Visual analysis of anatomy ontologies and related genomic information

Challenges in scientific research include the difficulty in obtaining overviews of the large amount of data required for analysis, and in resolving the differences in terminology used to store and interpret information in multiple, independently created data sets. Ontologies provide one solution for analysis involving multiple data sources, improving cross-referencing and data integration. This thesis looks at harnessing advanced human perception to reduce the cognitive load in the analysis of the multiple, complex data sets the bioinformatics user group studied use in research, taking advantage also of users’ domain knowledge, to build mental models of data that map to its underlying structure. Guided by a user-centred approach, prototypes were developed to provide a visual method for exploring users’ information requirements and to identify solutions for these requirements. 2D and 3D node-link graphs were built to visualise the hierarchically structured ontology data, to improve analysis of individual and comparison of multiple data sets, by providing overviews of the data, followed by techniques for detailed analysis of regions of interest. Iterative, heuristic and structured user evaluations were used to assess and refine the options developed for the presentation and analysis of the ontology data. The evaluation results confirmed the advantages that visualisation provides over text-based analysis, and also highlighted the advantages of each of 2D and 3D for visual data analysis.Overseas Research Students Awards SchemeJames Watt Scholarshi

Embedded 3D Web Based Content for the Creation of an Interactive Medical Browser

The research project set out to examine the possibility of presenting 3D medical visualisations through a web browser to help suffers and their families understand their conditions. Explaining complex medical subjects and communicating them simply and clearly to non-specialists is a continuing problem in modern medical practice. The study set out to complement current methods of health communication via pamphlets, posters, books, magazines, 2D & 3D animations and text based websites as all of these have disadvantages which an interactive 3D system might be able to overcome. The reason a Web Browser approach was adopted was due to the wide availability of browsers for a large number of users. Additionally modern web based 3D content delivery methods negate the need to continually download and install additional software, at the same time allowing for a high quality user experience associated with traditional 3D interactive software. To help answer the research questions, a prototype artefact focused on Asthma was produced which was then tested and validated through user testing with a small group of Asthma suffers and evaluated by medical professionals. The study concluded that effective communication of medical information to sufferers and their families using 3D browser based systems is possible and can form a useful part of a medical communication system for non-specialists

Data hosting infrastructure for primary biodiversity data

© The Author(s), 2011. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Bioinformatics 12 Suppl. 15 (2011): S5, doi:10.1186/1471-2105-12-S15-S5.Today, an unprecedented volume of primary biodiversity data are being generated worldwide, yet significant amounts of these data have been and will continue to be lost after the conclusion of the projects tasked with collecting them. To get the most value out of these data it is imperative to seek a solution whereby these data are rescued, archived and made available to the biodiversity community. To this end, the biodiversity informatics community requires investment in processes and infrastructure to mitigate data loss and provide solutions for long-term hosting and sharing of biodiversity data. We review the current state of biodiversity data hosting and investigate the technological and sociological barriers to proper data management. We further explore the rescuing and re-hosting of legacy data, the state of existing toolsets and propose a future direction for the development of new discovery tools. We also explore the role of data standards and licensing in the context of data hosting and preservation. We provide five recommendations for the biodiversity community that will foster better data preservation and access: (1) encourage the community's use of data standards, (2) promote the public domain licensing of data, (3) establish a community of those involved in data hosting and archival, (4) establish hosting centers for biodiversity data, and (5) develop tools for data discovery. The community's adoption of standards and development of tools to enable data discovery is essential to sustainable data preservation. Furthermore, the increased adoption of open content licensing, the establishment of data hosting infrastructure and the creation of a data hosting and archiving community are all necessary steps towards the community ensuring that data archival policies become standardized

Web Tracking: Mechanisms, Implications, and Defenses

This articles surveys the existing literature on the methods currently used by web services to track the user online as well as their purposes, implications, and possible user's defenses. A significant majority of reviewed articles and web resources are from years 2012-2014. Privacy seems to be the Achilles' heel of today's web. Web services make continuous efforts to obtain as much information as they can about the things we search, the sites we visit, the people with who we contact, and the products we buy. Tracking is usually performed for commercial purposes. We present 5 main groups of methods used for user tracking, which are based on sessions, client storage, client cache, fingerprinting, or yet other approaches. A special focus is placed on mechanisms that use web caches, operational caches, and fingerprinting, as they are usually very rich in terms of using various creative methodologies. We also show how the users can be identified on the web and associated with their real names, e-mail addresses, phone numbers, or even street addresses. We show why tracking is being used and its possible implications for the users (price discrimination, assessing financial credibility, determining insurance coverage, government surveillance, and identity theft). For each of the tracking methods, we present possible defenses. Apart from describing the methods and tools used for keeping the personal data away from being tracked, we also present several tools that were used for research purposes - their main goal is to discover how and by which entity the users are being tracked on their desktop computers or smartphones, provide this information to the users, and visualize it in an accessible and easy to follow way. Finally, we present the currently proposed future approaches to track the user and show that they can potentially pose significant threats to the users' privacy.Comment: 29 pages, 212 reference

Open-source magnetic resonance imaging : Improving access, science, and education through global collaboration

The authors would like to thank all the authors that are sharing their work open-source and all the supporters of the Open Source Imaging Initiative (OSI2). The project (21NRM05 and 22HLT02 A4IM) has received funding from the European Partnership on Metrology, co-financed by the European Union's Horizon Europe Research and Innovation Programme and by the Participating States. This research is funded by dtec.bw- Digitalization and Technology Research Center of the Bundeswehr. dtec.bw is funded by the European Union - NextGeneration EU. Part of the image reconstruction used here was developed by the CCP PETMR and CCP SynerBi (https://www.ccppetmr.ac.uk/), UK EPSRC grants EP/P022200/1, EP/M022587/1 and EP/T026693/1. This work made use of computational support by CoSeC, the Computational Science Centre for Research Communities via CCP-SyneRBI and CCPi. RG Nunes acknowledges funding from Fundação para a Ciência e a Tecnologia (grants UIDP/50009/2020 and LA/P/0083/2020). Ruben Pellicer-Guridi has been funded by the European Union's Marie Skłodowska-Curie project nr. 101030868. Open Access funding enabled and organized by Projekt DEAL.Peer reviewe

IAIMS newsletter

NewsletterThe IAIMS Newsletter (1996-2005) provides valuable information about library activities and resources as well as informative articles related to information technology

Simple identification tools in FishBase

Simple identification tools for fish species were included in the FishBase information system from its inception. Early tools made use of the relational model and characters like fin ray meristics. Soon pictures and drawings were added as a further help, similar to a field guide. Later came the computerization of existing dichotomous keys, again in combination with pictures and other information, and the ability to restrict possible species by country, area, or taxonomic group. Today, www.FishBase.org offers four different ways to identify species. This paper describes these tools with their advantages and disadvantages, and suggests various options for further development. It explores the possibility of a holistic and integrated computeraided strategy