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  1. Article ; Online: Ali-Bey - an open collaborative georeferencing web application

    Arnald Marcer / Agustí Escobar / Víctor Garcia-Font / Francesc Uribe

    Biodiversity Data Journal, Vol 10, Iss , Pp 1-

    2022  Volume 13

    Abstract: Georeferencing preserved specimens represents a major effort at the Museu de Ciències Naturals de Barcelona (MCNB), given the available resources and limited staff that can be allocated to the task. Georeferencing is a labour-intensive and hard-to- ... ...

    Abstract Georeferencing preserved specimens represents a major effort at the Museu de Ciències Naturals de Barcelona (MCNB), given the available resources and limited staff that can be allocated to the task. Georeferencing is a labour-intensive and hard-to-automate task that requires software tools that can help in making it as efficient as possible. The tool we present, Ali-Bey, has been slowly developed over 15 years and its functionalities have been gradually built in a process of development, testing, use in production and refinement, rather than as a single development cycle out of a comprehensive specifications requirement document. At the start, the MCNB could not find a tool that fully satisfied the requirements listed as essential and made the decision to develop a custom tool. At the end, the initiative has proved successful since it has delivered a new georeferencing tool that meets the MCNB's needs, all in a context of yearly scarce availability of funds. The tool has been gradually matured and developed over the years, in line with the scarce financing. Only recently, after reaching a notable set of novel features, we considered to release it as an open-source project. The MCNB has supported its development up until this date and decided to open it in order to give the NHC community the opportunity to contribute to its development.We present the software tool Ali-Bey that provides new functionality for the georeferencing of specimens in Natural History Collections, namely the possibility of cooperation between different institutions, the traceability of georeferences and the capability of managing different versions of a same site name, namely for historical reasons. The tool is an open-source web application implemented in Python and the Django framework that leverages other commonly-used specialised geodatabase and map server tools. An API provides access to the geodatabase to externally-developed tools. In addition, for an easy installation, the tool is provided as a multi-container Docker application.
    Keywords georeferencing ; web application ; site name version ; Biology (General) ; QH301-705.5
    Subject code 020
    Language English
    Publishing date 2022-04-01T00:00:00Z
    Publisher Pensoft Publishers
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Deciphering the adjustment between environment and life history in annuals

    Esperanza Manzano-Piedras / Arnald Marcer / Carlos Alonso-Blanco / F Xavier Picó

    PLoS ONE, Vol 9, Iss 2, p e

    lessons from a geographically-explicit approach in Arabidopsis thaliana.

    2014  Volume 87836

    Abstract: The role that different life-history traits may have in the process of adaptation caused by divergent selection can be assessed by using extensive collections of geographically-explicit populations. This is because adaptive phenotypic variation shifts ... ...

    Abstract The role that different life-history traits may have in the process of adaptation caused by divergent selection can be assessed by using extensive collections of geographically-explicit populations. This is because adaptive phenotypic variation shifts gradually across space as a result of the geographic patterns of variation in environmental selective pressures. Hence, large-scale experiments are needed to identify relevant adaptive life-history traits as well as their relationships with putative selective agents. We conducted a field experiment with 279 geo-referenced accessions of the annual plant Arabidopsis thaliana collected across a native region of its distribution range, the Iberian Peninsula. We quantified variation in life-history traits throughout the entire life cycle. We built a geographic information system to generate an environmental data set encompassing climate, vegetation and soil data. We analysed the spatial autocorrelation patterns of environmental variables and life-history traits, as well as the relationship between environmental and phenotypic data. Almost all environmental variables were significantly spatially autocorrelated. By contrast, only two life-history traits, seed weight and flowering time, exhibited significant spatial autocorrelation. Flowering time, and to a lower extent seed weight, were the life-history traits with the highest significant correlation coefficients with environmental factors, in particular with annual mean temperature. In general, individual fitness was higher for accessions with more vigorous seed germination, higher recruitment and later flowering times. Variation in flowering time mediated by temperature appears to be the main life-history trait by which A. thaliana adjusts its life history to the varying Iberian environmental conditions. The use of extensive geographically-explicit data sets obtained from field experiments represents a powerful approach to unravel adaptive patterns of variation. In a context of current global warming, ...
    Keywords Medicine ; R ; Science ; Q
    Subject code 333
    Language English
    Publishing date 2014-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article: Genome‐wide signatures of flowering adaptation to climate temperature: Regional analyses in a highly diverse native range of Arabidopsis thaliana

    Tabas‐Madrid, Daniel / Alberto Pascual‐Montano / Arnald Marcer / Belén Méndez‐Vigo / Carlos Alonso‐Blanco / Detlef Weigel / F. Xavier Picó / Noelia Arteaga

    Plant, cell and environment. 2018 Aug., v. 41, no. 8

    2018  

    Abstract: Current global change is fueling an interest to understand the genetic and molecular mechanisms of plant adaptation to climate. In particular, altered flowering time is a common strategy for escape from unfavourable climate temperature. In order to ... ...

    Abstract Current global change is fueling an interest to understand the genetic and molecular mechanisms of plant adaptation to climate. In particular, altered flowering time is a common strategy for escape from unfavourable climate temperature. In order to determine the genomic bases underlying flowering time adaptation to this climatic factor, we have systematically analysed a collection of 174 highly diverse Arabidopsis thaliana accessions from the Iberian Peninsula. Analyses of 1.88 million single nucleotide polymorphisms provide evidence for a spatially heterogeneous contribution of demographic and adaptive processes to geographic patterns of genetic variation. Mountains appear to be allele dispersal barriers, whereas the relationship between flowering time and temperature depended on the precise temperature range. Environmental genome‐wide associations supported an overall genome adaptation to temperature, with 9.4% of the genes showing significant associations. Furthermore, phenotypic genome‐wide associations provided a catalogue of candidate genes underlying flowering time variation. Finally, comparison of environmental and phenotypic genome‐wide associations identified known (Twin Sister of FT, FRIGIDA‐like 1, and Casein Kinase II Beta chain 1) and new (Epithiospecifer Modifier 1 and Voltage‐Dependent Anion Channel 5) genes as candidates for adaptation to climate temperature by altered flowering time. Thus, this regional collection provides an excellent resource to address the spatial complexity of climate adaptation in annual plants.
    Keywords alleles ; annuals ; Arabidopsis thaliana ; climatic factors ; flowering date ; genetic variation ; genomics ; global change ; mountains ; non-specific serine/threonine protein kinase ; phenotype ; plant adaptation ; single nucleotide polymorphism ; temperature ; temporal variation ; Iberian Peninsula
    Language English
    Dates of publication 2018-08
    Size p. 1806-1820.
    Publishing place John Wiley & Sons, Ltd
    Document type Article
    Note JOURNAL ARTICLE
    ZDB-ID 391893-2
    ISSN 1365-3040 ; 0140-7791
    ISSN (online) 1365-3040
    ISSN 0140-7791
    DOI 10.1111/pce.13189
    Database NAL-Catalogue (AGRICOLA)

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  4. Article ; Online: Community engagement

    Dimitrios Koureas / Christos Arvanitidis / Lee Belbin / Walter Berendsohn / Christian Damgaard / Quentin Groom / Anton Güntsch / Gregor Hagedorn / Alex Hardisty / Donald Hobern / Arnald Marcer / Daniel Mietchen / David Morse / Matthias Obst / Lyubomir Penev / Lars Pettersson / Soraya Sierra / Vincent Smith / Rutger Vos

    Research Ideas and Outcomes, Vol 2, Iss , Pp 1-

    The ‘last mile’ challenge for European research e-infrastructures

    2016  Volume 7

    Abstract: Europe is building its Open Science Cloud; a set of robust and interoperable e-infrastructures with the capacity to provide data and computational solutions through cloud-based services. The development and sustainable operation of such e-infrastructures ...

    Abstract Europe is building its Open Science Cloud; a set of robust and interoperable e-infrastructures with the capacity to provide data and computational solutions through cloud-based services. The development and sustainable operation of such e-infrastructures are at the forefront of European funding priorities. The research community, however, is still reluctant to engage at the scale required to signal a Europe-wide change in the mode of operation of scientific practices. The striking differences in uptake rates between researchers from different scientific domains indicate that communities do not equally share the benefits of the above European investments. We highlight the need to support research communities in organically engaging with the European Open Science Cloud through the development of trustworthy and interoperable Virtual Research Environments. These domain-specific solutions can support communities in gradually bridging technical and socio-cultural gaps between traditional and open digital science practice, better diffusing the benefits of European e-infrastructures.
    Keywords e-infrastructure ; Virtual Research Environment ; Science ; Q
    Subject code 020
    Language English
    Publishing date 2016-07-01T00:00:00Z
    Publisher Pensoft Publishers
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: Unifying European Biodiversity Informatics (BioUnify)

    Dimitrios Koureas / Alex Hardisty / Rutger Vos / Donat Agosti / Christos Arvanitidis / Peter Bogatencov / Pier Luigi Buttigieg / Yde de Jong / Ferenc Horvath / Georgios Gkoutos / Quentin Groom / Tomas Kliment / Urmas Kõljalg / Ioannis Manakos / Arnald Marcer / Karol Marhold / David Morse / Patricia Mergen / Lyubomir Penev /
    Lars Pettersson / Jens-Christian Svenning / Anton van de Putte / Vincent Smith

    Research Ideas and Outcomes, Vol 2, Iss , Pp 1-

    2016  Volume 23

    Keywords COST Action ; Biodiversity Informatics ; Environm ; Science ; Q
    Language English
    Publishing date 2016-01-01T00:00:00Z
    Publisher Pensoft Publishers
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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