Collaborating with our community to increase code sharing.
Ontology highlight
ABSTRACT:
SUBMITTER: Cadwallader L
PROVIDER: S-EPMC8009435 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description: Not available
| S-EPMC9162310 | biostudies-literature
Project description:Data-driven computational analysis is becoming increasingly important in biomedical research, as the amount of data being generated continues to grow. However, the lack of practices of sharing research outputs, such as data, source code and methods, affects transparency and reproducibility of studies, which are critical to the advancement of science. Many published studies are not reproducible due to insufficient documentation, code, and data being shared. We conducted a comprehensive analysis of 453 manuscripts published between 2016-2021 and found that 50.1% of them fail to share the analytical code. Even among those that did disclose their code, a vast majority failed to offer additional research outputs, such as data. Furthermore, only one in ten papers organized their code in a structured and reproducible manner. We discovered a significant association between the presence of code availability statements and increased code availability (p=2.71×10 -9 ). Additionally, a greater proportion of studies conducting secondary analyses were inclined to share their code compared to those conducting primary analyses (p=1.15*10 -07 ). In light of our findings, we propose raising awareness of code sharing practices and taking immediate steps to enhance code availability to improve reproducibility in biomedical research. By increasing transparency and reproducibility, we can promote scientific rigor, encourage collaboration, and accelerate scientific discoveries. We must prioritize open science practices, including sharing code, data, and other research products, to ensure that biomedical research can be replicated and built upon by others in the scientific community.
| S-EPMC10441317 | biostudies-literature
Project description:Making scientific analyses reproducible, well documented, and easily shareable is crucial to maximizing their impact and ensuring that others can build on them. However, accomplishing these goals is not easy, requiring careful attention to organization, workflow, and familiarity with tools that are not a regular part of every scientist's toolbox. We have developed an R package, workflowr, to help all scientists, regardless of background, overcome these challenges. Workflowr aims to instill a particular "workflow" - a sequence of steps to be repeated and integrated into research practice - that helps make projects more reproducible and accessible.This workflow integrates four key elements: (1) version control (via Git); (2) literate programming (via R Markdown); (3) automatic checks and safeguards that improve code reproducibility; and (4) sharing code and results via a browsable website. These features exploit powerful existing tools, whose mastery would take considerable study. However, the workflowr interface is simple enough that novice users can quickly enjoy its many benefits. By simply following the workflowr "workflow", R users can create projects whose results, figures, and development history are easily accessible on a static website - thereby conveniently shareable with collaborators by sending them a URL - and accompanied by source code and reproducibility safeguards. The workflowr R package is open source and available on CRAN, with full documentation and source code available at https://github.com/jdblischak/workflowr.
| S-EPMC6833990 | biostudies-literature
Project description:This research aimed to understand the needs and habits of researchers in relation to code sharing and reuse; gather feedback on prototype code notebooks created by NeuroLibre; and help determine strategies that publishers could use to increase code sharing. We surveyed 188 researchers in computational biology. Respondents were asked about how often and why they look at code, which methods of accessing code they find useful and why, what aspects of code sharing are important to them, and how satisfied they are with their ability to complete these tasks. Respondents were asked to look at a prototype code notebook and give feedback on its features. Respondents were also asked how much time they spent preparing code and if they would be willing to increase this to use a code sharing tool, such as a notebook. As a reader of research articles the most common reason (70%) for looking at code was to gain a better understanding of the article. The most commonly encountered method for code sharing-linking articles to a code repository-was also the most useful method of accessing code from the reader's perspective. As authors, the respondents were largely satisfied with their ability to carry out tasks related to code sharing. The most important of these tasks were ensuring that the code was running in the correct environment, and sharing code with good documentation. The average researcher, according to our results, is unwilling to incur additional costs (in time, effort or expenditure) that are currently needed to use code sharing tools alongside a publication. We infer this means we need different models for funding and producing interactive or executable research outputs if they are to reach a large number of researchers. For the purpose of increasing the amount of code shared by authors, PLOS Computational Biology is, as a result, focusing on policy rather than tools.
| S-EPMC9406794 | biostudies-literature
Project description:To qualitatively assess pharmacists' perspectives on the barriers and facilitators of collaborating with community health workers (CHWs) when caring for patients with diabetes.Eight pharmacists were invited to participate in a focus group. All pharmacists had worked with CHWs for 12 months as part of a larger study. Seven pharmacists participated in a single focus group while one pharmacist participated in an individual interview. Data were analyzed by two investigators to identify common themes.Perceived barriers included issues associated with maintaining patient confidentiality, pharmacists' level of comfort with CHWs, uncertainty about CHW roles, and inconsistent communication between pharmacists and CHWs. However, pharmacists reported that the care model fostered improvement in patient-pharmacist communication, patient adherence to medication, and assessment of patients' overall condition.Pharmacists expressed positive attitudes and experiences in working with CHWs caring for a minority patient population with poorly controlled diabetes. Most believed that CHWs acted as facilitators and aided them in producing positive clinical outcomes by addressing the multiple psychosocial and contextual dimensions of patient health. Developing approaches for more frequent and effective communication between pharmacists and CHWs was the primary perceived challenge.
| S-EPMC5549615 | biostudies-literature
Project description:Background: The reproducibility policy at the journal Biostatistics rewards articles with badges for data and code sharing. This study investigates the effect of badges at increasing reproducible research. Methods: The setting of this observational study is the Biostatistics and Statistics in Medicine (control journal) online research archives. The data consisted of 240 randomly sampled articles from 2006 to 2013 (30 articles per year) per journal. Data analyses included: plotting probability of data and code sharing by article submission date, and Bayesian logistic regression modelling. Results: The probability of data sharing was higher at Biostatistics than the control journal but the probability of code sharing was comparable for both journals. The probability of data sharing increased by 3.9 times (95% credible interval: 1.5 to 8.44 times, p-value probability that sharing increased: 0.998) after badges were introduced at Biostatistics. On an absolute scale, this difference was only a 7.6% increase in data sharing (95% CI: 2 to 15%, p-value: 0.998). Badges did not have an impact on code sharing at the journal (mean increase: 1 time, 95% credible interval: 0.03 to 3.58 times, p-value probability that sharing increased: 0.378). 64% of articles at Biostatistics that provide data/code had broken links, and at Statistics in Medicine, 40%; assuming these links worked only slightly changed the effect of badges on data (mean increase: 6.7%, 95% CI: 0.0% to 17.0%, p-value: 0.974) and on code (mean increase: -2%, 95% CI: -10.0 to 7.0%, p-value: 0.286). Conclusions: The effect of badges at Biostatistics was a 7.6% increase in the data sharing rate, 5 times less than the effect of badges at Psychological Science. Though badges at Biostatistics did not impact code sharing, and had a moderate effect on data sharing, badges are an interesting step that journals are taking to incentivise and promote reproducible research.
| S-EPMC5843843 | biostudies-literature
Project description:BackgroundSystems science approaches like simulation modeling can offer an opportunity for community voice to shape policies. In the episteme of many communities there are elders, leaders, and researchers who are seen as bearers of historic knowledge and can contextualize and interpret contemporary research using knowledge systems of the community. There is a need for a systematic methodology to collaborate with community Knowledge Bearers and Knowledge Interpreters. In this paper we report the results of piloting a systematic methodology for collaborating with a community Knowledge-Bearer and Knowledge-Interpreter to develop a conceptual model revealing the local-level influences and architecture of systems shaping community realities. The use case for this pilot is 'persistent poverty' in the United States, specifically within the inner-city African American community in Baltimore City.MethodsThis pilot of a participatory modeling approach was conducted over a span of 7 sessions and included the following steps, each with an associated script: Step 1: Knowledge-Bearer and Knowledge-Interpreter recruitment Step 2: Relationship building Step 3: Session introduction, Vignette development & enrichment Step 4: Vignette analysis & constructing architecture of systems map Step 5: Augmenting architecture of systems map RESULTS: Each step of the participatory modeling approach resulted in artifacts that were valuable for both the communities and the research effort. Vignette construction resulted in narratives representing a spectrum of lived experiences, trajectories, and outcomes within a community. The collaborative analysis of vignettes yielded the Architecture of Systemic Factors map, that revealed how factors inter-relate to form a system in which lived experience of poverty occurs. A literature search provided an opportunity for the community to contextualize existing research about them using realities of lived experience.ConclusionThis methodology showed that a community Knowledge Bearer can function as communicators and interpreters of their community's knowledge base, can develop coherent narratives of lived experiences within which research and knowledge is contextualized, and can collaboratively construct conceptual mappings necessary for simulation modeling. This participatory modeling approach showed that even if there already exists a vast body of research about a community, collaborating with community gives context to that research and brings together disparate findings within narratives of lived experience.
| S-EPMC10010640 | biostudies-literature
Project description:Being able to replicate research results is the hallmark of science. Replication of research findings using computational models should, in principle, be possible. In this manuscript, we assess code sharing and model documentation practices of 7500 publications about individual-based and agent-based models. The code availability increased over the years, up to 18% in 2018. Model documentation does not include all the elements that could improve the transparency of the models, such as mathematical equations, flow charts, and pseudocode. We find that articles with equations and flow charts being cited more among other model papers, probably because the model documentation is more transparent. The practices of code sharing improve slowly over time, partly due to the emergence of more public repositories and archives, and code availability requirements by journals and sponsors. However, a significant change in norms and habits need to happen before computational modeling becomes a reproducible science.
| S-EPMC7493807 | biostudies-literature
Project description:BackgroundTo improve health-care delivery, care providers must base their services on community health needs and create a seamless continuum of care in which these needs can be met. Though, it is not obvious that providers apply this vision. Experiments with regulated competition in the health systems of many industrialized countries trigger providers to optimize individual organizational goals rather than improve population health from a community perspective. Thus, a tension exists between the need to collaborate and the need to compete. Despite or because of this tension, community health partnerships are being promoted, and this should enforce a needs-based and integrated care delivery.MethodsIn this single case study, we retrospectively explored how local health-care providers in Amsterdam collaborated for more than 30 years, interacting with the changes to the national health-care system. In-depth analysis of interviews, documents and literature focused on the complex relationship between the activities of this health partnership, its nature and its changing context.ResultsThe findings revealed that the partnership itself was successful and sustainable over time, although the partnership lost its initial broad explorative nature and narrowed its strategic focus towards care of the elderly. Furthermore, the realized projects--although they enforced integrated care--lost their community-based character. This declining scope of community-based integrated care seems to have been influenced by the incremental introduction of regulated competition in Dutch health care. This casts doubts on the ability of health partnerships to apply a vision of community-based integrated care within the context of competition.ConclusionCollaborating health-care providers can build seamless continuums of care in a competitive environment, although these will not automatically maximize community health with limited resources. Active policies with regard to health system design, incentive structures and population-based performance measures are warranted in order to insure that community-based integrated care through health partnerships will be more than just policy rhetoric.
| S-EPMC1464130 | biostudies-literature
Project description:Biological Pathway Exchange (BioPAX) is a standard language to represent biological pathways at the molecular and cellular level and to facilitate the exchange of pathway data. The rapid growth of the volume of pathway data has spurred the development of databases and computational tools to aid interpretation; however, use of these data is hampered by the current fragmentation of pathway information across many databases with incompatible formats. BioPAX, which was created through a community process, solves this problem by making pathway data substantially easier to collect, index, interpret and share. BioPAX can represent metabolic and signaling pathways, molecular and genetic interactions and gene regulation networks. Using BioPAX, millions of interactions, organized into thousands of pathways, from many organisms are available from a growing number of databases. This large amount of pathway data in a computable form will support visualization, analysis and biological discovery.
| S-EPMC3001121 | biostudies-literature