10,504 research outputs found
DEEP: a provenance-aware executable document system
The concept of executable documents is attracting growing interest from both academics and publishers since it is a promising technology for the dissemination of scientific results. Provenance is a kind of metadata that provides a rich description of the derivation history of data products starting from their original sources. It has been used in many different e-Science domains and has shown great potential in enabling reproducibility of scientific results. However, while both executable documents and provenance are aimed at enhancing the dissemination of scientific results, little has been done to explore the integration of both techniques. In this paper, we introduce the design and development of DEEP, an executable document environment that generates scientific results dynamically and interactively, and also records the provenance for these results in the document. In this system, provenance is exposed to users via an interface that provides them with an alternative way of navigating the executable document. In addition, we make use of the provenance to offer a document rollback facility to users and help to manage the system's dynamic resources
Automatic vs Manual Provenance Abstractions: Mind the Gap
In recent years the need to simplify or to hide sensitive information in
provenance has given way to research on provenance abstraction. In the context
of scientific workflows, existing research provides techniques to semi
automatically create abstractions of a given workflow description, which is in
turn used as filters over the workflow's provenance traces. An alternative
approach that is commonly adopted by scientists is to build workflows with
abstractions embedded into the workflow's design, such as using sub-workflows.
This paper reports on the comparison of manual versus semi-automated approaches
in a context where result abstractions are used to filter report-worthy results
of computational scientific analyses. Specifically; we take a real-world
workflow containing user-created design abstractions and compare these with
abstractions created by ZOOM UserViews and Workflow Summaries systems. Our
comparison shows that semi-automatic and manual approaches largely overlap from
a process perspective, meanwhile, there is a dramatic mismatch in terms of data
artefacts retained in an abstracted account of derivation. We discuss reasons
and suggest future research directions.Comment: Preprint accepted to the 2016 workshop on the Theory and Applications
of Provenance, TAPP 201
A posteriori metadata from automated provenance tracking: Integration of AiiDA and TCOD
In order to make results of computational scientific research findable,
accessible, interoperable and re-usable, it is necessary to decorate them with
standardised metadata. However, there are a number of technical and practical
challenges that make this process difficult to achieve in practice. Here the
implementation of a protocol is presented to tag crystal structures with their
computed properties, without the need of human intervention to curate the data.
This protocol leverages the capabilities of AiiDA, an open-source platform to
manage and automate scientific computational workflows, and TCOD, an
open-access database storing computed materials properties using a well-defined
and exhaustive ontology. Based on these, the complete procedure to deposit
computed data in the TCOD database is automated. All relevant metadata are
extracted from the full provenance information that AiiDA tracks and stores
automatically while managing the calculations. Such a protocol also enables
reproducibility of scientific data in the field of computational materials
science. As a proof of concept, the AiiDA-TCOD interface is used to deposit 170
theoretical structures together with their computed properties and their full
provenance graphs, consisting in over 4600 AiiDA nodes
Data Provenance and Management in Radio Astronomy: A Stream Computing Approach
New approaches for data provenance and data management (DPDM) are required
for mega science projects like the Square Kilometer Array, characterized by
extremely large data volume and intense data rates, therefore demanding
innovative and highly efficient computational paradigms. In this context, we
explore a stream-computing approach with the emphasis on the use of
accelerators. In particular, we make use of a new generation of high
performance stream-based parallelization middleware known as InfoSphere
Streams. Its viability for managing and ensuring interoperability and integrity
of signal processing data pipelines is demonstrated in radio astronomy. IBM
InfoSphere Streams embraces the stream-computing paradigm. It is a shift from
conventional data mining techniques (involving analysis of existing data from
databases) towards real-time analytic processing. We discuss using InfoSphere
Streams for effective DPDM in radio astronomy and propose a way in which
InfoSphere Streams can be utilized for large antennae arrays. We present a
case-study: the InfoSphere Streams implementation of an autocorrelating
spectrometer, and using this example we discuss the advantages of the
stream-computing approach and the utilization of hardware accelerators
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