An innovative collaborative high-performance platform for simulation

This paper presents an innovative collaborative visualization platform for the simulation-based design applications. Following the scope and the main objectives, the general architecture based on the internet standard technologies is explained. Based on a multi-domain approach, several demonstrators are involved crossing interests of industrial and academic communities. Related to the field of process engineering, we adapt and deploy a web-based architecture research application on the targeted platform

MACBenAbim: A Multi-platform Mobile Application for searching keyterms in Computational Biology and Bioinformatics

Computational biology and bioinformatics are gradually gaining grounds in Africa and other developing nations of the world. However, in these countries, some of the challenges of computational biology and bioinformatics education are inadequate infrastructures, and lack of readily-available complementary and motivational tools to support learning as well as research. This has lowered the morale of many promising undergraduates, postgraduates and researchers from aspiring to undertake future study in these fields. In this paper, we developed and described MACBenAbim (Multi-platform Mobile Application for Computational Biology and Bioinformatics), a flexible user-friendly tool to search for, define and describe the meanings of keyterms in computational biology and bioinformatics, thus expanding the frontiers of knowledge of the users. This tool also has the capability of achieving visualization of results on a mobile multi-platform context

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

Visualization of flow fields in the web platform

Visualization of vector fields plays an important role in research activities nowadays -- Web applications allow a fast, multi-platform and multi-device access to data, which results in the need of optimized applications to be implemented in both high-performance and low-performance devices -- Point trajectory calculation procedures usually perform repeated calculations due to the fact that several points might lie over the same trajectory -- This paper presents a new methodology to calculate point trajectories over highly-dense and uniformly-distributed grid of points in which the trajectories are forced to lie over the points in the grid -- Its advantages rely on a highly parallel computing architecture implementation and in the reduction of the computational effort to calculate the stream paths since unnecessary calculations are avoided, reusing data through iterations -- As case study, the visualization of oceanic currents through in the web platform is presented and analyzed, using WebGL as the parallel computing architecture and the rendering Application Programming Interfac

Hardware-accelerated Web Visualization of Vector Fields. Case Study in Oceanic Currents

Visualization of vector fields plays an important role in research activities nowadays -- Increasing web applications allow a fast, multi-platform and multi-device access to data -- As a result, web applications must be optimized in order to be performed heterogeneously as well as on high-performance as on low capacity devices -- This paper presents a hardware-accelerated scheme for integration-based flow visualization techniques, based on a hierarchical integration procedure which reduces the computational effort of the algorithm from linear to logarithmic, compared to serial integration methodologies -- The contribution relies on the fact that the optimization is only implemented using the graphics application programming interface (API), instead of requiring additional APIs or plug-ins -- This is achieved by using images as data storing elements instead of graphical information matrices -- A case study in oceanic currents is implemente

Evoplex: A platform for agent-based modeling on networks

Agent-based modeling and network science have been used extensively to advance our understanding of emergent collective behavior in systems that are composed of a large number of simple interacting individuals or agents. With the increasing availability of high computational power in affordable personal computers, dedicated efforts to develop multi-threaded, scalable and easy-to-use software for agent-based simulations are needed more than ever. Evoplex meets this need by providing a fast, robust and extensible platform for developing agent-based models and multi-agent systems on networks. Each agent is represented as a node and interacts with its neighbors, as defined by the network structure. Evoplex is ideal for modeling complex systems, for example in evolutionary game theory and computational social science. In Evoplex, the models are not coupled to the execution parameters or the visualization tools, and there is a user-friendly graphical interface which makes it easy for all users, ranging from newcomers to experienced, to create, analyze, replicate and reproduce the experiments.Comment: 6 pages, 5 figures; accepted for publication in SoftwareX [software available at https://evoplex.org

DoctorEye: A clinically driven multifunctional platform, for accurate processing of tumors in medical images

Copyright @ Skounakis et al.This paper presents a novel, open access interactive platform for 3D medical image analysis, simulation and visualization, focusing in oncology images. The platform was developed through constant interaction and feedback from expert clinicians integrating a thorough analysis of their requirements while having an ultimate goal of assisting in accurately delineating tumors. It allows clinicians not only to work with a large number of 3D tomographic datasets but also to efficiently annotate multiple regions of interest in the same session. Manual and semi-automatic segmentation techniques combined with integrated correction tools assist in the quick and refined delineation of tumors while different users can add different components related to oncology such as tumor growth and simulation algorithms for improving therapy planning. The platform has been tested by different users and over large number of heterogeneous tomographic datasets to ensure stability, usability, extensibility and robustness with promising results. AVAILABILITY: THE PLATFORM, A MANUAL AND TUTORIAL VIDEOS ARE AVAILABLE AT: http://biomodeling.ics.forth.gr. It is free to use under the GNU General Public License