Gregory Giuliani

WPS mediation: An approach to process geospatial data on different computing backends

The OGC Web Processing Service (WPS) specification allows generating information by processing distributed geospatial data made available through Spatial Data Infrastructures (SDIs). However, current SDIs have limited analytical capacities and various problems emerge when trying to use them in data and computing-intensive domains such as environmental sciences. These problems are usually not or only partially solvable using single computing resources. Therefore, the Geographic Information (GI) community is trying to benefit from the superior storage and computing capabilities offered by distributed computing (e.g., Grids, Clouds) related methods and technologies. Currently, there is no commonly agreed approach to grid-enable WPS. No implementation allows one to seamlessly execute a geoprocessing calculation following user requirements on different computing backends, ranging from a stand-alone GIS server up to computer clusters and large Grid infrastructures. Considering this issue, this paper presents a proof of concept by mediating different geospatial and Grid software packages, and by proposing an extension of WPS specification through two optional parameters. The applicability of this approach will be demonstrated using a Normalized Difference Vegetation Index (NDVI) mediated WPS process, highlighting benefits, and issues that need to be further investigated to improve performances.

Hospital Effluents Are One of Several Sources of Metal, Antibiotic Resistance Genes, and Bacterial Markers Disseminated in Sub-Saharan Urban Rivers

Data concerning the occurrence of emerging biological contaminants such as antibiotic resistance genes (ARGs) and fecal indicator bacteria (FIB) in aquatic environments in Sub-Saharan African countries is limited. On the other hand, antibiotic resistance remains a worldwide problem which may pose serious potential risks to human and animal health. Consequently, there is a growing number of reports concerning the prevalence and dissemination of these contaminants into various environmental compartments. Sediments provide the opportunity to reconstruct the pollution history and evaluate impacts so this study investigates the abundance and distribution of toxic metals, FIB, and ARGs released from hospital effluent wastewaters and their presence in river sediments receiving systems. ARGs (blaTEM, blaCTX-M, blaSHV, and aadA), total bacterial load, and selected bacterial species FIB [Escherichia coli, Enterococcus (ENT)] and species (Psd) were quantified by targeting species specific genes using quantitative PCR (qPCR) in total DNA extracted from the sediments recovered from 4 hospital outlet pipes (HOP) and their river receiving systems in the City of Kinshasa in the Democratic Republic of the Congo. The results highlight the great concentration of toxic metals in HOP, reaching the values (in mg kg−1) of 47.9 (Cr), 213.6 (Cu), 1434.4 (Zn), 2.6 (Cd), 281.5 (Pb), and 13.6 (Hg). The results also highlight the highest (P < 0.05) values of 16S rRNA, FIB, and ARGs copy numbers in all sampling sites including upstream (control site), discharge point, and downstream of receiving rivers, indicating that the hospital effluent water is not an exclusive source of the biological contaminants entering the urban rivers. Significant correlation were observed between (i) all analyzed ARGs and total bacterial load (16S rRNA) 0.51 to 0.72 (p < 0.001, n = 65); (ii) ARGs (except blaTEM) and FIB and Psd 0.57 < r < 0.82 (p < 0.001, n = 65); and (iii) ARGs (except blaTEM) and toxic metals (Cd, Cr, Cu, and Zn) 0.44 to 0.72, (p < 0.001, n = 65). These findings demonstrate that several sources including hospital and urban wastewaters contribute to the spread of toxic metals and biological emerging contaminants in aquatic ecosystems.

Leachates draining from controlled municipal solid waste landfill: Detailed geochemical characterization and toxicity tests

Management of municipal solid wastes in many countries consists of waste disposal into landfill without treatment or selective collection of solid waste fractions including plastics, paper, glass, metals, electronic waste, and organic fraction leading to the unsolved problem of contamination of numerous ecosystems such as air, soil, surface, and ground water. Knowledge of leachate composition is critical in risk assessment of long-term impact of landfills on human health and the environment as well as for prevention of negative outcomes. The research presented in this paper investigates the seasonal variation of draining leachate composition and resulting toxicity as well as the contamination status of soil/sediment from lagoon basins receiving leachates from landfill in Mpasa, a suburb of Kinshasa in the Democratic Republic of the Congo. Samples were collected during the dry and rainy seasons and analyzed for pH, electrical conductivity, dissolved oxygen, soluble ions, toxic metals, and were then subjected to toxicity tests. Results highlight the significant seasonal difference in leachate physicochemical composition. Affected soil/sediment showed higher values for toxic metals than leachates, indicating the possibility of using lagoon system for the purification of landfill leachates, especially for organic matter and heavy metal sedimentation. However, the ecotoxicity tests demonstrated that leachates are still a significant source of toxicity for terrestrial and benthic organisms. Therefore, landfill leachates should not be discarded into the environment (soil or surface water) without prior treatment. Interest in the use of macrophytes in lagoon system is growing and toxic metal retention in lagoon basin receiving systems needs to be fully investigated in the future. This study presents useful tools for evaluating landfill leachate quality and risk in lagoon systems which can be applied to similar environmental compartments.

Bringing GEOSS Services into Practice: A Capacity Building Resource on Spatial Data Infrastructures (SDI)

Data discoverability, accessibility, and integration are frequent barriers for scientists and a major obstacle for favorable results on environmental research. To tackle this issue, the Group on Earth Observations (GEO) is leading the development of the Global Earth Observation System of Systems (GEOSS), a voluntary effort that connects Earth Observation resources world-wide, acting as a gateway between producers and users of environmental data. GEO recognizes the importance of capacity building and education to reach large adoption, acceptance and commitment on data sharing principles to increase the capacity to access and use Earth Observations data. This article presents “Bringing GEOSS services into practice” (BGSIP), an integrated set of teaching material and software to facilitate the publication and use of environmental data through standardized discovery, view, download, and processing services, further facilitating the registration of data into GEOSS. So far, 520 participants in 10 countries have been trained using this material, leading to numerous Spatial Data Infrastructure implementations and 1,000 tutorial downloads. This workshop lowers the entry barriers for both data providers and users, facilitates the development of technical skills, and empowers people.

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

Software Platform Interoperability Throughout EnviroGRIDS Portal

The Black Sea Catchment area is well known for subjects such as ecologically unsustainable development or inadequate resource management. The EnviroGRIDS project addresses these issues by using emerging information technologies. The enviroGRIDS Web Portal allows the users to access the geospatial functionality given by Web infrastructure, and to high power computation resources given by Grid infrastructure. The Black Sea Catchment Observation System portal provides a single point of access to the enviroGRIDS applications and tools. Both the vertical and horizontal interoperability are available between the platforms and applications throughout the portal. The horizontal interoperability is accomplished through services, meaning the applications are working together by the exposed services. The vertical interoperability is supported by the communication between the layers of end user applications, Web infrastructure, and Grid infrastructure. The basic solution of interoperability is accomplished by services, messages, and data. The paper highlights the solutions developed by the Black Sea Catchment Observation System portal to support various types of interoperability between the modules of geospatial data management, hydrological model calibration and running, satellite image processing, spatial data visualization, and virtual training center.

Facilitating the production of ISO-compliant metadata of geospatial datasets

Abstract Metadata are recognized as an essential element to enable efficient and effective discovery of geospatial data published in spatial data infrastructures (SDI). However, metadata production is still perceived as a complex, tedious and time-consuming task. This typically results in little metadata production and can seriously hinder the objective of facilitating data discovery. In response to this issue, this paper presents a proof of concept based on an interoperable workflow between a data publication server and a metadata catalog to automatically generate ISO-compliant metadata. The proposed approach facilitates metadata creation by embedding this task in daily data management workflows; ensures that data and metadata are permanently up-to-date; significantly reduces the obstacles of metadata production; and potentially facilitates contributions to initiatives like the Global Earth Observation System of Systems (GEOSS) by making geospatial resources discoverable.

An interoperable cloud-based scientific GATEWAY for NDVI time series analysis

Processing of high-resolution time series satellite images typically requires a large amount of computational resources and time. We introduce here a scientific gateway for computing the Normalized Difference Vegetation Index (NDVI) time series data. Based on a distributed workflow using the Web Processing Service (WPS) standard, the gateway aims to be completely interoperable with other standardized tools. The availability of this gateway may help researchers to acquire knowledge of land cover changes more efficiently over very large spatial and temporal extents, which is especially important in the context of Armenia for which timely decision-making is needed. A scientific gateway for computing the NDVI time series data based on a distributed workflow using the WPS standard.An optimal NDVI times series geoprocessing services based on cloud infrastructures.Experimental results in the study area that include some part of the territory of Armenia.

Grid based data processing tools and applications for black sea catchment basin

This paper highlights the main functionalities, tools and applications provided by the BSC-OS portal, developed through the enviroGRIDS project. The presentation highlights the main issues of interoperability between geospatial and grid infrastructures, and between different platforms supporting the Earth Science oriented tools and applications. Other subjects such as spatial data management, hydrological model calibration, environmental scenario development and running, satellite image classification and data mining, tools and applications for data reporting and scenarios visualization, and development of Earth Science oriented training materials, are approached by the BSC-OS portal development.

Assessing the Dynamics of Organic Aerosols over the North Atlantic Ocean

The influence of aerosols on climate is highly dependent on the particle size distribution, concentration, and composition. In particular, the latter influences their ability to act as cloud condensation nuclei, whereby they impact cloud coverage and precipitation. Here, we simultaneously measured the concentration of aerosols from sea spray over the North Atlantic on board the exhaust-free solar-powered vessel “PlanetSolar”, and the sea surface physico-chemical parameters. We identified organic-bearing particles based on individual particle fluorescence spectra. Organic-bearing aerosols display specific spatio-temporal distributions as compared to total aerosols. We propose an empirical parameterization of the organic-bearing particle concentration, with a dependence on water salinity and sea-surface temperature only. We also show that a very rich mixture of organic aerosols is emitted from the sea surface. Such data will certainly contribute to providing further insight into the influence of aerosols on cloud formation, and be used as input for the improved modeling of aerosols and their role in global climate processes.