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

Footprints of information foragers: Behaviour semantics of visual exploration

Social navigation exploits the knowledge and experience of peer users of information resources. A wide variety of visual–spatial approaches become increasingly popular as a means to optimize information access as well as to foster and sustain a virtual community among geographically distributed users. An information landscape is among the most appealing design options of representing and communicating the essence of distributed information resources to users. A fundamental and challenging issue is how an information landscape can be designed such that it will not only preserve the essence of the underlying information structure, but also accommodate the diversity of individual users. The majority of research in social navigation has been focusing on how to extract useful information from what is in common between users' profiles, their interests and preferences. In this article, we explore the role of modelling sequential behaviour patterns of users in augmenting social navigation in thematic landscapes. In particular, we compare and analyse the trails of individual users in thematic spaces along with their cognitive ability measures. We are interested in whether such trails can provide useful guidance for social navigation if they are embedded in a visual–spatial environment. Furthermore, we are interested in whether such information can help users to learn from each other, for example, from the ones who have been successful in retrieving documents. In this article, we first describe how users' trails in sessions of an experimental study of visual information retrieval can be characterized by Hidden Markov Models. Trails of users with the most successful retrieval performance are used to estimate parameters of such models. Optimal virtual trails generated from the models are visualized and animated as if they were actual trails of individual users in order to highlight behavioural patterns that may foster social navigation. The findings of the research will provide direct input to the design of social navigation systems as well as to enrich theories of social navigation in a wider context. These findings will lead to the further development and consolidation of a tightly coupled paradigm of spatial, semantic and social navigation

Development of Distributed Research Center for analysis of regional climatic and environmental changes

We present an approach and first results of a collaborative project being carried out by a joint team of researchers from the Institute of Monitoring of Climatic and Ecological Systems, Russia and Earth Systems Research Center UNH, USA. Its main objective is development of a hardware and software platform prototype of a Distributed Research Center (DRC) for monitoring and projecting of regional climatic and environmental changes in the Northern extratropical areas. The DRC should provide the specialists working in climate related sciences and decision-makers with accurate and detailed climatic characteristics for the selected area and reliable and affordable tools for their in-depth statistical analysis and studies of the effects of climate change. Within the framework of the project, new approaches to cloud processing and analysis of large geospatial datasets (big geospatial data) inherent to climate change studies are developed and deployed on technical platforms of both institutions. We discuss here the state of the art in this domain, describe web based information-computational systems developed by the partners, justify the methods chosen to reach the project goal, and briefly list the results obtained so far

Training of Crisis Mappers and Map Production from Multi-sensor Data: Vernazza Case Study (Cinque Terre National Park, Italy)

This aim of paper is to presents the development of a multidisciplinary project carried out by the cooperation between Politecnico di Torino and ITHACA (Information Technology for Humanitarian Assistance, Cooperation and Action). The goal of the project was the training in geospatial data acquiring and processing for students attending Architecture and Engineering Courses, in order to start up a team of "volunteer mappers". Indeed, the project is aimed to document the environmental and built heritage subject to disaster; the purpose is to improve the capabilities of the actors involved in the activities connected in geospatial data collection, integration and sharing. The proposed area for testing the training activities is the Cinque Terre National Park, registered in the World Heritage List since 1997. The area was affected by flood on the 25th of October 2011. According to other international experiences, the group is expected to be active after emergencies in order to upgrade maps, using data acquired by typical geomatic methods and techniques such as terrestrial and aerial Lidar, close-range and aerial photogrammetry, topographic and GNSS instruments etc.; or by non conventional systems and instruments such us UAV, mobile mapping etc. The ultimate goal is to implement a WebGIS platform to share all the data collected with local authorities and the Civil Protectio