Sharing and caring of eScience data

This commentary reflects on the issues presented in this volume from the perspective of a large eScience project, GEON, whose aim is to promote data integration in the geosciences within the US and abroad. Technical, social, and regulatory challenges accompanying the collection, curation, and sharing of eScience data are discussed. Opportunities and barriers to engaging in international eScience collaborations are highlighted.     

Neuroscience instrumentation and distributed analysis of brain activity data: a case for eScience on global Grids

The distribution of knowledge (by scientists) and data sources (advanced scientific instruments), and the need for large‐scale computational resources for analyzing massive scientific data are two major problems commonly observed in scientific disciplines. Two popular scientific disciplines of this nature are brain science and high‐energy physics. The analysis of brain‐activity data gathered from the MEG (magnetoencephalography) instrument is an important research topic in medical science since it helps doctors in identifying symptoms of diseases. The data needs to be analyzed exhaustively to efficiently diagnose and analyze brain functions and requires access to large‐scale computational resources. The potential platform for solving such resource intensive applications is the Grid. This paper presents the design and development of MEG data analysis system by leveraging Grid technologies, primarily Nimrod‐G, Gridbus, and Globus. It describes the composition of the neuroscience (brain‐activity analysis) application as parameter‐sweep application and its on‐demand deployment on global Grids for distributed execution. The results of economic‐based scheduling of analysis jobs for three different optimizations scenarios on the world‐wide Grid testbed resources are presented along with their graphical visualization. Copyright © 2005 John Wiley & Sons, Ltd.     

eScience today and tomorrow—Part 2

This special section contains the second part of a set of top papers from the 10th IEEE International eScience Conference (eScience 2014), held in October 2014 in Guarujá, Brazil). The authors of strongly-reviewed papers published in that conference were invited to extend their papers, which then went through a second peer review. This special section contains the three papers that comprise the second set of the extended papers. Part 1, with another seven extended papers, was already published in a previous issue of FGCS  [1].     

Automated data provenance capture in spreadsheets,with case studies

One of the most important tasks in eScience is capturing the provenance of data. While scientists frequently use off-the-shelf analysis tools to process and manipulate data, current provenance techniques such as those based on scientific workflows are typically not able to trace internal data manipulations that occur within these tools. In this paper, we focus on one such off-the-shelf tool, MS Excel, which is used by many scientists; specifically, we propose InSituTrac, an automated in situ provenance approach for spreadsheet data in Excel. Our framework captures data provenance unobtrusively in the background, allows for user annotations, provides undo/redo functionality at various levels of granularity, presents the captured provenance in an accessible format, and visualizes captured provenance to support analysis of the provenance log. We highlight several motivating use case scenarios which show how provenance queries can be answered by our approach. Finally, case studies with an atmospheric science research group and a fisheries research group suggest that the automated provenance approach is both efficient and useful to scientists.     

A Web‐based resource model for scholarship 2.0: object reuse & exchange

Digital scholarship offers the opportunity to move beyond the limitations of traditional scholarly publication. Rather than limiting scholarly communication to text‐based static documents, the Web makes it possible for scholars to expose and share the full evidence of their research including data, images, video, and other genre of materials. These aggregations of evidence, or compound documents, can then be integrated into a linked data cloud, the basis of Scholarship 2.0—an open environment in which scholars collaborate and build new knowledge on the existing scholarship. We present Open Archives Initiative–Object Reuse and Exchange (OAI–ORE), a set of standards to identify and describe aggregations of WebResources, thereby making the Scholarship 2.0 vision possible. Copyright © 2010 John Wiley & Sons, Ltd.     

eScience today and tomorrow

This special issue contains extended versions of many of the top papers from the 10th IEEE International eScience Conference (eScience 2014), held in October 2014 in Guarujá, Brazil. The authors of strongly reviewed papers published in that conference were invited to extend their papers, which then went through a second peer review. This special issue contains the first set (seven) of the extended papers selected as the result of this review. Part 2, with three additional extended papers, will follow in a future issue of FGCS.     

Assessment of SDN technology for an easy-to-use VPN service

This paper describes how state-of-the-art SDN technology can be used to create and validate a user configurable, on-demand VPN service. In the Community Connection (CoCo) project an architecture for the VPN service was designed and a prototype was developed based on the OpenFlow protocol and the OpenDaylight controller. The CoCo prototype enables automatic setup and tear down of CoCo instances (VPNs) by end-users via an easy to use web portal, without needing the help of network administrators to do manual configuration of the network switches. Users from the research community, amongst others, expressed their interest in using such an easy-to-use VPN service for on-demand interconnection of their eScience resources (servers, VMs, laptops, storage, scientific instruments, etc.) that may only be reachable for their closed group. The developed CoCo prototype was validated in an SDN testbed and via Mininet simulation. Using the calibrated Mininet simulation the impact was analysed for larger scale deployments of the CoCo prototype.     

eScience and the humanities

Humanists face problems that are comparable to their colleagues in the sciences. Like scientists, humanists have electronic sources and datasets that are too large for traditional labor intensive analysis. They also need to work with materials that presuppose more background knowledge than any one researcher can master: no one can, for example, know all the languages needed for subjects that cross multiple disciplines. Unlike their colleagues in the sciences, however, humanists have relatively few resources with which to develop this new infrastructure. They must therefore systematically cultivate alliances with better funded disciplines, learning how to build on emerging infrastructure from other disciplines and, where possible, contributing to the design of a cyberinfrastructure that serves all of academia, including the humanities.     

Provenance Explorer-a graphical interface for constructing scientific publication packages from provenance trails

Scientific communities are under increasing pressure from funding organizations to publish their raw data, in addition to their traditional publications, in open archives. Many scientists would be willing to do this if they had tools that streamlined the process and exposed simple provenance information, i.e., enough to explain the methodology and validate the results without compromising the author’s intellectual property or competitive advantage. This paper presents Provenance Explorer, a tool that enables the provenance trail associated with a scientific discovery process to be visualized and explored through a graphical user interface (GUI). Based on RDF graphs, it displays the sequence of data, states and events associated with a scientific workflow, illustrating the methodology that led to the published results. The GUI also allows permitted users to expand selected links between nodes to reveal more fine-grained information and sub-workflows. But more importantly, the system enables scientists to selectively construct “scientific publication packages” by choosing particular nodes from the visual provenance trail and dragging-and-dropping them into an RDF package which can be uploaded to an archive or repository for publication or e-learning. The provenance relationships between the individual components in the package are automatically inferred using a rules-based inferencing engine.     

Collaborative eScience libraries

In the context of collaborative eScience, digital libraries are one of many distributed, interoperable resources available to scientists that facilitate both human and machine collaboration: machine collaboration in the form of standards such as the Open Archives Initiative Protocol for Metadata Harvesting and human collaboration in the form of collaborative workspaces. This paper describes a set of collaborative workspaces created at the Los Alamos National Laboratory Research Library, initial patterns of use, and additional user requirements determined based on these initial patterns of use.