SOLE: Linking Research Papers with Science Objects

Pham, Quan; Malik, Tanu; Foster, Ian; Lauro, Roberto Di; Montella, Raffaele

doi:10.1007/978-3-642-34222-6_16

Cited by 23 publications

(20 citation statements)

References 6 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…A custom Java/Android friendly front-end implementation will enable to GPGPU computing the most part of low-power integrated systems and devices. The final destination of this research is provisioning a full production software environment for advanced earth system simulations and analysis based on science gateways, workflow engines and high performance cloud computing [27], giving a support for the next generation of scientific dissemination tools [29] and the smart city management in case of extreme weather events.…”

Section: Discussionmentioning

confidence: 99%

On the Virtualization of CUDA Based GPU Remoting on ARM and X86 Machines in the GVirtuS Framework

Montella

Giunta

Laccetti

et al. 2016

Int J Parallel Prog

Self Cite

View full text Add to dashboard Cite

The astonishing development of diverse and different hardware platforms is twofold: on one side, the challenge for the exascale performance for big data processing and management; on the other side, the mobile and embedded devices for data collection and human machine interaction. This drove to a highly hierarchical evolution of programming models. GVirtuS is the general virtualization system developed in 2009 and firstly introduced in 2010 enabling a completely transparent layer among GPUs and VMs. This paper shows the latest achievements and developments of GVirtuS, now supporting CUDA 6.5, memory management and scheduling. Thanks to the new and improved remoting capabilities, GVirtus now enables GPU sharing among physical and virtual machines based on x86 and ARM CPUs on local workstations, computing clusters and distributed cloud appliances.

show abstract

Section: Discussionmentioning

confidence: 99%

On the Virtualization of CUDA Based GPU Remoting on ARM and X86 Machines in the GVirtuS Framework

Montella

Giunta

Laccetti

et al. 2016

Int J Parallel Prog

Self Cite

View full text Add to dashboard Cite

show abstract

“…Science Object Linking and Embedding (SOLE) is a system that allows linking articles with science objects [56]. A science object can be a source code of a software, a dataset or a workflow.…”

Section: Representation Of Packaging Structurementioning

confidence: 99%

Using a suite of ontologies for preserving workflow-centric research objects

Belhajjame

Zhao

Garijo

et al. 2015

Journal of Web Semantics

110

View full text Add to dashboard Cite

a b s t r a c tScientific workflows are a popular mechanism for specifying and automating data-driven in silico experiments. A significant aspect of their value lies in their potential to be reused. Once shared, workflows become useful building blocks that can be combined or modified for developing new experiments. However, previous studies have shown that storing workflow specifications alone is not sufficient to ensure that they can be successfully reused, without being able to understand what the workflows aim to achieve or to re-enact them. To gain an understanding of the workflow, and how it may be used and repurposed for their needs, scientists require access to additional resources such as annotations describing the workflow, datasets used and produced by the workflow, and provenance traces recording workflow executions.In this article, we present a novel approach to the preservation of scientific workflows through the application of research objects-aggregations of data and metadata that enrich the workflow specifications. Our approach is realised as a suite of ontologies that support the creation of workflow-centric research objects. Their design was guided by requirements elicited from previous empirical analyses of workflow decay and repair. The ontologies developed make use of and extend existing well known ontologies, namely the Object Reuse and Exchange (ORE) vocabulary, the Annotation Ontology (AO) and the W3C PROV ontology (PROVO). We illustrate the application of the ontologies for building Workflow Research Objects with a case-study that investigates Huntington's disease, performed in collaboration with a team from the Leiden University Medial Centre (HG-LUMC). Finally we present a number of tools developed for creating and managing workflow-centric research objects.

show abstract

“…Besides this drawback, the way a research paper is presented to readers, i.e. as a PDF or HTML rendering, has not yet adapted to facilitate inspection of the used materials, such as source code and data (Pham et al, 2012). These materials are wrapped into a folder and attached to the article or stored in external repositories, if available at all.…”

Section: List Of Figuresmentioning

confidence: 99%

“…Readers have to download the folder or visit the repository and can then examine the included materials. Aside from these efforts, another drawback of this approach is that the results in the paper and the materials are disconnected (Pham et al, 2012). Reviewers and readers need to handle three separate components: the actual paper and several potentially complex source code scripts and data files.…”

Section: List Of Figuresmentioning

confidence: 99%

Publishing Reproducible Geoscientific Papers: Status quo, benefits, and opportunities

Konkol¹

2019

Preprint

View full text Add to dashboard Cite

Open reproducible research (ORR) is the practice of publishing the source code andthe datasets that are needed to produce the computational results reported in a paper.Since geoscientific articles often include geostatistical analyses and spatiotemporaldata, reproducibility should be a cornerstone of the computational geosciences butis rarely realized. In addition, the current way of publishing scientific outcomes, i.e.as static PDFs, does not adequately report on computational aspects. Thus, readerscannot fully understand how the authors came to the conclusions and how robustthese are to changes in the analysis. Consequently, it is difficult for reviewers tofollow the analysis steps, and for other researchers to reuse existing materials. Thisdissertation has two overarching goals to tackle these issues: First, it aims at assistingauthors in adhering to ORR principles to ensure high scientific standards. The secondgoal is to reap the benefits that come with papers supplemented by code and data. Toachieve these objectives, this thesis reports on five complementary studies to collectand analyze qualitative (i.e. through interviews and a focus group) and quantitativedata (i.e. through surveys and reproducibility studies). Based on these studies, thiswork provides four key contributions: First, it identifies obstacles that preventedgeoscientists from publishing ORR. To overcome these barriers, this dissertationsuggests concrete and directly applicable strategies. One of these strategies is theexecutable research compendium (ERC) which encapsulates the paper, code, data,and the entire software environment needed to produce the computational results.Based on that, this work presents the design and implementation of an ERC-basedworkflow. It allows authors to convey their computational methods and results byalso providing interactive access to code and data, and readers to deeply investigatethe computational analysis while reading the actual article, e.g. by changing theparameters of the analysis. Finally, this work describes the concept of a binding; abinding connects those code lines and data subsets that produce a specific result, e.g.a figure or number. By also considering user interface widgets (e.g. a slider), thisapproach allows readers to interactively manipulate the parameters of the analysisto see how these changes affect the result. To conclude, the contributions include (i)a set of obstacles which prevent geoscientists from publishing ORR, (ii) conceptsand tools to overcome the identified barriers, (iii) incentives and opportunities thatcome with attached code and data, and (iv) solutions to realize the incentives whicheventually result in a higher number of open and reproducible research.

show abstract

SOLE: Linking Research Papers with Science Objects

Cited by 23 publications

References 6 publications

On the Virtualization of CUDA Based GPU Remoting on ARM and X86 Machines in the GVirtuS Framework

On the Virtualization of CUDA Based GPU Remoting on ARM and X86 Machines in the GVirtuS Framework

Using a suite of ontologies for preserving workflow-centric research objects

Publishing Reproducible Geoscientific Papers: Status quo, benefits, and opportunities

Contact Info

Product

Resources

About