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Overview

This demonstration illustrates how a LifeWatch researcher can easily upload and integrate an R-based algorithm in D4science, making it available to other researches, in particular members of the VRE in which the algorithm was published. Once published, researchers can discover the algorithm and use it with their own data. It is also possible to adapt the algorithm and to share improved versions. When processing data-intensive analysis algorithms, the computation can be outsourced on federated resources, such as those provided by the EGI e-Infrastructures.

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The proposed service architecture is shown in Figure 171. It combines different infrastructures: at a lower layer is the LifeWatch RI, containing the Swedish LifeWatch Portal that provides high-quality biological data for mosquito species, and the community data repositories that preserves environmental information and a series of ecological modelling algorithms. Datasets to be exploited include species data (95,730 abundance measurements from Sweden, Denmark, and Germany for 40 disease-carrying species in 2016), and hydrological data (generated by a regional hydrological model using 15 land use types and 8 soil types).

Figure 171. Use Case Architecture includes three layers: 1) Physical Infrastructure, 2) e-Infrastructure, and 3) VRE

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The D4Science/gCube-based VRE for mosquito disease study has been set up with the support from T7.1. The interfaces are shown in Figure 12. It provides a programming environment (shown in Figure 12, b), and it allows biodiversity researchers to develop and compile own/customised analysis algorithms using R, CLI etc. A researcher can decide to share his/her data, algorithms, or workflows by publishing it in the group area (shown in Figure 12, a) that enables social communications via  messages, comments, etc.

a. VRE area for sharing data, algorithms, and workflows

1. b. VRE area for developing an analysis algorithm

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2. VRE interfaces for mosquito disease study

Advantages

Using the VRE, there is no more need for manual sharing of data and algorithms. Information is always synchronized, and data and algorithms are joined in a single place. Users can enjoy an easy and user friendly access interface. The D4Science/gCube-based VRE has an interface to EGI Cloud/HTC resources. If needed, it can outsource the computation on the large-scale e-Infrastructure that can handle computation in parallel and store and share large volumes of data.

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This demonstrator illustrates a proof of concept of the proposed architecture that uses D4Science to setup a community-centric VRE, allowing researchers to share a simple algorithm with some data and allowing running computations on EGI FedCloud e-Infrastructure. The data was gathered and produced by the involved RIs and the dynamic computation was executed on EGI Federation’s resources.

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Youtube video is at https://youtubeyoutu.com/watch?v=IBJkSys5tVoheight460be/XtcCxkFX98I

Contributors

• Baptiste Grenier, EGI, baptiste.grenier@egi.eu
• Dr Matthias Obst, Swedish Lifewatch, matthias.obst@marine.gu.se
• Dr Leonardo Candela, CNR-ISTI, leonardo.candela@isti.cnr.it
• Dr Gianpaolo Coro, CNR-ISTI, gianpaolo.coro@isti.cnr.it