a GPU, but also to render not-so-large models in mobile GPUs, which are less capable than their desktop counterparts. Moreover, it can also be used to accelerate rendering frame rates using lower levels of the multiresolution hierarchy while still maintaining high-quality results in a focus and context approach. We also show an evaluation of these results based on perceptual metrics.Peer ReviewedPostprint (author's final draft

Exploring Uncertainty in Geodemographics with Interactive Graphics

Geodemographic classifiers characterise populations by categorising geographical areas according to the demographic and lifestyle characteristics of those who live within them. The dimension-reducing quality of such classifiers provides a simple and effective means of characterising population through a manageable set of categories, but inevitably hides heterogeneity, which varies within and between the demographic categories and geographical areas, sometimes systematically. This may have implications for their use, which is widespread in government and commerce for planning, marketing and related activities. We use novel interactive graphics to delve into OAC – a free and open geodemographic classifier that classifies the UK population in over 200,000 small geographical areas into 7 super-groups, 21 groups and 52 sub-groups. Our graphics provide access to the original 41 demographic variables used in the classification and the uncertainty associated with the classification of each geographical area on-demand. It also supports comparison geographically and by category. This serves the dual purpose of helping understand the classifier itself leading to its more informed use and providing a more comprehensive view of population in a comprehensible manner. We assess the impact of these interactive graphics on experienced OAC users who explored the details of the classification, its uncertainty and the nature of between – and within – class variation and then reflect on their experiences. Visualization of the complexities and subtleties of the classification proved to be a thought-provoking exercise both confirming and challenging users’ understanding of population, the OAC classifier and the way it is used in their organisations. Users identified three contexts for which the techniques were deemed useful in the context of local government, confirming the validity of the proposed methods

GODIVA2: interactive visualization of environmental data on the Web

GODIVA2 is a dynamic website that provides visual access to several terabytes of physically distributed, four-dimensional environmental data. It allows users to explore large datasets interactively without the need to install new software or download and understand complex data. Through the use of open international standards, GODIVA2 maintains a high level of interoperability with third-party systems, allowing diverse datasets to be mutually compared. Scientists can use the system to search for features in large datasets and to diagnose the output from numerical simulations and data processing algorithms. Data providers around Europe have adopted GODIVA2 as an INSPIRE-compliant dynamic quick-view system for providing visual access to their data

Animating the evolution of software

The use and development of open source software has increased significantly in the last decade. The high frequency of changes and releases across a distributed environment requires good project management tools in order to control the process adequately. However, even with these tools in place, the nature of the development and the fact that developers will often work on many other projects simultaneously, means that the developers are unlikely to have a clear picture of the current state of the project at any time. Furthermore, the poor documentation associated with many projects has a detrimental effect when encouraging new developers to contribute to the software. A typical version control repository contains a mine of information that is not always obvious and not easy to comprehend in its raw form. However, presenting this historical data in a suitable format by using software visualisation techniques allows the evolution of the software over a number of releases to be shown. This allows the changes that have been made to the software to be identified clearly, thus ensuring that the effect of those changes will also be emphasised. This then enables both managers and developers to gain a more detailed view of the current state of the project. The visualisation of evolving software introduces a number of new issues. This thesis investigates some of these issues in detail, and recommends a number of solutions in order to alleviate the problems that may otherwise arise. The solutions are then demonstrated in the definition of two new visualisations. These use historical data contained within version control repositories to show the evolution of the software at a number of levels of granularity. Additionally, animation is used as an integral part of both visualisations - not only to show the evolution by representing the progression of time, but also to highlight the changes that have occurred. Previously, the use of animation within software visualisation has been primarily restricted to small-scale, hand generated visualisations. However, this thesis shows the viability of using animation within software visualisation with automated visualisations on a large scale. In addition, evaluation of the visualisations has shown that they are suitable for showing the changes that have occurred in the software over a period of time, and subsequently how the software has evolved. These visualisations are therefore suitable for use by developers and managers involved with open source software. In addition, they also provide a basis for future research in evolutionary visualisations, software evolution and open source development