13,625 research outputs found
The Research Object Suite of Ontologies: Sharing and Exchanging Research Data and Methods on the Open Web
Research in life sciences is increasingly being conducted in a digital and
online environment. In particular, life scientists have been pioneers in
embracing new computational tools to conduct their investigations. To support
the sharing of digital objects produced during such research investigations, we
have witnessed in the last few years the emergence of specialized repositories,
e.g., DataVerse and FigShare. Such repositories provide users with the means to
share and publish datasets that were used or generated in research
investigations. While these repositories have proven their usefulness,
interpreting and reusing evidence for most research results is a challenging
task. Additional contextual descriptions are needed to understand how those
results were generated and/or the circumstances under which they were
concluded. Because of this, scientists are calling for models that go beyond
the publication of datasets to systematically capture the life cycle of
scientific investigations and provide a single entry point to access the
information about the hypothesis investigated, the datasets used, the
experiments carried out, the results of the experiments, the people involved in
the research, etc. In this paper we present the Research Object (RO) suite of
ontologies, which provide a structured container to encapsulate research data
and methods along with essential metadata descriptions. Research Objects are
portable units that enable the sharing, preservation, interpretation and reuse
of research investigation results. The ontologies we present have been designed
in the light of requirements that we gathered from life scientists. They have
been built upon existing popular vocabularies to facilitate interoperability.
Furthermore, we have developed tools to support the creation and sharing of
Research Objects, thereby promoting and facilitating their adoption.Comment: 20 page
Designing an automated prototype tool for preservation quality metadata extraction for ingest into digital repository
We present a viable framework for the automated extraction of preservation quality metadata, which is adjusted to meet the needs of, ingest to digital repositories. It has three distinctive features: wide coverage, specialisation and emphasis on quality. Wide coverage is achieved through the use of a distributed system of tool repositories, which helps to implement it over a broad range of document object types. Specialisation is maintained through the selection of the most appropriate metadata extraction tool for each case based on the identification of the digital object genre. And quality is sustained by introducing control points at selected stages of the workflow of the system. The integration of these three features as components in the ingest of material into digital repositories is a defining step ahead in the current quest for improved management of digital resources
Workflows and service discovery: a mobile device approach
Bioinformatics has moved from command-line standalone
programs to web-service based environments. Such trend has resulted
in an enormous amount of online resources which can be hard to find
and identify, let alone execute and exploit. Furthermore, these resources
are aimed -in general- to solve specific tasks. Usually, this tasks need to
be combined in order to achieve the desired results. In this line, finding
the appropriate set of tools to build up a workflow to solve a problem
with the services available in a repository is itself a complex exercise. Issues
such as services discovering, composition and representation appear.
On the technological side, mobile devices have experienced an incredible
growth in the number of users and technical capabilities. Starting from
this reality, in the present paper, we propose a solution for service discovering
and workflow generation while distinct approaches of representing
workflows in a mobile environment are reviewed and discussed. As a
proof of concept, a specific use case has been developed: we have embedded
an expanded version of our Magallanes search engine into mORCA,
our mobile client for bioinformatics. Such composition delivers a powerful
and ubiquitous solution that provides the user with a handy tool for
not only generate and represent workflows, but also services, data types,
operations and service types discoveryUniversidad de Málaga. Campus de Excelencia Internacional AndalucĂa Tech
AiiDA: Automated Interactive Infrastructure and Database for Computational Science
Computational science has seen in the last decades a spectacular rise in the
scope, breadth, and depth of its efforts. Notwithstanding this prevalence and
impact, it is often still performed using the renaissance model of individual
artisans gathered in a workshop, under the guidance of an established
practitioner. Great benefits could follow instead from adopting concepts and
tools coming from computer science to manage, preserve, and share these
computational efforts. We illustrate here our paradigm sustaining such vision,
based around the four pillars of Automation, Data, Environment, and Sharing. We
then discuss its implementation in the open-source AiiDA platform
(http://www.aiida.net), that has been tuned first to the demands of
computational materials science. AiiDA's design is based on directed acyclic
graphs to track the provenance of data and calculations, and ensure
preservation and searchability. Remote computational resources are managed
transparently, and automation is coupled with data storage to ensure
reproducibility. Last, complex sequences of calculations can be encoded into
scientific workflows. We believe that AiiDA's design and its sharing
capabilities will encourage the creation of social ecosystems to disseminate
codes, data, and scientific workflows.Comment: 30 pages, 7 figure
E-BioFlow: Different Perspectives on Scientific Workflows
We introduce a new type of workflow design system called\ud
e-BioFlow and illustrate it by means of a simple sequence alignment workflow. E-BioFlow, intended to model advanced scientific workflows, enables the user to model a workflow from three different but strongly coupled perspectives: the control flow perspective, the data flow perspective, and the resource perspective. All three perspectives are of\ud
equal importance, but workflow designers from different domains prefer different perspectives as entry points for their design, and a single workflow designer may prefer different perspectives in different stages of workflow design. Each perspective provides its own type of information, visualisation and support for validation. Combining these three perspectives in a single application provides a new and flexible way of modelling workflows
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