Cloud computing in a distributed e‐infrastructure using the web processing service standard

Coro, Gianpaolo; Panichi, Giancarlo; Scarponi, Paolo; Pagano, Pasquale

doi:10.1002/cpe.4219

Cited by 31 publications

(23 citation statements)

References 67 publications

(98 reference statements)

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“…In this section we will briefly describe only the two services we exploit the capabilities of during our activity, namely the DataMiner and the D4Science Data Catalogue. DataMiner : DataMiner is an open source computational system which is able to interoperate with the other services of the D4Science Research e-Infrastructure [2] . It uses the Web Processing Service (WPS, see [4] ) standard to publish/describe the hosted processes and produces a provenance XML file for each experiment in the Prov-O ontological format [7] .…”

Section: Experimental Design Materials and Methodsmentioning

confidence: 99%

A collection of Aquamaps native layers in NetCDF format

2018

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Many research communities working in biology and related fields are deeply interested in having a wide collection of environmental and species distribution data. Obviously, for these communities to be able to carry out their studies in a fast and efficient manner, these data need to be well organized, meticulously described and possibly represented in a standard format that allows for a direct usage. In fact, being the final goal of these communities to extract information from the data and applying some kind of data processing workflows, cutting down the data preparation and preprocessing time is key. This is the main reason that triggered the activity presented in this paper that aimed at converting the whole collection of 10,385 species distribution models published by the Aquamaps consortium (Aquamaps Native Distributions) into NetCDF files, creating a re-usable, portable and self-describing collection of native habitat datasets.

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Section: Experimental Design Materials and Methodsmentioning

confidence: 99%

A collection of Aquamaps native layers in NetCDF format

2018

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“…The D4Science e‐Infrastructure hosts a cloud computing platform named DataMiner, an open‐source system developed to meet < Science criteria of re‐usability, reproducibility, and repeatability of experiments. It relies on the Web Processing Service standard (WPS) to represent processes.…”

Section: Methodsmentioning

confidence: 99%

Reconstructing 3D virtual environments within a collaborative e‐infrastructure

Coro

Palma

Ellenbroek

et al. 2018

Concurrency and Computation

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Summary Sets of two‐dimensional images are insufficient to capture the development in time and space of three‐dimensional structures. The 2D “flattening” of photographs results in a significant loss of features especially if the photos were taken by one person. Automatically collecting and aligning photos in order to render 3D structures from 2D images without specialised equipment is currently a complex process that requires specialist knowledge with often limited results. In this paper, an Open Science oriented workflow is proposed where an on‐line file system is used to share photos of an object or an environment and to produce a virtual reality scene as a navigable 3D reconstruction that can be shared with other people. Our workflow is based on a distributed e‐Infrastructure and overcomes common limitations of other approaches by having all the used technology integrated on the same platform and by not requiring specialist knowledge. A performance evaluation of the 3D reconstruction process embedded in the workflow is reported against a commercial software and an open‐source software in terms of computational efficiency and reconstruction accuracy, and three marine science use cases are reported to show potential applications of the workflow.

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“…Data of number of dives per reef site were not included in the analysis. The approach, which involves a series of steps performed sequentially to the harmonized data was applied at seascape scale and carried out using the DataMiner system of the D4Science e-Infrastructure (Italy) [61,62].…”

Section: Study Area and Experimental Designmentioning

confidence: 99%

Quantifying Coral Reef Composition of Recreational Diving Sites: A Structure from Motion Approach at Seascape Scale

et al. 2019

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Recreational diving is known to have both direct and indirect impacts on coral habitats. Direct impacts include increasing sedimentation, breaks and diseases that lead to a decrease in the richness and abundances of hard corals. Indirect impacts include urban development, land management and sewage disposal. The ecological effects of scuba diving on the spatial composition metrics of reef benthic communities are less well studied, and they have not been investigated at seascape scale. In this study, we combine orthomosaics derived from Structure from Motion (SfM) photogrammetry and data-mining techniques to study the spatial composition of reef benthic communities of recreational diving sites at seascape scale (>25 m 2 ). The study focuses on the case study area of Ponta do Ouro Partial Marine Reserve (Mozambique). Results showed that scuba-diving resistant taxa (i.e., sponges and algae) were abundant at small (>850 m 2 ) and highly dived sites (>3000 dives yr − 1 ), characterized by low diversity and density, and big organisms with complex shapes. Fragile taxa (i.e., Acropora spp.) were abundant at low (365 dives yr − 1 ) and moderately dived sites (1000–3000 dives yr − 1 ) where the greater depth and wider coral reef surfaces attenuate the abrasive effect of waves and re-suspended sediments. Highest taxa diversity and density, and lowest abundance of resistant taxa were recorded at large (>2000 m 2 ) and rarely dived sites. This study highlights the potential applications for a photogrammetric approach to support monitoring programs at Ponta do Ouro Partial Marine Reserve (Mozambique), and provides some insight to understand the influence of scuba diving on benthic communities.

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Cloud computing in a distributed e‐infrastructure using the web processing service standard

Cited by 31 publications

References 67 publications

A collection of Aquamaps native layers in NetCDF format

A collection of Aquamaps native layers in NetCDF format

Reconstructing 3D virtual environments within a collaborative e‐infrastructure

Quantifying Coral Reef Composition of Recreational Diving Sites: A Structure from Motion Approach at Seascape Scale

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