Concept: System software
We describe a set of best practices for scientific software development, based on research and experience, that will improve scientists' productivity and the reliability of their software.
Increasing an individual’s awareness and understanding of their dietary habits and reasons for eating may help facilitate positive dietary changes. Mobile technologies allow individuals to record diet-related behavior in real time from any location; however, the most popular software applications lack empirical evidence supporting their efficacy as health promotion tools.
- Journal of the American Medical Informatics Association : JAMIA
- Published almost 6 years ago
We present SHARE, a new system for statistical health information release with differential privacy. We present two case studies that evaluate the software on real medical datasets and demonstrate the feasibility and utility of applying the differential privacy framework on biomedical data.
This paper outlines preliminary research of an innovative software program that enables the use of an electronic health record in a nursing education curriculum. The software application program is called EHRNE, which stands for Electronic Heath Record for Nursing Education. The aim of EHRNE is to enhance student’s learning of health informatics when they are working in the simulation laboratory. Integrating EHRNE into the nursing curriculum exposes students to electronic health records before they go into the workplace. A qualitative study was conducted using focus group interviews of nine nursing students. Nursing students' perceptions of using the EHRNE application were explored. The interviews were audio-taped and transcribed verbatim. The data was analyzed following the Colaizzi (1978) guideline. Four main categories that related to the EHRNE application were identified from the interviews: functionality, data management, timing and complexity, and accessibility. The analysis of the data revealed advantages and limitations of using EHRNE in the classroom setting. Integrating the EHRNE program into the curriculum will promote students' awareness of electronic documentation and enhance students' learning in the simulation laboratory. Preliminary findings suggested that before integrating the EHRNE program into the nursing curriculum, educational sessions for both students and faculty outlining the software’s purpose, advantages, and limitations were needed. Following the educational sessions, further investigation of students' perceptions and learning using the EHRNE program is recommended.
The Raven-II is a platform for collaborative research on advances in surgical robotics. Seven Universities have begun research using this platform. The Raven-II system has two three DOF spherical positioning mechanisms capable of attaching interchangeable four DOF instruments. The Raven-II software is based on open standards such as Linux and ROS to maximally facilitate software development. The mechnism is robust enough for repeated experiments and animal surgery experiments, but is not engineered to sufficient safety standards for human use. Mechanisms in place for interaction among the user community and dissemination of results include an electronic forum, an online software SVN repository, and meetings and workshops at major robotics conferences.
With Next Generation Sequencing data being routinely used, evolutionary biology is transforming into a computational science. Thus, researchers have to rely on a growing number of increasingly complex software. All widely used core tools in the field have grown considerably, in terms of the number of features as well as lines of code and consequently, also with respect to software complexity. A topic that has received little attention is the software engineering quality of widely used core analysis tools. Software developers appear to rarely assess the quality of their code, and this can have potential negative consequences for end-users. To this end, we assessed the code quality of 16 highly cited and compute-intensive tools mainly written in C/C ++ (e.g., MrBayes, MAFFT, SweepFinder etc.) and JAVA (BEAST) from the broader area of evolutionary biology that are being routinely used in current data analysis pipelines. Since, the software engineering quality of the tools we analyzed is rather unsatisfying, we provide a list of best practices for improving the quality of existing tools and list techniques that can be deployed for developing reliable, high quality scientific software from scratch. Finally, we also discuss journal as well as science policy and, more importantly, funding issues that need to be addressed for improving software engineering quality as well as ensuring support for developing new and maintaining existing software. Our intention is to raise the awareness of the community regarding software engineering quality issues and to emphasize the substantial lack of funding for scientific software development.
Molecular descriptors are widely employed to present molecular characteristics in cheminformatics. Various molecular-descriptor-calculation software programs have been developed. However, users of those programs must contend with several issues, including software bugs, insufficient update frequencies, and software licensing constraints. To address these issues, we propose Mordred, a developed descriptor-calculation software application that can calculate more than 1800 two- and three-dimensional descriptors. It is freely available via GitHub. Mordred can be easily installed and used in the command line interface, as a web application, or as a high-flexibility Python package on all major platforms (Windows, Linux, and macOS). Performance benchmark results show that Mordred is at least twice as fast as the well-known PaDEL-Descriptor and it can calculate descriptors for large molecules, which cannot be accomplished by other software. Owing to its good performance, convenience, number of descriptors, and a lax licensing constraint, Mordred is a promising choice of molecular descriptor calculation software that can be utilized for cheminformatics studies, such as those on quantitative structure-property relationships.
Almost all research work in computational neuroscience involves software. As researchers try to understand ever more complex systems, there is a continual need for software with new capabilities. Because of the wide range of questions being investigated, new software is often developed rapidly by individuals or small groups. In these cases, it can be hard to demonstrate that the software gives the right results. Software developers are often open about the code they produce and willing to share it, but there is little appreciation among potential users of the great diversity of software development practices and end results, and how this affects the suitability of software tools for use in research projects. To help clarify these issues, we have reviewed a range of software tools and asked how the culture and practice of software development affects their validity and trustworthiness. We identified four key questions that can be used to categorize software projects and correlate them with the type of product that results. The first question addresses what is being produced. The other three concern why, how, and by whom the work is done. The answers to these questions show strong correlations with the nature of the software being produced, and its suitability for particular purposes. Based on our findings, we suggest ways in which current software development practice in computational neuroscience can be improved and propose checklists to help developers, reviewers, and scientists to assess the quality of software and whether particular pieces of software are ready for use in research.
Breast cancer is the most common cancer in women. The use of mobile software applications for health and wellbeing promotion has grown exponentially in recent years. We systematically reviewed the breast cancer apps available in today’s leading smartphone application stores and characterized them based on their features, evidence base and target audiences.
This article demonstrates a new smartphone-based reusable glucose meter. The glucose meter includes a custom-built smartphone case that houses a permanent bare sensor strip, a stylus that is loaded with enzyme-carbon composite pellets, and sensor instrumentation circuits. A custom-designed Android-based software application was developed to enable easy and clear display of measured glucose concentration. A typical test involves the user loading the software, using the stylus to dispense an enzymatic pellet on top of the bare sensor strip affixed to the case, and then introducing the sample. The electronic module then acquires and wirelessly transmits the data to the application software to be displayed on the screen. The deployed pellet is then discarded to regain the fresh bare sensor surface. Such a unique working principle allows the system to overcome challenges faced by previously reported reusable sensors, such as enzyme degradation, leaching, and hysteresis effects. Studies reveal that the enzyme loaded in the pellets are stable for up to 8 months at ambient conditions, and generate reproducible sensor signals. The work illustrates the significance of the pellet-based sensing system towards realizing a reusable, point-of-care sensor that snugly fits around a smartphone and which does not face issues usually common to reusable sensors. The versatility of this system allows it to be easily modified to detect other analytes for application in a wide range of healthcare, environmental and defense domains.