scholarly journals Taking a fresh look at FAIR for research software

Patterns ◽  
2021 ◽  
Vol 2 (5) ◽  
pp. 100267
Author(s):  
Daniel S. Katz ◽  
Morane Gruenpeter ◽  
Tom Honeyman
Keyword(s):  
Research Software

scholarly journals Workplace Health in Kentucky: A Statewide Comparison

2021 ◽  
Vol 18 (10) ◽  
pp. 5473
Author(s):  
Gretchen Macy ◽  
Jacqueline Basham ◽  
Cecilia Watkins ◽  
Vijay Golla
Keyword(s):  
Health Promotion ◽  
Occupational Safety ◽  
Workplace Health Promotion ◽  
Cost Effective ◽  
Occupational Safety And Health ◽  
Workplace Health ◽  
Positive Direction ◽  
Research Software ◽  
Safety And Health ◽  
Statewide Assessment

The objectives of this study were to assess the state of Kentucky’s workplace health promotion and occupational safety and health programs, to ensure the ability to comprehend any possible trends over the past six years in the state’s progress in offering workplace health promotion and health protection programs, to compare the results of this survey with the 2013 Kentucky state-wide assessment, and to identify gaps in Kentucky’s workplace health promotion and occupational safety and health based on Total Worker Health® (TWH) concepts. Using Qualtrics research software, the Workplace Health in America assessment was sent to companies located in Kentucky and having 10 or more employees. Participants were identified using Dun and Bradstreet’s Hoover’s database. The results showed that, as with the 2013 survey, larger workplaces significantly were more likely to offer workplace health promotion programs than smaller companies (X2 = 24.30; p < 0.001). However, more companies (78%) reported offering programs compared to the 2013 assessment (49%). Given the results of the current study as compared to the statewide assessment conducted in 2013, Kentucky’s WHP is moving in a positive direction; yet, there is still much to be done. There remains a strong need to provide cost-effective and accessible resources for all elements of TWH to small workplaces.

scholarly journals biotoolsSchema: a formalized schema for bioinformatics software description

GigaScience ◽  
2021 ◽  
Vol 10 (1) ◽  
Author(s):  
Jon Ison ◽  
Hans Ienasescu ◽  
Emil Rydza ◽  
Piotr Chmura ◽  
Kristoffer Rapacki ◽  
...  
Keyword(s):  
Scientific Community ◽  
Life Science ◽  
Technical Information ◽  
Heterogeneous Data ◽  
Digital Resources ◽  
Data Intensive ◽  
Research Software ◽  
Bioinformatics Software ◽  
Scientific Context ◽  
Machine Readable

Abstract Background Life scientists routinely face massive and heterogeneous data analysis tasks and must find and access the most suitable databases or software in a jungle of web-accessible resources. The diversity of information used to describe life-scientific digital resources presents an obstacle to their utilization. Although several standardization efforts are emerging, no information schema has been sufficiently detailed to enable uniform semantic and syntactic description—and cataloguing—of bioinformatics resources. Findings Here we describe biotoolsSchema, a formalized information model that balances the needs of conciseness for rapid adoption against the provision of rich technical information and scientific context. biotoolsSchema results from a series of community-driven workshops and is deployed in the bio.tools registry, providing the scientific community with &gt;17,000 machine-readable and human-understandable descriptions of software and other digital life-science resources. We compare our approach to related initiatives and provide alignments to foster interoperability and reusability. Conclusions biotoolsSchema supports the formalized, rigorous, and consistent specification of the syntax and semantics of bioinformatics resources, and enables cataloguing efforts such as bio.tools that help scientists to find, comprehend, and compare resources. The use of biotoolsSchema in bio.tools promotes the FAIRness of research software, a key element of open and reproducible developments for data-intensive sciences.

Software Design of College Students' Physical Activity Energy Monitor

2013 ◽  
Vol 464 ◽  
pp. 424-428
Author(s):  
Qi Luo
Keyword(s):  
Physical Activity ◽  
College Students ◽  
Software Design ◽  
Electronic Circuit ◽  
Physiological Condition ◽  
Research Software ◽  
Movement Condition ◽  
Tracking Module ◽  
Activity Energy ◽  
Hardware Structure

The hardware structure of college students physical activity energy monitor has been designed through electronic circuit method in the previous research. Software Design of college students physical activity energy monitor by using LabVIEW is also proposed. User login module, physiological condition module, movement condition module, diet tracking module, virtual coaches module and other modules are also realized in the paper.

Computing in the statistical office

2021 ◽  
pp. 1-14
Author(s):  
Mark P.J. van der Loo
Keyword(s):  
Business Process ◽  
Process Model ◽  
Software Engineer ◽  
Business Process Model ◽  
Official Statistics ◽  
Research Software

Computing with data is at the hart activity of the statistical office. Yet, the area of technical computing often falls between the two stools of data analysts and IT developers. In this paper we analyze the importance of computational skills in the Generic Statistical Business Process Model. Next, we give an overview of computational topics that are of importance to the statistical office. Many of these skills turn out to be of highly technical nature. After this, we try to provoke a wider discussion on the role of technical computing by 1) introducing the role of the Research Software Engineer into the field of official statistics and 2) propose a six semester bachelor’s curriculum in official statistics.

scholarly journals Are Academic Libraries Changing Fast Enough?

2018 ◽  
Vol 42 (3) ◽  
pp. 433-440
Author(s):  
Wolfram Horstmann
Keyword(s):  
Academic Libraries ◽  
Information Organization ◽  
Digital Content ◽  
Learning Space ◽  
Software Support ◽  
Data Intensive ◽  
Research Software ◽  
Management Plans ◽  
Mission Critical ◽  
Academic Information

AbstractAcademic libraries are under a severe pressure of transforming towards a novel form of information organization. Book circulation, learning space and licensing digital content continue to be core services. But the sciences and the humanities are increasingly requesting support for their novel publishing activities. Open Access in science or digital editions in the humanities, and data-intensive operations in research, e.g. data management plans, research software support or data curation and preservation services become mission critical. Thus, in order to stay the central partner for academic information within the institution, libraries need to change. But how fast could libraries possibly change, if the existing services were also to be continued, particularly considering that budget increases are rare? Experiences at the State and University Library Göttingen (SUB) shall elucidate opportunities and challenges.

scholarly journals Automating Finite Element Methods for Geodynamics via Firedrake

2022 ◽  
Author(s):  
D. Rhodri Davies ◽  
Stephan C. Kramer ◽  
Siavash Ghelichkhan ◽  
Angus Gibson
Keyword(s):  
Finite Element ◽  
Code Generation ◽  
Automated System ◽  
Plate Motion ◽  
Reproducible Research ◽  
Surface Boundary ◽  
Problem Size ◽  
Mantle Dynamics ◽  
Research Software ◽  
Wide Range

Abstract. Firedrake is an automated system for solving partial differential equations using the finite element method. By applying sophisticated performance optimisations through automatic code-generation techniques, it provides a means to create accurate, efficient, flexible, easily extensible, scalable, transparent and reproducible research software, that is ideally suited to simulating a wide-range of problems in geophysical fluid dynamics. Here, we demonstrate the applicability of Firedrake for geodynamical simulation, with a focus on mantle dynamics. The accuracy and efficiency of the approach is confirmed via comparisons against a suite of analytical and benchmark cases of systematically increasing complexity, whilst parallel scalability is demonstrated up to 12288 compute cores, where the problem size and the number of processing cores are simultaneously increased. In addition, Firedrake's flexibility is highlighted via straightforward application to different physical (e.g. complex nonlinear rheologies, compressibility) and geometrical (2-D and 3-D Cartesian and spherical domains) scenarios. Finally, a representative simulation of global mantle convection is examined, which incorporates 230 Myr of plate motion history as a kinematic surface boundary condition, confirming its suitability for addressing research problems at the frontiers of global mantle dynamics research.

scholarly journals UCEasy: A software package for automating and simplifying the analysis of ultraconserved elements (UCEs)

2021 ◽  
Vol 9 ◽  
Author(s):  
Caio Ribeiro ◽  
Lucas Oliveira ◽  
Romina Batista ◽  
Marcos De Sousa
Keyword(s):  
Best Practices ◽  
Software Package ◽  
Phylogenetic Trees ◽  
Computational Analysis ◽  
Data Matrix ◽  
Command Line ◽  
Command Line Interface ◽  
Ultraconserved Elements ◽  
Research Software ◽  
Different Levels

The use of Ultraconserved Elements (UCEs) as genetic markers in phylogenomics has become popular and has provided promising results. Although UCE data can be easily obtained from targeted enriched sequencing, the protocol for in silico analysis of UCEs consist of the execution of heterogeneous and complex tools, a challenge for scientists without training in bioinformatics. Developing tools with the adoption of best practices in research software can lessen this problem by improving the execution of computational experiments, thus promoting better reproducibility. We present UCEasy, an easy-to-install and easy-to-use software package with a simple command line interface that facilitates the computational analysis of UCEs from sequencing samples, following the best practices of research software. UCEasy is a wrapper that standardises, automates and simplifies the quality control of raw reads, assembly and extraction and alignment of UCEs, generating at the end a data matrix with different levels of completeness that can be used to infer phylogenetic trees. We demonstrate the functionalities of UCEasy by reproducing the published results of phylogenomic studies of the bird genus Turdus (Aves) and of Adephaga families (Coleoptera) containing genomic datasets to efficiently extract UCEs.

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