Andréa De Bono

MetaLook: a 3D visualisation software for marine ecological genomics

BackgroundMarine ecological genomics can be defined as the application of genomic sciences to understand the structure and function of marine ecosystems. In this field of research, the analysis of genomes and metagenomes of environmental relevance must take into account the corresponding habitat (contextual) data, e.g. water depth, physical and chemical parameters. The creation of specialised software tools and databases is requisite to allow this new kind of integrated analysis.ResultsWe implemented the MetaLook software for visualisation and analysis of marine ecological genomic and metagenomic data with respect to habitat parameters. MetaLook offers a three-dimensional user interface to interactively visualise DNA sequences on a world map, based on a centralised georeferenced database. The user can define environmental containers to organise the sequences according to different habitat criteria. To find similar sequences, the containers can be queried with either genes from the georeferenced database or user-imported sequences, using the BLAST algorithm. This allows an interactive assessment of the distribution of gene functions in the environment.ConclusionMetaLook allows scientists to investigate sequence data in their environmental context and to explore correlations between genes and habitat parameters. This software is a step towards the creation of specialised tools to study constrained distributions and habitat specificity of genes correlated with specific processes.MetaLook is available at: http://www.megx.net/metalook

Building an Earth Observations Data Cube: lessons learned from the Swiss Data Cube (SDC) on generating Analysis Ready Data (ARD)

Abstract Pressures on natural resources are increasing and a number of challenges need to be overcome to meet the needs of a growing population in a period of environmental variability. Some of these environmental issues can be monitored using remotely sensed Earth Observations (EO) data that are increasingly available from a number of freely and openly accessible repositories. However, the full information potential of EO data has not been yet realized. They remain still underutilized mainly because of their complexity, increasing volume, and the lack of efficient processing capabilities. EO Data Cubes (DC) are a new paradigm aiming to realize the full potential of EO data by lowering the barriers caused by these Big data challenges and providing access to large spatio-temporal data in an analysis ready form. Systematic and regular provision of Analysis Ready Data (ARD) will significantly reduce the burden on EO data users. Nevertheless, ARD are not commonly produced by data providers and therefore getting uniform and consistent ARD remains a challenging task. This paper presents an approach to enable rapid data access and pre-processing to generate ARD using interoperable services chains. The approach has been tested and validated generating Landsat ARD while building the Swiss Data Cube.

A web platform for landuse, climate, demography, hydrology and beach erosion in the Black Sea catchment

The Black Sea catchment (BSC) is facing important demographic, climatic and landuse changes that may increase pollution, vulnerability and scarcity of water resources, as well as beach erosion through sea level rise. Limited access to reliable time-series monitoring data from environmental, statistical, and socio-economical sources is a major barrier to policy development and decision-making. To address these issues, a web-based platform was developed to enable discovery and access to key environmental information for the region. This platform covers: landuse, climate, and demographic scenarios; hydrology and related water vulnerability and scarcity; as well as beach erosion. Each data set has been obtained with state-of-the-art modelling tools from available monitoring data using appropriate validation methods. These analyses were conducted using global and regional data sets. The data sets are intended for national to regional assessments, for instance for prioritizing environmental protection projects and investments. Together they form a unique set of information, which lay out future plausible change scenarios for the BSC, both for scientific and policy purposes.