What Google Maps can do for biomedical data dissemination: examples and a design study

BACKGROUND: Biologists often need to assess whether unfamiliar datasets warrant the time investment required for more detailed exploration. Basing such assessments on brief descriptions provided by data publishers is unwieldy for large datasets that contain insights dependent on specific scientific questions. Alternatively, using complex software systems for a preliminary analysis may be deemed as too time consuming in itself, especially for unfamiliar data types and formats. This may lead to wasted analysis time and discarding of potentially useful data. RESULTS: We present an exploration of design opportunities that the Google Maps interface offers to biomedical data visualization. In particular, we focus on synergies between visualization techniques and Google Maps that facilitate the development of biological visualizations which have both low-overhead and sufficient expressivity to support the exploration of data at multiple scales. The methods we explore rely on displaying pre-rendered visualizations of biological data in browsers, with sparse yet powerful interactions, by using the Google Maps API. We structure our discussion around five visualizations: a gene co-regulation visualization, a heatmap viewer, a genome browser, a protein interaction network, and a planar visualization of white matter in the brain. Feedback from collaborative work with domain experts suggests that our Google Maps visualizations offer multiple, scale-dependent perspectives and can be particularly helpful for unfamiliar datasets due to their accessibility. We also find that users, particularly those less experienced with computer use, are attracted by the familiarity of the Google Maps API. Our five implementations introduce design elements that can benefit visualization developers. CONCLUSIONS: We describe a low-overhead approach that lets biologists access readily analyzed views of unfamiliar scientific datasets. We rely on pre-computed visualizations prepared by data experts, accompanied by sparse and intuitive interactions, and distributed via the familiar Google Maps framework. Our contributions are an evaluation demonstrating the validity and opportunities of this approach, a set of design guidelines benefiting those wanting to create such visualizations, and five concrete example visualizations

Visual parameter optimisation for biomedical image processing

Background: Biomedical image processing methods require users to optimise input parameters to ensure high quality output. This presents two challenges. First, it is difficult to optimise multiple input parameters for multiple input images. Second, it is difficult to achieve an understanding of underlying algorithms, in particular, relationships between input and output. Results: We present a visualisation method that transforms users’ ability to understand algorithm behaviour by integrating input and output, and by supporting exploration of their relationships. We discuss its application to a colour deconvolution technique for stained histology images and show how it enabled a domain expert to identify suitable parameter values for the deconvolution of two types of images, and metrics to quantify deconvolution performance. It also enabled a breakthrough in understanding by invalidating an underlying assumption about the algorithm. Conclusions: The visualisation method presented here provides analysis capability for multiple inputs and outputs in biomedical image processing that is not supported by previous analysis software. The analysis supported by our method is not feasible with conventional trial-and-error approaches

Interfaces for science: Conceptualizing an interactive graphical interface

6,849.32 new research journal articles are published every day. The exponential growth of Scientific Knowledge Objects (SKOs) on the Web, makes searches time-consuming. Access to the right and relevant SKOs is vital for research, which calls for several topics, including the visualization of science dynamics. We present an interface model aimed to represent of the relations that emerge in the science social space dynamics, namely through the visualization and navigation of the relational structures between researchers, SKOs, knowledge domains, subdomains, and topics. This interface considers the relationship between the researcher who reads and shares the relevant articles and the researcher who wants to find the most relevant SKOs within a subject matter. This article presents the first iteration of the conceptualization process of the interface layout, its interactivity and visualization structures. It is essential to consider the hierarchical and relational structures/algorithms to represent the science social space dynamics. These structures are not being used as analysis tools, because it is not objective to show the linkage properties of these relationships. Instead, they are used as a means of representing, navigating and exploring these relationships. To sum up, this article provides a framework and fundamental guidelines for an interface layout that explores the social science space dynamics between the researcher who seeks relevant SKOs and the researchers who read and share them.This work has been supported by COMPETE: POCI-01-0145-FEDER- 007043 and FCT - Fundação para a Ciência e Tecnologia within the Project Scope: (UID/CEC/00319/2013) and the Project IViSSEM: ref: POCI-010145-FEDER-28284

Genomorama: genome visualization and analysis

<p>Abstract</p> <p>Background</p> <p>The ability to visualize genomic features and design experimental assays that can target specific regions of a genome is essential for modern biology. To assist in these tasks, we present Genomorama, a software program for interactively displaying multiple genomes and identifying potential DNA hybridization sites for assay design.</p> <p>Results</p> <p>Useful features of Genomorama include genome search by DNA hybridization (probe binding and PCR amplification), efficient multi-scale display and manipulation of multiple genomes, support for many genome file types and the ability to search for and retrieve data from the National Center for Biotechnology Information (NCBI) Entrez server.</p> <p>Conclusion</p> <p>Genomorama provides an efficient computational platform for visualizing and analyzing multiple genomes.</p

ERYTHROPOIETIN FOR THE TREATMENT OF SUBARACHNOID HEMORRAGE: A FEASIBLE INGREDIENT FOR A SUCCESS MEDICAL RECIPE

Subaracnhoid hemorrage (SAH) following aneurysm bleeding accounts for 6% to 8% of all cerebrovascular accidents. Althoug an aneurysm can be effectively managed by surgery or endovascular therapy, delayed cerebral ischemia is diagnosed in a high percentage of patients resulting in significant morbility and mortality. Cerebral vasospasm occurs in more than half of all patients after aneurysm rupture and is recognized as the leading cause of delayed cerebral ischemia after SAH. Hemodynamic strategies and endovascular procedures may be considered fo the treatment of cerebral vasospasm. In recent years, the mechanism contributing to the development of vasospasm, abnormal reactivity of cerebral arteries and cerebral ischemia following SAH, have been intensively investigated. A number of pathological processes have been identified in the pathogenesis of vasospasm including endothelial injury, smooth muscle cell contraction from spasmogenic substances produced by the subarachnoid blood clots, changes in vascular responsiveness and inflammatory response of the vascular endothelium. to date, the current therapeutic interventions remain ineffective being limited to the manipulation os systemic blood pressure, variation of blood volume and viscosity, and control of arterial carbon dioxide tension. In this scenario, the hormone erythropoietin (EPO), has been found to exert neuroprotective action during experimental SAH when its recombinant form (rHuEPO) is systematically administered. However, recent translation of experimental data into clinical trials has suggested an unclear role of recombinant human EPO in the setting of SAH. In this context, the aim of the recurrent review is to present current evidence on the potential role of EPO in cerebrovascular dysfunction following aneurysmal subarachnoid hemorrage

Comparing speed-dependent automatic zooming with traditional scroll, pan and zoom methods

Speed-dependent automatic zooming couples the user’s rate of motion through an information space with the zoom level—the faster the user moves the ‘higher’ they fly above the work surface. Igarashi and Hinckley [2000] proposed using the technique to improve scrolling through large documents. Their informal preliminary evaluation showed mixed results with participants completing scrolling tasks in roughly the same time, or more slowly, than when using traditional methods. In this paper, we describe the implementation and formal evaluation of two rapidly interactive speed-dependent automatic zooming interfaces. The ecologically oriented evaluation shows that scrolling tasks are solved significantly faster with automatic zooming in both text document and map browsing tasks. Subjective preferences and workload measures also strongly favour the automatic zooming systems. Implications for the future of scrolling interfaces are substantial, and directions for further work are presented

Utilising a Geographic Space Metaphor in a Software Development Environment

Current software systems are growing ever larger and more complex. This increase in size and complexity is of course reflected in the data produced in the development process and overviewing and navigating the structure are becoming daunting tasks. This paper presents a model for visualising many important aspects of the complex, multi-dimensional, data in a software development project. The model is based on a geographic space metaphor: Entities in the software architecture are organised geographically in what becomes a design `landscape&apos;. Thereby overview and navigation is supported by tapping into humans fine spatial and visual perception. The landscape is shared in the project team, and mediates daily development activities thereby providing a common reference frame, and a framework for visualising aspects of the software. A prototype implementation of a software development environment, Ragnarok, based on this model is presented and some preliminary experiences outli..

KidPad: a Collaborative Storytelling Tool for Children

Collaborative storytelling occurs frequently when children play, but relatively few efforts have been made to support it with computers. This demonstration presents KidPad, a collaborative storytelling tool that supports children creating hyperlinked stories in a large two-dimensional zoomable space. Through the use of local tools, KidPad provides children with advanced interaction techniques in a collaborative environment