VIOLA - A multi-purpose and web-based visualization tool for neuronal-network simulation output

Neuronal network models and corresponding computer simulations are invaluable tools to aid the interpretation of the relationship between neuron properties, connectivity and measured activity in cortical tissue. Spatiotemporal patterns of activity propagating across the cortical surface as observed experimentally can for example be described by neuronal network models with layered geometry and distance-dependent connectivity. The interpretation of the resulting stream of multi-modal and multi-dimensional simulation data calls for integrating interactive visualization steps into existing simulation-analysis workflows. Here, we present a set of interactive visualization concepts called views for the visual analysis of activity data in topological network models, and a corresponding reference implementation VIOLA (VIsualization Of Layer Activity). The software is a lightweight, open-source, web-based and platform-independent application combining and adapting modern interactive visualization paradigms, such as coordinated multiple views, for massively parallel neurophysiological data. For a use-case demonstration we consider spiking activity data of a two-population, layered point-neuron network model subject to a spatially confined excitation originating from an external population. With the multiple coordinated views, an explorative and qualitative assessment of the spatiotemporal features of neuronal activity can be performed upfront of a detailed quantitative data analysis of specific aspects of the data. Furthermore, ongoing efforts including the European Human Brain Project aim at providing online user portals for integrated model development, simulation, analysis and provenance tracking, wherein interactive visual analysis tools are one component. Browser-compatible, web-technology based solutions are therefore required. Within this scope, with VIOLA we provide a first prototype.Comment: 38 pages, 10 figures, 3 table

Interactive Web-based Visualization of Atomic Position-time Series Data

Extracting and interpreting the information contained in large sets of time-varying three dimensional positional data for the constituent atoms of simulated material system is a challenging task. This thesis work reports our initial implementation of a web-based visualization system and its use-case study. The system allows the users to perform the desired visualization task on a web browser for the position-time series data extracted from the local or remote hosts. It involves a pre-processing step for data reduction, which involves skipping uninteresting parts of the data uniformly (at full atomic configuration level) or non-uniformly (at atomic species level or individual atom level). Atomic configuration at a given time step (snapshot) is rendered using the ball-stick representation and can be animated by rendering successive configurations. The entire atomic dynamics can be captured as the trajectories by rendering the atomic positions at all time steps together as points. The trajectories can be manipulated at both species and atomic levels so that we can focus on one or more trajectories of interest. They can be color-coded according to the additional information including the time elapsed and the distance traveled. The instantaneous atomic structure and the complete trajectories can be superimposed to help assess the 3D geometries and extents of the selected trajectories. The implementation was done using WebGL and Three.js for graphical rendering, HTML5 and Javascript for GUI, and Elasticsearch and JSON for data storage and retrieval within the Grails Framework. We have demonstrated the usefulness of our visualization system by analyzing the simulated position-time series for proton-bearing forsterite (Mg2SiO4) system – an abundant mineral of Earths upper mantle. Visualization reveals that protons (hydrogen ions) incorporated as interstitials are much more mobile than protons substituting the host Mg and Si cation sites. The proton diffusion appears to be anisotropic with high mobility along the x-direction, showing limited discrete jumps in other two directions. Our work at the present represents a simplistic (direct) web-based rendering of large atomic data sets. While the atomic structure can be animated at an interactive rate, the trajectory processing is slow, taking several minutes. We anticipate to further improve the system and use it in gaining useful structural and dynamical information from more materials simulation data

Accessible user interface support for multi-device ubiquitous applications: architectural modifiability considerations

The market for personal computing devices is rapidly expanding from PC, to mobile, home entertainment systems, and even the automotive industry. When developing software targeting such ubiquitous devices, the balance between development costs and market coverage has turned out to be a challenging issue. With the rise of Web technology and the Internet of things, ubiquitous applications have become a reality. Nonetheless, the diversity of presentation and interaction modalities still drastically limit the number of targetable devices and the accessibility toward end users. This paper presents webinos, a multi-device application middleware platform founded on the Future Internet infrastructure. Hereto, the platform's architectural modifiability considerations are described and evaluated as a generic enabler for supporting applications, which are executed in ubiquitous computing environments

Web Based Prognostics and 24/7 Monitoring

We created a general framework for analysts to store and view data in a way that removes the boundaries created by operating systems, programming languages, and proximity. With the advent of HTML5 and CSS3 with JavaScript the distribution of information is limited to only those who lack a browser. We created a framework based on the methodology: one server, one web based application. Additional benefits are increased opportunities for collaboration. Today the idea of a group in a single room is antiquated. Groups will communicate and collaborate with others from other universities, organizations, as well as other continents across times zones. There are many varieties of data gathering and condition-monitoring software available as well as companies who specialize in customizing software to individual applications. One single group will depend on multiple languages, environments, and computers to oversee recording and collaborating with one another in a single lab. The heterogeneous nature of the system creates challenges for seamless exchange of data and ideas between members. To address these limitations we designed a framework to allow users seamless accessibility to their data. Our framework was deployed using the data feed on the NASA Ames' planetary rover testbed. Our paper demonstrates the process and implementation we followed on the rover

BlogForever D2.6: Data Extraction Methodology

This report outlines an inquiry into the area of web data extraction, conducted within the context of blog preservation. The report reviews theoretical advances and practical developments for implementing data extraction. The inquiry is extended through an experiment that demonstrates the effectiveness and feasibility of implementing some of the suggested approaches. More specifically, the report discusses an approach based on unsupervised machine learning that employs the RSS feeds and HTML representations of blogs. It outlines the possibilities of extracting semantics available in blogs and demonstrates the benefits of exploiting available standards such as microformats and microdata. The report proceeds to propose a methodology for extracting and processing blog data to further inform the design and development of the BlogForever platform