FAIRness and Usability for Open-access Omics Data Systems

Omics data sharing is crucial to the biological research community, and the last decade or two has seen a huge rise in collaborative analysis systems, databases, and knowledge bases for omics and other systems biology data. We assessed the FAIRness of NASAs GeneLab Data Systems (GLDS) along with four similar kinds of systems in the research omics data domain, using 14 FAIRness metrics. The range of overall FAIRness scores was 6-12 (out of 14), average 10.1, and standard deviation 2.4. The range of Pass ratings for the metrics was 29-79%, Partial Pass 0-21%, and Fail 7-50%. The systems we evaluated performed the best in the areas of data findability and accessibility, and worst in the area of data interoperability. Reusability of metadata, in particular, was frequently not well supported. We relate our experiences implementing semantic integration of omics data from some of the assessed systems for federated querying and retrieval functions, given their shortcomings in data interoperability. Finally, we propose two new principles that Big Data system developers, in particular, should consider for maximizing data accessibility

Open Science principles for accelerating trait-based science across the Tree of Life.

Synthesizing trait observations and knowledge across the Tree of Life remains a grand challenge for biodiversity science. Species traits are widely used in ecological and evolutionary science, and new data and methods have proliferated rapidly. Yet accessing and integrating disparate data sources remains a considerable challenge, slowing progress toward a global synthesis to integrate trait data across organisms. Trait science needs a vision for achieving global integration across all organisms. Here, we outline how the adoption of key Open Science principles-open data, open source and open methods-is transforming trait science, increasing transparency, democratizing access and accelerating global synthesis. To enhance widespread adoption of these principles, we introduce the Open Traits Network (OTN), a global, decentralized community welcoming all researchers and institutions pursuing the collaborative goal of standardizing and integrating trait data across organisms. We demonstrate how adherence to Open Science principles is key to the OTN community and outline five activities that can accelerate the synthesis of trait data across the Tree of Life, thereby facilitating rapid advances to address scientific inquiries and environmental issues. Lessons learned along the path to a global synthesis of trait data will provide a framework for addressing similarly complex data science and informatics challenges

Towards a service-oriented e-infrastructure for multidisciplinary environmental research

Research e-infrastructures are considered to have generic and thematic parts. The generic part provids high-speed networks, grid (large-scale distributed computing) and database systems (digital repositories and data transfer systems) applicable to all research commnities irrespective of discipline. Thematic parts are specific deployments of e-infrastructures to support diverse virtual research communities. The needs of a virtual community of multidisciplinary envronmental researchers are yet to be investigated. We envisage and argue for an e-infrastructure that will enable environmental researchers to develop environmental models and software entirely out of existing components through loose coupling of diverse digital resources based on the service-oriented achitecture. We discuss four specific aspects for consideration for a future e-infrastructure: 1) provision of digital resources (data, models & tools) as web services, 2) dealing with stateless and non-transactional nature of web services using workflow management systems, 3) enabling web servce discovery, composition and orchestration through semantic registries, and 4) creating synergy with existing grid infrastructures

Transforming Technical Services: Evolving Functions in Large Research University Libraries

Technical services functions in academic libraries have evolved in response to fiscal pressures and advances in technology. In this study the author investigates how technical services in large research university libraries are adapting to support the changing roles of academic libraries. The author conducted hour-long phone interviews in early 2014 with the representatives from nineteen out of the twenty-five university libraries in the Technical Services Directors Large Research Libraries Interest Group. This paper presents the results and discussion based on the interview data: use of the name, Technical Services; new and emerging functions of technical services; organizational structure of technical services units; change drivers that are affecting technical services now, and those that will soon; and challenges in managing technical services. Five models of a technical services organizational structure were developed from participants’ organizational charts and interview data. This research also highlights the skills needed among technical services personnel.UT Librarie

Report of the user requirements and web based access for eResearch workshops

The User Requirements and Web Based Access for eResearch Workshop, organized jointly by NeSC and NCeSS, was held on 19 May 2006. The aim was to identify lessons learned from e-Science projects that would contribute to our capacity to make Grid infrastructures and tools usable and accessible for diverse user communities. Its focus was on providing an opportunity for a pragmatic discussion between e-Science end users and tool builders in order to understand usability challenges, technological options, community-specific content and needs, and methodologies for design and development. We invited members of six UK e-Science projects and one US project, trying as far as possible to pair a user and developer from each project in order to discuss their contrasting perspectives and experiences. Three breakout group sessions covered the topics of user-developer relations, commodification, and functionality. There was also extensive post-meeting discussion, summarized here. Additional information on the workshop, including the agenda, participant list, and talk slides, can be found online at http://www.nesc.ac.uk/esi/events/685/ Reference: NeSC report UKeS-2006-07 available from http://www.nesc.ac.uk/technical_papers/UKeS-2006-07.pd

High Energy Physics Forum for Computational Excellence: Working Group Reports (I. Applications Software II. Software Libraries and Tools III. Systems)

Computing plays an essential role in all aspects of high energy physics. As computational technology evolves rapidly in new directions, and data throughput and volume continue to follow a steep trend-line, it is important for the HEP community to develop an effective response to a series of expected challenges. In order to help shape the desired response, the HEP Forum for Computational Excellence (HEP-FCE) initiated a roadmap planning activity with two key overlapping drivers -- 1) software effectiveness, and 2) infrastructure and expertise advancement. The HEP-FCE formed three working groups, 1) Applications Software, 2) Software Libraries and Tools, and 3) Systems (including systems software), to provide an overview of the current status of HEP computing and to present findings and opportunities for the desired HEP computational roadmap. The final versions of the reports are combined in this document, and are presented along with introductory material.Comment: 72 page

Considering Human Aspects on Strategies for Designing and Managing Distributed Human Computation

A human computation system can be viewed as a distributed system in which the processors are humans, called workers. Such systems harness the cognitive power of a group of workers connected to the Internet to execute relatively simple tasks, whose solutions, once grouped, solve a problem that systems equipped with only machines could not solve satisfactorily. Examples of such systems are Amazon Mechanical Turk and the Zooniverse platform. A human computation application comprises a group of tasks, each of them can be performed by one worker. Tasks might have dependencies among each other. In this study, we propose a theoretical framework to analyze such type of application from a distributed systems point of view. Our framework is established on three dimensions that represent different perspectives in which human computation applications can be approached: quality-of-service requirements, design and management strategies, and human aspects. By using this framework, we review human computation in the perspective of programmers seeking to improve the design of human computation applications and managers seeking to increase the effectiveness of human computation infrastructures in running such applications. In doing so, besides integrating and organizing what has been done in this direction, we also put into perspective the fact that the human aspects of the workers in such systems introduce new challenges in terms of, for example, task assignment, dependency management, and fault prevention and tolerance. We discuss how they are related to distributed systems and other areas of knowledge.Comment: 3 figures, 1 tabl

Planets: Integrated Services for Digital Preservation

The Planets Project is developing services and technology to address core challenges in digital preservation. This article introduces the motivation for this work, describes the extensible technical architecture and places the Planets approach into the context of the Open Archival Information System (OAIS) Reference Model. It also provides a scenario demonstrating Planets’ usefulness in solving real-life digital preservation problems and an overview of the project’s progress to date