scholarly journals Community curation of bioinformatics software and data resources

2019 ◽  
Vol 21 (5) ◽  
pp. 1697-1705 ◽  
Author(s):  
Jon Ison ◽  
Hervé Ménager ◽  
Bryan Brancotte ◽  
Erik Jaaniso ◽  
Ahto Salumets ◽  
...  
Keyword(s):  
Systematic Approach ◽  
Service Providers ◽  
Biological Information ◽  
Scientific Communities ◽  
Bioinformatics Software ◽  
Research Infrastructures ◽  
Community Curation ◽  
Comprehensive Registry

Abstract The corpus of bioinformatics resources is huge and expanding rapidly, presenting life scientists with a growing challenge in selecting tools that fit the desired purpose. To address this, the European Infrastructure for Biological Information is supporting a systematic approach towards a comprehensive registry of tools and databases for all domains of bioinformatics, provided under a single portal (https://bio.tools). We describe here the practical means by which scientific communities, including individual developers and projects, through major service providers and research infrastructures, can describe their own bioinformatics resources and share these via bio.tools.

Physical and remote access to the European Volcano Research Infrastructures as a strategy to promote the community building: efforts, challenges, and results.

2020 ◽  
Author(s):  
Letizia Spampinato ◽  
Giuseppe Puglisi
Keyword(s):  
Community Building ◽  
Volcanic Rocks ◽  
Remote Access ◽  
Research Topics ◽  
Scientific Communities ◽  
Research Infrastructures ◽  
Physical Access ◽  
Selection Of ◽  
Volcano Observatories ◽  
The Ideal

<p>Indeed, nowadays data sharing via internet is one of the most used approaches to networking scientific communities. However, the opportunity to physically access Research Infrastructures (RIs) and their installations and facilities is potentially the most powerful mean to build up a community. Physically access, in fact, makes the ideal conditions for the RI’s providers and users to work side by side on specific research topics. This is recently the case of the European trans-national access activities promoted in order to allow and push the volcanology community to use either the volcano observatories, to carry out experiments or fieldworks, or laboratories, for exploiting analytical and computational facilities, belonging to the main European volcano research institutions.</p><p>The EUROVOLC project has granted the access to 11 RIs for an overall of 45 installations, including single facilities of pools of mobile instrumentation and of laboratories, and remote access to collections of volcanic rocks, of 5 European countries (France, Iceland, Italy, Portugal, and Spain). In the frame of the project, the trans-national access offer has come from 7 partners (IMO, UI, INGV&CNR, CIVISA, IPGP, and CSIC) acting in 7 WPs (13, 14, 16, 16, 17, 18, and 19).</p><p>The EUROVOLC work-plan has foreseen two calls, one in 2018 and the other in 2019, allowing users to apply for access the RIs, and the effective physical access in 2019 and 2020, respectively. Each call has been managed according to a stepwise process based on an excellence-driven criterion, in which the roles of the various actors and the schedule have been previously defined.</p><p>This contribution aims at presenting the management and coordination efforts related to the trans-national access activities in the frame of EUROVOLC including the preparation and the launch of the 1<sup>st</sup> call, the process of the selection of the proposals, the feedback from the management of the 1<sup>st</sup> call, the preparation of the 2<sup>nd</sup> call, and a critical analysis for improving the management of the 2<sup>nd</sup> call.</p>

A Systematic Approach to Biologically-Inspired Engineering Design

2011 ◽  
Author(s):  
Jacquelyn K. S. Nagel ◽  
Robert B. Stone
Keyword(s):  
Engineering Design ◽  
Systematic Approach ◽  
Biological Information ◽  
Biological Knowledge ◽  
Biologically Inspired ◽  
Design Methodologies ◽  
Functional Representation ◽  
Engineering Designs ◽  
Engineered Systems ◽  
Biologically Inspired Design

To facilitate systematic biologically-inspired design, a design methodology that integrates with function-based design methodologies has been formalized. The goals of this methodology are to go beyond the element of chance, reduce the amount of time and effort required for developing biologically-inspired engineering solutions, and bridge the seemingly immense disconnect between the engineering and biological domains. Using functional representation and abstraction to describe biological systems presents the natural designs in an engineering context and allows designers to make connections between biological and engineered systems. Thus, the biological information is accessible to engineering designers with varying biological knowledge, but a common understanding of engineering design methodologies. Two approaches to validation are presented. One examines current biologically-inspired products either in production or in literature to see if the systematic approach to biologically-inspired design can reproduce the existing designs. The second investigates needs-based design problems that lead to plausible biologically-inspired solutions. This work has demonstrated the feasibility of using systematic design for the discovery of innovative engineering designs without requiring expert-level knowledge, but rather broad knowledge of many fields.

Sustainable FAIR Data management is challenging for RIs and it is challenging to solid Earth scientists

2020 ◽  
Author(s):  
Massimo Cocco ◽  
Daniele Bailo ◽  
Keith G. Jeffery ◽  
Rossana Paciello ◽  
Valerio Vinciarelli ◽  
...  
Keyword(s):  
Data Management ◽  
Solid Earth ◽  
Service Management ◽  
Open Science ◽  
Adoption Process ◽  
Scientific Communities ◽  
Research Infrastructures ◽  
Data Products ◽  
Data Stewardship ◽  
Fair Principles

<p>Interoperability has long been an objective for research infrastructures dealing with research data to foster open access and open science. More recently, FAIR principles (Findability, Accessibility, Interoperability and Reusability) have been proposed. The FAIR principles are now reference criteria for promoting and evaluating openness of scientific data. FAIRness is considered a necessary target for research infrastructures in different scientific domains at European and global level.</p><p>Solid Earth RIs have long been committed to engage scientific communities involved in data collection, standardization and quality management as well as providing metadata and services for qualification, storage and accessibility. They are working to adopt FAIR principles, thus addressing the onerous task of turning these principles into practices. To make FAIR principles a reality in terms of service provision for data stewardship, some RI implementers in EPOS have proposed a FAIR-adoption process leveraging a four stage roadmap that reorganizes FAIR principles to better fit to scientists and RI implementers mindset. The roadmap considers FAIR principles as requirements in the software development life cycle, and reorganizes them into data, metadata, access services and use services. Both the implementation and the assessment of “FAIRness” level by means of questionnaire and metrics is made simple and closer to day-to-day scientists works.</p><p>FAIR data and service management is demanding, requiring resources and skills and more importantly it needs sustainable IT resources. For this reason, FAIR data management is challenging for many Research Infrastructures and data providers turning FAIR principles into reality through viable and sustainable practices. FAIR data management also includes implementing services to access data as well as to visualize, process, analyse and model them for generating new scientific products and discoveries.</p><p>FAIR data management is challenging to Earth scientists because it depends on their perception of finding, accessing and using data and scientific products: in other words, the perception of data sharing. The sustainability of FAIR data and service management is not limited to financial sustainability and funding; rather, it also includes legal, governance and technical issues that concern the scientific communities.</p><p>In this contribution, we present and discuss some of the main challenges that need to be urgently tackled in order to run and operate FAIR data services in the long-term, as also envisaged by the European Open Science Cloud initiative: a) sustainability of the IT solutions and resources to support practices for FAIR data management (i.e., PID usage and preservation, including costs for operating the associated IT services); b) re-usability, which on one hand requires clear and tested methods to manage heterogeneous metadata and provenance, while on the other hand can be considered a frontier research field; c) FAIR services provision, which presents many open questions related to the application of FAIR principles to services for data stewardship, and to services for the creation of data products taking in input FAIR raw data, for which is not clear how FAIRness compliancy of data products can be still guaranteed.</p>

scholarly journals The Collaborative Potential of Research Infrastructures in Addressing Global Scientific Questions

2019 ◽  
Vol 3 ◽  
Author(s):  
Christos Arvanitidis ◽  
Richard Warwick ◽  
Paul Somerfield ◽  
Christina Pavloudi ◽  
Evangelos Pafilis ◽  
...  
Keyword(s):  
Data Access ◽  
Marine Species ◽  
Biological Information ◽  
Valid Species ◽  
Marine Biota ◽  
Taxonomic Distinctness ◽  
Micro Ct ◽  
European Research ◽  
Ecosystem Research ◽  
Research Infrastructures

Research Infrastructures (RIs) are facilities, resources and services used by scientists to perform research and support innovation. A number of EU research infrastructures [e.g. e-Science and Technology European Infrastructure for Biodiversity and Ecosystem Research (LifeWatch) European Research Iinfrastructures Consortium (ERIC); The European life-sciences Infrastructure for biological Information (ELIXIR); the European Marine Biological Resource Centre (EMBRC ERIC); the European Research Infrastructure for Imaging Technologies in Biological and Biomedical Sciences (uroBioImaging ERIC)] have been building Virtual Research Environments (VREs), which include many virtual laboratories (vLabs) offering, one stop data access to scientists, high computational capacity and collaborative research platforms in support of the requirements of the digital science. This presentation gives examples on the use of the vLabs developed by LifeWatch ERIC which have subsequently been taken up as web services by other RIs. The RvLab operates on a high-performance computer cluster, and has been used in order to analyse various properties of taxon equality, with a focus on marine species. This taxonomic information on marine biota is organized and made publicly available through the World Register of Marine Species (WoRMS) that delivers more than 250,000 described valid species names. Although scientists consider an equal status (in terms of contribution to overall diversity) to each taxon used in taxonomy, biogeography, ecology and biodiversity, the question “are all taxa equal?” has never been tested at a global scale. We present evidence that this question can be addressed by applying relatedness indices (Taxonomic Distinctness) over the entire WoRMS metazoan tree. The virtual micro-CT laboratory (Micro-CT vLab), which can be used by the members of the scientific community interested in the digitisation methods and biological collections, makes the micro-CT data exploration of natural history specimens freely available over the internet. Micro-CT vLab makes it possible the online exploration and dissemination of micro-CT datasets, which are only rarely made available to the public due to their very large size and a lack of dedicated online platforms supporting the interactive manipulation of 3D data. Examples of how these vLabs can be used by other RIs are provided.

The Need for a Systematic Approach to Disaster Psychosocial Response: A Suggested Competency Framework

2014 ◽  
Vol 29 (2) ◽  
pp. 183-189 ◽  
Author(s):  
Robin S. Cox ◽  
Taryn Danford
Keyword(s):  
Performance Appraisal ◽  
Systematic Approach ◽  
Service Providers ◽  
Psychosocial Support ◽  
Competency Framework ◽  
Job Descriptions ◽  
Publication Type ◽  
Behavioral Indicators ◽  
Competency Based ◽  
Competency Domains

AbstractCompetency models attempt to define what makes expert performers “experts.” Successful disaster psychosocial planning and the institutionalizing of psychosocial response within emergency management require clearly-defined skill sets. This necessitates anticipating both the short- and long-term psychosocial implications of a disaster or health emergency (ie, pandemic) by developing effective and sustained working relationships among psychosocial providers, programs, and other planning partners. The following article outlines recommended competencies for psychosocial responders to enable communities and organizations to prepare for and effectively manage a disaster response.Competency-based models are founded on observable performance or behavioral indicators, attitudes, traits, or personalities related to effective performance in a specific role or job. After analyzing the literature regarding competency-based frameworks, a proposed competency framework that details 13 competency domains is suggested. Each domain describes a series of competencies and suggests behavioral indicators for each competency and, where relevant, associated training expectations. These domains have been organized under three distinct categories or types of competencies: general competency domains; disaster psychosocial intervention competency domains; and disaster psychosocial program leadership and coordination competency domains.Competencies do not replace job descriptions nor should they be confused with performance assessments. What they can do is update and revise job descriptions; orient existing and new employees to their disaster/emergency roles and responsibilities; target training needs; provide the basis for ongoing self-assessment by agencies and individuals as they evaluate their readiness to respond; and provide a job- or role-relevant basis for performance appraisal dimensions or standards and review discussions.Using a modular approach to psychosocial planning, service providers can improve their response capacity by utilizing differences in levels of expertise and training. The competencies outlined in this paper can thus be used to standardize expectations about levels of psychosocial support interventions. In addition this approach provides an adaptable framework that can be adjusted for various contexts.CoxRS, DanfordT. The need for a systematic approach to disaster psychosocial response: a suggested competency framework. Prehosp Disaster Med. 2014;29(2):1-7.

scholarly journals Secure Encapsulation and Publication of Biological Services in the Cloud Computing Environment

2013 ◽  
Vol 2013 ◽  
pp. 1-8 ◽  
Author(s):  
Weizhe Zhang ◽  
Xuehui Wang ◽  
Bo Lu ◽  
Tai-hoon Kim
Keyword(s):  
Cloud Computing ◽  
Basic Function ◽  
Biological Information ◽  
Prototype System ◽  
Computing Environment ◽  
Job Status ◽  
Cloud Computing Environment ◽  
Software Products ◽  
Bioinformatics Software ◽  
And Function

Secure encapsulation and publication for bioinformatics software products based on web service are presented, and the basic function of biological information is realized in the cloud computing environment. In the encapsulation phase, the workflow and function of bioinformatics software are conducted, the encapsulation interfaces are designed, and the runtime interaction between users and computers is simulated. In the publication phase, the execution and management mechanisms and principles of the GRAM components are analyzed. The functions such as remote user job submission and job status query are implemented by using the GRAM components. The services of bioinformatics software are published to remote users. Finally the basic prototype system of the biological cloud is achieved.

Perceptions of a Collaborative Professional Learning Program: Seeing the “Bigger Picture”

2020 ◽  
Vol 5 (1) ◽  
pp. 290-303
Author(s):  
P. Charlie Buckley ◽  
Kimberly A. Murza ◽  
Tami Cassel
Keyword(s):  
Data Analysis ◽  
Professional Learning ◽  
Social Communication ◽  
Special Educators ◽  
Service Providers ◽  
Integrative Approach ◽  
Theory Approach ◽  
Learning Program ◽  
Speech Language Pathologists ◽  
Related Service

Purpose The purpose of this study was to explore the perceptions of special education practitioners (i.e., speech-language pathologists, special educators, para-educators, and other related service providers) on their role as communication partners after participation in the Social Communication and Engagement Triad (Buckley et al., 2015 ) yearlong professional learning program. Method A qualitative approach using interviews and purposeful sampling was used. A total of 22 participants who completed participation in either Year 1 or Year 2 of the program were interviewed. Participants were speech-language pathologists, special educators, para-educators, and other related service providers. Using a grounded theory approach (Glaser & Strauss, 1967 ) to data analysis, open, axial, and selective coding procedures were followed. Results Three themes emerged from the data analysis and included engagement as the goal, role as a communication partner, and importance of collaboration. Conclusions Findings supported the notion that educators see the value of an integrative approach to service delivery, supporting students' social communication and engagement across the school day but also recognizing the challenges they face in making this a reality.

Talking Across Cultures in Early Intervention: Finding Common Ground to Meet Children's Communication Needs

2009 ◽  
Vol 16 (3) ◽  
pp. 79-85 ◽  
Author(s):  
Elizabeth D. Peña ◽  
Christine Fiestas
Keyword(s):  
Early Intervention ◽  
Cultural Values ◽  
Common Ground ◽  
Service Providers ◽  
Cultural Orientation ◽  
Speech Language Pathology ◽  
Provider Perspectives ◽  
Language Pathology ◽  
Communication Needs ◽  
Caregiver Role

Abstract In this paper, we explore cultural values and expectations that might vary among different groups. Using the collectivist-individualist framework, we discuss differences in beliefs about the caregiver role in teaching and interacting with young children. Differences in these beliefs can lead to dissatisfaction with services on the part of caregivers and with frustration in service delivery on the part of service providers. We propose that variation in caregiver and service provider perspectives arise from cultural values, some of which are instilled through our own training as speech-language pathologists. Understanding where these differences in cultural orientation originate can help to bridge these differences. These can lead to positive adaptations in the ways that speech-language pathology services are provided within an early intervention setting that will contribute to effective intervention.

Systems of Oppression in Geriatric Clinical Service Delivery

2021 ◽  
pp. 1-3
Author(s):  
Diane L. Kendall
Keyword(s):  
Higher Education ◽  
Service Delivery ◽  
Clinical Setting ◽  
Service Providers ◽  
Hard Work ◽  
Clinical Service ◽  
Meaningful Change ◽  
Important Work ◽  
Speech Language Pathologists ◽  
Medical Institutions

Purpose The purpose of this article was to extend the concepts of systems of oppression in higher education to the clinical setting where communication and swallowing services are delivered to geriatric persons, and to begin a conversation as to how clinicians can disrupt oppression in their workplace. Conclusions As clinical service providers to geriatric persons, it is imperative to understand systems of oppression to affect meaningful change. As trained speech-language pathologists and audiologists, we hold power and privilege in the medical institutions in which we work and are therefore obligated to do the hard work. Suggestions offered in this article are only the start of this important work.

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