The SoftWipe tool and benchmark for assessing coding standards adherence of scientific software.
Ontology highlight
ABSTRACT:
SUBMITTER: Zapletal A
PROVIDER: S-EPMC8113446 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:ObjectivesWe seek to develop a prototype software analytical tool to augment FDA regulatory reviewers' capacity to harness scientific literature reports in PubMed/MEDLINE for pharmacovigilance and adverse drug event (ADE) safety signal detection. We also aim to gather feedback through usability testing to assess design, performance, and user satisfaction with the tool.MethodsA prototype, open source, web-based, software analytical tool generated statistical disproportionality data mining signal scores and dynamic visual analytics for ADE safety signal detection and management. We leveraged Medical Subject Heading (MeSH) indexing terms assigned to published citations in PubMed/MEDLINE to generate candidate drug-adverse event pairs for quantitative data mining. Six FDA regulatory reviewers participated in usability testing by employing the tool as part of their ongoing real-life pharmacovigilance activities to provide subjective feedback on its practical impact, added value, and fitness for use.ResultsAll usability test participants cited the tool's ease of learning, ease of use, and generation of quantitative ADE safety signals, some of which corresponded to known established adverse drug reactions. Potential concerns included the comparability of the tool's automated literature search relative to a manual 'all fields' PubMed search, missing drugs and adverse event terms, interpretation of signal scores, and integration with existing computer-based analytical tools.ConclusionsUsability testing demonstrated that this novel tool can automate the detection of ADE safety signals from published literature reports. Various mitigation strategies are described to foster improvements in design, productivity, and end user satisfaction.
| S-EPMC5373771 | biostudies-literature
Project description:BackgroundModern high throughput experimental techniques such as DNA microarrays often result in large lists of genes. Computational biology tools such as clustering are then used to group together genes based on their similarity in expression profiles. Genes in each group are probably functionally related. The functional relevance among the genes in each group is usually characterized by utilizing available biological knowledge in public databases such as Gene Ontology (GO), KEGG pathways, association between a transcription factor (TF) and its target genes, and/or gene networks.ResultsWe developedGoalGene Ontology AnaLyzer, a software tool specifically designed for the functional evaluation of gene groups. GOAL implements and supports efficient and statistically rigorous functional interpretations of gene groups through its integration with available GO, TF-gene association data, and association with KEGG pathways. In order to facilitate more specific functional characterization of a gene group, we implement three GO-tree search strategies rather than one as in most existing GO analysis tools. Furthermore, GOAL offers flexibility in deployment. It can be used as a standalone tool, a plug-in to other computational biology tools, or a web server application.ConclusionWe developed a functional evaluation software tool, GOAL, to perform functional characterization of a gene group. GOAL offers three GO-tree search strategies and combines its strength in function integration, portability and visualization, and its flexibility in deployment. Furthermore, GOAL can be used to evaluate and compare gene groups as the output from computational biology tools such as clustering algorithms.
| S-EPMC2873542 | biostudies-literature
Project description:Teaching of responsible conduct of research is largely predicated on the assumption that there are accepted standards of conduct that can be taught. However there is little evidence of consensus in the scientific community about such standards, at least for the practices of authorship, collaboration, and data management. To assess whether such differences in standards are based on disciplinary differences, a survey, described previously, addressing standards, practices, and perceptions about teaching and learning was distributed in November 2010 to US faculty from 50 graduate programs for the biomedical disciplines of microbiology, neuroscience, nursing, and psychology. Despite evidence of statistically significant differences across the four disciplines, actual differences were quite small. Stricter measures of effect size indicated practically significant disciplinary differences for fewer than 10% of the questions. This suggests that the variation in individual standards of practice within each discipline is at least as great as variation due to differences among disciplines. Therefore, the need for discipline-specific training may not be as important as sometimes thought.
| S-EPMC4375091 | biostudies-literature
Project description:Background: Code selection is crucial to the accuracy and reproducibility of studies using administrative data, however a comprehensive assessment of coding trends for major cardiac diagnoses and procedures is lacking. We aimed to evaluate trends in administrative code utilization for major cardiac diagnoses and procedures, and adherence to required methodological practices in cardiac research using the National Inpatient Sample (NIS). Methods: In this observational study of 445 articles, ICD-9-CM codes corresponding to acute myocardial infarction (AMI), heart failure, atrial fibrillation, percutaneous coronary intervention, and coronary artery bypass grafting were collected and analyzed. The NIS was used to compare the number of hospitalizations between the most frequently encountered AMI case definitions. Key elements were abstracted from each article to evaluate adherence to required methodological practices. Results: Variation in code utilization was observed for each diagnosis and procedure assessed, and the number of unique case definitions published per year increased throughout the study period (P < 0.001), driven largely by the significant increase in articles per year (P < 0.001). Off-target codes were observed in 39 (8.8%) studies. Upon reintroduction into the NIS for 2008-2012, the most commonly encountered case definitions for AMI were found to yield significantly different estimates of AMI hospitalizations and hospitalization trends over time. Three hundred and ninety-nine articles (84%) did not adhere to one or more required research practices. Overall adherence was superior for publications in higher-impact journals (P = 0.002). Conclusions: Substantial variation in code selection exists for major cardiac diagnoses and procedures, and non-adherence to methodological standards is widespread. These data have important implications for the accuracy and generalizability of analyses using the NIS.
| S-EPMC8592936 | biostudies-literature
Project description:The practice of research is full of ethical challenges, many of which might be addressed through the teaching of responsible conduct of research (RCR). Although such training is increasingly required, there is no clear consensus about either the goals or content of an RCR curriculum. The present study was designed to assess community standards in three domains of research practice: authorship, collaboration, and data management. A survey, developed through advice from content matter experts, focus groups, and interviews, was distributed in November 2010 to U.S. faculty from 50 graduate programs for each of four different disciplines: microbiology, neuroscience, nursing, and psychology. The survey addressed practices and perceived standards, as well as perceptions about teaching and learning. Over 1,300 responses (response rate of 21 %) yielded statistically significant differences in responses to nearly all questions. However the magnitude of these differences was typically small, leaving little reason to argue for community consensus on standards. For nearly all questions asked, the clear finding was that there was nothing approaching consensus. These results may be useful not so much to teach what the standards are, but to increase student awareness of the diversity of those standards in reported practice.
| S-EPMC4057364 | biostudies-literature
Project description:Science depends heavily on reliable and easy-to-use software packages, such as mathematical libraries or data analysis tools. Developing such packages requires a lot of effort, which is too often avoided due to the lack of funding or recognition. In order to reduce the efforts required to create sustainable software packages, we present a project skeleton that ensures the best software engineering practices from the start of a project, or serves as reference for existing projects.
| S-EPMC7089539 | biostudies-literature
Project description:The opportunities for both subtle and profound errors in software and data management are boundless, yet they remain surprisingly underappreciated. Here I estimate that any reported scientific result could very well be wrong if data have passed through a computer, and that these errors may remain largely undetected. It is therefore necessary to greatly expand our efforts to validate scientific software and computed results.
| S-EPMC4629271 | biostudies-literature
Project description:The proliferation of web-based integrative analysis frameworks has enabled users to perform complex analyses directly through the web. Unfortunately, it also revoked the freedom to easily select the most appropriate tools. To address this, we have developed Galaxy ToolShed.
| S-EPMC4038738 | biostudies-literature
Project description:Science outreach and communication are gaining more and more importance for conveying the meaning of today's research to the general public. Public exhibitions of scientific instruments can provide hands-on experience with technical advances and their applications in the life sciences. The software of such devices, however, is oftentimes not appropriate for this purpose. In this study, we describe a software framework and the necessary computer configuration that is well suited for exposing a complex self-built and software-controlled instrument such as a microscope to laymen under limited supervision, e.g. in museums or schools. We identify several aspects that must be met by such software, and we describe a design that can simultaneously be used to control either (i) a fully functional instrument in a robust and fail-safe manner, (ii) an instrument that has low-cost or only partially working hardware attached for illustration purposes or (iii) a completely virtual instrument without hardware attached. We describe how to assess the educational success of such a device, how to monitor its operation and how to facilitate its maintenance. The introduced concepts are illustrated using our software to control eduSPIM, a fluorescent light sheet microscope that we are currently exhibiting in a technical museum.
| S-EPMC5003368 | biostudies-literature
Project description:The increasing complexity of data and analysis methods has created an environment where scientists, who may not have formal training, are finding themselves playing the impromptu role of software engineer. While several resources are available for introducing scientists to the basics of programming, researchers have been left with little guidance on approaches needed to advance to the next level for the development of robust, large-scale data analysis tools that are amenable to integration into workflow management systems, tools, and frameworks. The integration into such workflow systems necessitates additional requirements on computational tools, such as adherence to standard conventions for robustness, data input, output, logging, and flow control. Here we provide a set of 10 guidelines to steer the creation of command-line computational tools that are usable, reliable, extensible, and in line with standards of modern coding practices.
| S-EPMC6532757 | biostudies-literature