NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps

Molecular biology knowledge can be systematically represented in a computer-readable form as a comprehensive map of molecular interactions. There exist a number of maps of molecular interactions containing detailed description of various cell mechanisms. It is difficult to explore these large maps, to comment their content and to maintain them. Though there exist several tools addressing these problems individually, the scientific community still lacks an environment that combines these three capabilities together. NaviCell is a web-based environment for exploiting large maps of molecular interactions, created in CellDesigner, allowing their easy exploration, curation and maintenance. NaviCell combines three features: (1) efficient map browsing based on Google Maps engine; (2) semantic zooming for viewing different levels of details or of abstraction of the map and (3) integrated web-based blog for collecting the community feedback. NaviCell can be easily used by experts in the field of molecular biology for studying molecular entities of their interest in the context of signaling pathways and cross-talks between pathways within a global signaling network. NaviCell allows both exploration of detailed molecular mechanisms represented on the map and a more abstract view of the map up to a top-level modular representation. NaviCell facilitates curation, maintenance and updating the comprehensive maps of molecular interactions in an interactive fashion due to an imbedded blogging system. NaviCell provides an easy way to explore large-scale maps of molecular interactions, thanks to the Google Maps and WordPress interfaces, already familiar to many users. Semantic zooming used for navigating geographical maps is adopted for molecular maps in NaviCell, making any level of visualization meaningful to the user. In addition, NaviCell provides a framework for community-based map curation.Comment: 20 pages, 5 figures, submitte

That's 'é' not 'þ' '?' or '☐': a user-driven context-aware approach to erroneous metadata in digital libraries

In this paper we present a novel system for user-driven integration of name variants when interacting with web-based information systems. The growth and diversity of online information means that many users experience disambiguation and collocation errors in their information searching. We approach these issues via a client-side JavaScript browser extension that can reorganise web content and also integrate remote data sources. The system is illustrated through three worked examples using existing digital libraries

Database on coastal vulnerability and exposure

In this document, we report progress on the development of European layers on exposure and vulnerability. This involves the collection and cataloguing of relevant exposure factors (e.g., land use, population, settlements, infrastructures) and vulnerability indicators (coastal flood protection, damage functions) as well as the development and application of tools for the logging, spatial interpolation, statistical analysis and validation of the collected information. All data are available through the The Risk Data hub database the aim of which is to improve the accessibility and dissemination of EU-wide curated risk data for fostering Disaster Risk Management (DRM).JRC.E.1-Disaster Risk Managemen

User-centered development of a Virtual Research Environment to support collaborative research events

This paper discusses the user-centred development process within the Collaborative Research Events on the Web (CREW) project, funded under the JISC Virtual Research Environments (VRE) programme. After presenting the project, its aims and the functionality of the CREW VRE, we focus on the user engagement approach, grounded in the method of co-realisation. We describe the different research settings and requirements of our three embedded user groups and the respective activities conducted so far. Finally we elaborate on the main challenges of our user engagement approach and end with the project’s next steps

LookBook: pioneering Inclusive beauty with artificial intelligence and machine learning algorithms

Technology's imperfections and biases inherited from historical norms are crucial to acknowledge. Rapid perpetuation and amplification of these biases necessitate transparency and proactive measures to mitigate their impact. The online visual culture reinforces Eurocentric beauty ideals through prioritized algorithms and augmented reality filters, distorting reality and perpetuating unrealistic standards of beauty. Narrow beauty standards in technology pose a significant challenge to overcome. Algorithms personalize content, creating "filter bubbles" that reinforce these ideals and limit exposure to diverse representations of beauty. This cycle compels individuals to conform, hindering the embrace of their unique features and alternative definitions of beauty. LookBook counters prevalent narrow beauty standards in technology. It promotes inclusivity and representation through self-expression, community engagement, and diverse visibility. LookBook comprises three core sections: Dash, Books, and Community. In Dash, users curate their experience through personalization algorithms. Books allow users to collect curated content for inspiration and creativity, while Community fosters connections with like-minded individuals. Through LookBook, users create a reality aligned with their unique vision. They control consumed content, nurturing individualism through preferences and creativity. This personalization empowers individuals to break free from narrow beauty standards and embrace their distinctiveness. LookBook stands out with its algorithmic training and data representation. It offers transparency on how personalization algorithms operate and ensures a balanced and diverse representation of physicalities and ethnicities. By addressing biases and embracing a wide range of identities, LookBook sparks a conversation for a technology landscape that amplifies all voices, fostering an environment celebrating diversity and prioritizing inclusivity

A Workflow Approach to Visualization-Based Storytelling with Cultural Heritage Data

Stories are as old as human history - and a powerful means for the engaging communication of information, especially in combination with visualizations. The InTaVia project is built on this intersection and has developed a platform which supports the workflow of cultural heritage experts to create compelling visualization-based stories: From the search for relevant cultural objects and actors in a cultural knowledge graph, to the curation and visual analysis of the selected information, and to the creation of stories based on these data and visualizations, which can be shared with the interested public.Comment: VIS4DH 202

Chado Controller: advanced annotation management with a community annotation system

Summary: We developed a controller that is compliant with the Chado database schema, GBrowse and genome annotation-editing tools such as Artemis and Apollo. It enables the management of public and private data, monitors manual annotation (with controlled vocabularies, structural and functional annotation controls) and stores versions of annotation for all modified features. The Chado controller uses PostgreSQL and Perl