Digital libraries for the preservation of research methods and associated artifacts

New digital artifacts are emerging in data-intensive science. For example, scientific workflows are executable descriptions of scientific procedures that define the sequence of computational steps in an automated data analysis, supporting reproducible research and the sharing and replication of best-practice and know-how through reuse. Workflows are specified at design time and interpreted through their execution in a variety of situations, environments, and domains. Hence it is essential to preserve both their static and dynamic aspects, along with the research context in which they are used. To achieve this, we propose the use of multidimensional digital objects (Research Objects) that aggregate the resources used and/or produced in scientific investigations, including workflow models, provenance of their executions, and links to the relevant associated resources, along with the provision of technological support for their preservation and efficient retrieval and reuse. In this direction, we specified a software architecture for the design and implementation of a Research Object preservation system, and realized this architecture with a set of services and clients, drawing together practices in digital libraries, preservation systems, workflow management, social networking and Semantic Web technologies. In this paper, we describe the backbone system of this realization, a digital library system built on top of dLibra

Molecular mechanism of calcium induced trimerization of C1q-like domain of otolin-1 from human and zebrafish

Abstract The C1q superfamily includes proteins involved in innate immunity, insulin sensitivity, biomineralization and more. Among these proteins is otolin-1, which is a collagen-like protein that forms a scaffold for the biomineralization of inner ear stones in vertebrates. The globular C1q-like domain (gC1q), which is the most conserved part of otolin-1, binds Ca2+ and stabilizes its collagen-like triple helix. The molecular details of the assembly of gC1q otolin-1 trimers are not known. Here, we substituted putative Ca2+-binding acidic residues of gC1q otolin-1 with alanine to analyse how alanine influences the formation of gC1q trimers. We used human and zebrafish gC1q otolin-1 to assess how evolutionary changes affected the function of the protein. Surprisingly, the mutated forms of gC1q otolin-1 trimerized even in the absence of Ca2+, although they were less stable than native proteins saturated with Ca2+. We also found that the zebrafish gC1q domain was less stable than the human homologue under all tested conditions and became stabilized at higher concentrations of Ca2+, which showed that specific interactions leading to the neutralization of the negative charge at the axis of a gC1q trimer by Ca2+ are required for the trimers to form. Moreover, human gC1q otolin-1 seems to be optimized to function at lower concentrations of Ca2+, which is consistent with reported Ca2+ concentrations in the endolymphs of fish and mammals. Our results allow us to explain the molecular mechanism of assembly of proteins from the C1q superfamily, the modulating role of Ca2+ and expand the knowledge of biomineralization of vertebrate inner ear stones: otoliths and otoconia

ECONOMIC EVALUATION OF SPRING WHEAT PRODUCTION TECHNOLOGY WITH DIFFERENT INTENSITY LEVELS

The aim of the study was to compare the productive and economic effects of different production intensities of spring wheat. The study was based on the results of a twoyear (2015-2016) field study, conducted at the Agricultural Experimental Station in Osiny, belonging to the Institute of Soil Science and Plant Cultivation in Pulawy. Spring wheat cultivars (Arabella and KWS Torridon) were grown using intensive and integrated technologies. The technologies studied differed in the level of mineral fertilization and chemical plant protection. The cultivation of spring wheat of the KWS Torridon cultivar according to intensive technology, as compared with cultivation under conditions of integrated technology, resulted in a significant increase in grain yield by 10.6%, respectively. On the other hand, no effect of production technology was found on the yield of the Arabella cultivar. The research showed that the technology intensity level, determined by inputs of production means, determined the structure of direct costs and profitability of spring wheat cultivars. The compared technologies ensured the profitability of spring wheat grain production. The most advantageous index of direct profitability was recorded for the Arabella cultivar grown under integrated technology

ROHub – A Digital Library for Sharing and Preserving Research Objects: Poster (Poster) - iPRES 2014 - Melbourne

ROHub is a digital library system, enhanced with Semantic Web technologies, which supports the storage, lifecycle management, sharing and preservation of research objects – semantic aggregations of related scientific resources, their annotations and research context. ROHub includes a set of features to help scientists throughout the research lifecycle to create and maintain high-quality research objects that can be interpreted and reproduced in the future, including quality assessment, evolution management, navigation through provenance information and monitoring features. It provides a set of RESTful APIs along with a Web Interface for users and developers. A demo installation is available at: www.rohub.org

scufl2-wfdesc 0.3.7

<p>This is an extension to Scufl2 which provides the export capability to wfdesc ontology from the Wf4Ever  RO wfdesc ontology.</p> <p>This is exposed as a command line tool scufl2-to-wfdesc, but can also be accessed programmatically as a plugin for the SCUFL2 API.</p

ROHub – A Digital Library for Sharing and Preserving Research Objects: Poster (Text) - iPRES 2014 - Melbourne

ROHub is a digital library system, enhanced with Semantic Web technologies, which supports the storage, lifecycle management, sharing and preservation of research objects – semantic aggregations of related scientific resources, their annotations and research context. ROHub includes a set of features to help scientists throughout the research lifecycle to create and maintain high-quality research objects that can be interpreted and reproduced in the future, including quality assessment, evolution management, navigation through provenance information and monitoring features. It provides a set of RESTful APIs along with a Web Interface for users and developers. A demo installation is available at: www.rohub.org