BioClimate: a Science Gateway for Climate Change and Biodiversity research in the EUBrazilCloudConnect project

[EN] Climate and biodiversity systems are closely linked across a wide range of scales. To better understand the mutual interaction between climate change and biodiversity there is a strong need for multidisciplinary skills, scientific tools, and access to a large variety of heterogeneous, often distributed, data sources. Related to that, the EUBrazilCloudConnect project provides a user-oriented research environment built on top of a federated cloud infrastructure across Europe and Brazil, to serve key needs in different scientific domains, which is validated through a set of use cases. Among them, the most data-centric one is focused on climate change and biodiversity research. As part of this use case, the BioClimate Science Gateway has been implemented to provide end-users transparent access to (i) a highly integrated user-friendly environment, (ii) a large variety of data sources, and (iii) different analytics & visualization tools to serve a large spectrum of users needs and requirements. This paper presents a complete overview of BioClimate and the related scientific environment, in particular its Science Gateway, delivered to the end-user community at the end of the project.This work was supported by the EU FP7 EUBrazilCloudConnect Project (Grant Agreement 614048), and CNPq/Brazil (Grant Agreement no 490115/2013-6).Fiore, S.; Elia, D.; Blanquer Espert, I.; Brasileiro, FV.; Nuzzo, A.; Nassisi, P.; Rufino, LAA.... (2019). BioClimate: a Science Gateway for Climate Change and Biodiversity research in the EUBrazilCloudConnect project. Future Generation Computer Systems. 94:895-909. https://doi.org/10.1016/j.future.2017.11.034S8959099

Locating Pleistocene Refugia: Comparing Phylogeographic and Ecological Niche Model Predictions

Ecological niche models (ENMs) provide a means of characterizing the spatial distribution of suitable conditions for species, and have recently been applied to the challenge of locating potential distributional areas at the Last Glacial Maximum (LGM) when unfavorable climate conditions led to range contractions and fragmentation. Here, we compare and contrast ENM-based reconstructions of LGM refugial locations with those resulting from the more traditional molecular genetic and phylogeographic predictions. We examined 20 North American terrestrial vertebrate species from different regions and with different range sizes for which refugia have been identified based on phylogeographic analyses, using ENM tools to make parallel predictions. We then assessed the correspondence between the two approaches based on spatial overlap and areal extent of the predicted refugia. In 14 of the 20 species, the predictions from ENM and predictions based on phylogeographic studies were significantly spatially correlated, suggesting that the two approaches to development of refugial maps are converging on a similar result. Our results confirm that ENM scenario exploration can provide a useful complement to molecular studies, offering a less subjective, spatially explicit hypothesis of past geographic patterns of distribution

Building Networks to Promote Knowledge of Brazil’s Biodiversity: The experience of the INCT - Virtual Herbarium

The Botanical Society of Brazil (SBB) for many years discussed the need to improve the nation’s herbarium collections, by providing training and educating botanists as specialists in plant and fungal taxonomy. It was in this context that an audacious project was developed, which envisaged personnel training for studies in plant and fungal diversity (particularly taxonomy and curation of collections) and the organization and online delivery of the label data of plant and fungal specimens from the herbaria of Brazil - the National Institute of Science and Technology (INCT) Virtual Herbarium.The INCT-Virtual Herbarium had the benefit of the expertise from existing initiatives which, when brought together, made its development possible within a short period of time. These initiatives included: the Herbaria Network of SBB; the Herbarium Network of the Northeast; the Brazilian National Research and Education Network (RNP); and the Reference Center for Environmental Information (CRIA), responsible for the development and maintenance of the speciesLink Network. When it began in 2009, the INCT-Virtual Herbarium brought together 25 Brazilian herbaria sharing 48 plant and fungal databases online (one herbarium can share more than one data set, e.g., plants, fungi, carpological collection), and two US herbaria. Today, the network includes 140 Brazilian herbaria and 25 herbaria from other countries, which hold collections originating from Brazil, thus creating a national virtual herbarium with 190 data sets, sharing over 11 million data records and over 4.5 million associated images.The INCT-Virtual Herbarium is not only a data aggregator, but also an active and integrated community with common objectives such as: free sharing of good quality data; fomenting the important role of herbaria in documenting knowledge of the flora and funga, training, and developing tools and systems to improve data quality and in identifying data and knowledge gaps to help plan new collecting expeditions.The INCT-Virtual Herbarium chose to adopt a collegiate management model, led by a Management Committee of six members from different institutions, together with coordinators of the following subject areas: flowering plant taxonomy, taxonomy of cryptogams, personnel training, liaison with herbaria, product research, and online information systems. A variety of indicators and applications were developed to make online monitoring of activities viable and these are all freely available to anyone interested. Not only the Management Committee but also each partner herbarium can follow the evolution of the INCT, as well as that of each herbarium, in qualitative and quantitative terms.Besides the scientific community, the INCT reaches the general public and decision-makers, providing information that has improved the understanding of preservation and conservation of Brazil’s biological heritage, represented by the botanical and mycological collections. The INCT Virtual Herbarium adopted the speciesLink platform as the basis for its information system. This platform began its development in 2001 with support from the São Paulo Research Foundation (FAPESP), and in 2008 was the only network in Brazil with national scope and international recognition.Some initial decisions on the architecture of the network, which would serve the INCT-Virtual Herbarium were fundamental to its success: the use of international standards and protocols; the concept of minimum interference with the collections, where each data provider could retain sensitive data, having full control of its data; the acceptance of the data without a quality filter, as the network has important tools to identify errors; any changes or corrections are made only by those responsible for the curation of the data; recognition and credit awarded to each and every participant.The speciesLink network uses the Darwin Core data standard (Wieczorek et al. 2012) and participated actively with the Global Biodiversity Information Facility (GBIF) and other networks in developing the DiGIR protocol (Distributed Generic Information Retrieval) and its later evolution the TAPIR protocol (TDWG Access Protocol for Information Retrieval). The use of these standards and protocols facilitated the process of repatriating collection data of Brazilian material deposited in herbaria in other countries.In 2015 the INCT Virtual Herbarium started to transfer its data sets to GBIF and SiBBr, the Brazilian Biodiversity Information System and the Brazilian node of GBIF. These data sets are updated every month, but their updating in SiBBr and GBIF depends on indexing actions of these networks. The development of the INCT-Virtual Herbarium network has shown that a large community of widely dispersed scientists can work together around an important objective, providing Brazil's biodiversity data, and benefiting the whole community

Big data analytics for climate change and biodiversity in the EUBrazilCC federated cloud infrastructure

The analysis of large volumes of data is key for knowledge discovery in several scientific domains such as climate, astrophysics, life sciences among others. It requires a large set of computational and storage resources, as well as flexible and efficient software solutions able to dynamically exploit the available infrastructure and address issues related to data volume, distribution, velocity and heterogeneity. This paper presents a data-driven and cloud-based use case implemented in the context of the EUBrazilCC project for the analysis of climate change and biodiversity data. The use case architecture and main components, as well as a Platform as a Service (PaaS) framework for big data analytics named PDAS, together with its elastic deployment in the EUBrazilCC federated cloud infrastructure are presented and discussed in detail