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1.
Annu Rev Genomics Hum Genet ; 24: 369-391, 2023 08 25.
Artigo em Inglês | MEDLINE | ID: mdl-36791787

RESUMO

The Human Cell Atlas (HCA) is striving to build an open community that is inclusive of all researchers adhering to its principles and as open as possible with respect to data access and use. However, open data sharing can pose certain challenges. For instance, being a global initiative, the HCA must contend with a patchwork of local and regional privacy rules. A notable example is the implementation of the European Union General Data Protection Regulation (GDPR), which caused some concern in the biomedical and genomic data-sharing community. We examine how the HCA's large, international group of researchers is investing tremendous efforts into ensuring appropriate sharing of data. We describe the HCA's objectives and governance, how it defines open data sharing, and ethico-legal challenges encountered early in its development; in particular, we describe the challenges prompted by the GDPR. Finally, we broaden the discussion to address tools and strategies that can be used to address ethical data governance.


Assuntos
Aminas , Ascomicetos , Humanos , Impulso (Psicologia) , União Europeia , Segurança Computacional
2.
Plant J ; 118(2): 584-600, 2024 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-38141174

RESUMO

Phenotyping of model organisms grown on Petri plates is often carried out manually, despite the procedures being time-consuming and laborious. The main reason for this is the limited availability of automated phenotyping facilities, whereas constructing a custom automated solution can be a daunting task for biologists. Here, we describe SPIRO, the Smart Plate Imaging Robot, an automated platform that acquires time-lapse photographs of up to four vertically oriented Petri plates in a single experiment, corresponding to 192 seedlings for a typical root growth assay and up to 2500 seeds for a germination assay. SPIRO is catered specifically to biologists' needs, requiring no engineering or programming expertise for assembly and operation. Its small footprint is optimized for standard incubators, the inbuilt green LED enables imaging under dark conditions, and remote control provides access to the data without interfering with sample growth. SPIRO's excellent image quality is suitable for automated image processing, which we demonstrate on the example of seed germination and root growth assays. Furthermore, the robot can be easily customized for specific uses, as all information about SPIRO is released under open-source licenses. Importantly, uninterrupted imaging allows considerably more precise assessment of seed germination parameters and root growth rates compared with manual assays. Moreover, SPIRO enables previously technically challenging assays such as phenotyping in the dark. We illustrate the benefits of SPIRO in proof-of-concept experiments which yielded a novel insight on the interplay between autophagy, nitrogen sensing, and photoblastic response.


Assuntos
Germinação , Plântula , Fenótipo , Germinação/fisiologia , Sementes , Processamento de Imagem Assistida por Computador
3.
Trends Genet ; 38(2): 113-115, 2022 02.
Artigo em Inglês | MEDLINE | ID: mdl-34740452

RESUMO

Advocates of transparency in science often point to the benefits of open practices for the scientific process. Here, we focus on a possibly underappreciated effect of standards for transparency: their influence on non-scientific decisions. As a case study, we consider the current state of probabilistic genotyping software in forensics.


Assuntos
Genética Forense , Ciências Forenses , Humanos
4.
Genes Cells ; 29(4): 275-281, 2024 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-38351723

RESUMO

Our research activities would be better served if they were communicated in a manner that is openly accessible to the public and all researchers. The research we share is often limited to representative data included in research papers-science would be much more efficient if all reproducible research data were shared alongside detailed methods and protocols, in the paradigm called Open Science. On the other hand, one primary function of research journals is to select manuscripts of good quality, verify the authenticity of the data and its impact, and deliver to the appropriate audience for critical evaluation and verification. In the current paradigm, where publication in a subset of journals is intimately linked to research evaluation, a hypercompetitive "market" has emerged where authors compete to access a limited number of top-tier journals, leading to high rejection rates. Competition among publishers and scientific journals for market dominance resulted in an increase in both the number of journals and the cost of publishing and accessing scientific papers. Here we summarize the current problems and potential solutions from the development of AI technology discussed in the seminar at the 46th Annual Meeting of the Molecular Biology Society of Japan.


Assuntos
Acesso à Informação , Editoração , Japão
5.
Syst Biol ; 73(2): 470-485, 2024 Jul 27.
Artigo em Inglês | MEDLINE | ID: mdl-38507308

RESUMO

Chronograms-phylogenies with branch lengths proportional to time-represent key data on timing of evolutionary events, allowing us to study natural processes in many areas of biological research. Chronograms also provide valuable information that can be used for education, science communication, and conservation policy decisions. Yet, achieving a high-quality reconstruction of a chronogram is a difficult and resource-consuming task. Here we present DateLife, a phylogenetic software implemented as an R package and an R Shiny web application available at www.datelife.org, that provides services for efficient and easy discovery, summary, reuse, and reanalysis of node age data mined from a curated database of expert, peer-reviewed, and openly available chronograms. The main DateLife workflow starts with one or more scientific taxon names provided by a user. Names are processed and standardized to a unified taxonomy, allowing DateLife to run a name match across its local chronogram database that is curated from Open Tree of Life's phylogenetic repository, and extract all chronograms that contain at least two queried taxon names, along with their metadata. Finally, node ages from matching chronograms are mapped using the congruification algorithm to corresponding nodes on a tree topology, either extracted from Open Tree of Life's synthetic phylogeny or one provided by the user. Congruified node ages are used as secondary calibrations to date the chosen topology, with or without initial branch lengths, using different phylogenetic dating methods such as BLADJ, treePL, PATHd8, and MrBayes. We performed a cross-validation test to compare node ages resulting from a DateLife analysis (i.e, phylogenetic dating using secondary calibrations) to those from the original chronograms (i.e, obtained with primary calibrations), and found that DateLife's node age estimates are consistent with the age estimates from the original chronograms, with the largest variation in ages occurring around topologically deeper nodes. Because the results from any software for scientific analysis can only be as good as the data used as input, we highlight the importance of considering the results of a DateLife analysis in the context of the input chronograms. DateLife can help to increase awareness of the existing disparities among alternative hypotheses of dates for the same diversification events, and to support exploration of the effect of alternative chronogram hypotheses on downstream analyses, providing a framework for a more informed interpretation of evolutionary results.


Assuntos
Classificação , Filogenia , Software , Classificação/métodos , Bases de Dados Factuais
6.
Proc Natl Acad Sci U S A ; 119(4)2022 01 25.
Artigo em Inglês | MEDLINE | ID: mdl-35042810

RESUMO

The field of genomics has benefited greatly from its "openness" approach to data sharing. However, with the increasing volume of sequence information being created and stored and the growing number of international genomics efforts, the equity of openness is under question. The United Nations Convention of Biodiversity aims to develop and adopt a standard policy on access and benefit-sharing for sequence information across signatory parties. This standardization will have profound implications on genomics research, requiring a new definition of open data sharing. The redefinition of openness is not unwarranted, as its limitations have unintentionally introduced barriers of engagement to some, including Indigenous Peoples. This commentary provides an insight into the key challenges of openness faced by the researchers who aspire to protect and conserve global biodiversity, including Indigenous flora and fauna, and presents immediate, practical solutions that, if implemented, will equip the genomics community with both the diversity and inclusivity required to respectfully protect global biodiversity.


Assuntos
Povos Indígenas/genética , Disseminação de Informação/ética , Biodiversidade , Genômica/métodos , Humanos , Povos Indígenas/psicologia , Povos Indígenas/estatística & dados numéricos , Disseminação de Informação/métodos , Grupos Populacionais/genética
7.
Proteomics ; 24(3-4): e2300354, 2024 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-38088481

RESUMO

In recent years, there has been a tremendous evolution in the high-throughput, tandem mass spectrometry-based analysis of intact proteins, also known as top-down proteomics (TDP). Both hardware and software have developed to the point that the technique has largely entered the mainstream, and large-scale, ambitious, multi-laboratory initiatives have started to make their appearance in the literature. For this, however, more convenient and robust data sharing and reuse will be required. Walzer et al. have created TopDownApp, a customisable, open platform for visualisation and analysis of TDP data, which they hope will be a step in this direction. As they point out, other benefits of such data sharing and interoperability would include reanalysis of published datasets, as well as the prospect of using large amounts of data to train machine learning algorithms. In time, this work could prove to be a valuable resource in the move towards a future of greater TDP data findability, accessibility, interoperability and reusability.


Assuntos
Proteômica , Software , Proteômica/métodos , Algoritmos , Espectrometria de Massas em Tandem , Proteínas de Ligação a DNA
8.
Proteomics ; 24(3-4): e2200403, 2024 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-37787899

RESUMO

Although Top-down (TD) proteomics techniques, aimed at the analysis of intact proteins and proteoforms, are becoming increasingly popular, efforts are needed at different levels to generalise their adoption. In this context, there are numerous improvements that are possible in the area of open science practices, including a greater application of the FAIR (Findable, Accessible, Interoperable, and Reusable) data principles. These include, for example, increased data sharing practices and readily available open data standards. Additionally, the field would benefit from the development of open data analysis workflows that can enable data reuse of public datasets, something that is increasingly common in other proteomics fields.


Assuntos
Proteínas , Proteômica , Proteômica/métodos , Proteínas/análise , Fluxo de Trabalho
9.
BMC Bioinformatics ; 25(1): 110, 2024 Mar 12.
Artigo em Inglês | MEDLINE | ID: mdl-38475691

RESUMO

BACKGROUND: The analysis of large and complex biological datasets in bioinformatics poses a significant challenge to achieving reproducible research outcomes due to inconsistencies and the lack of standardization in the analysis process. These issues can lead to discrepancies in results, undermining the credibility and impact of bioinformatics research and creating mistrust in the scientific process. To address these challenges, open science practices such as sharing data, code, and methods have been encouraged. RESULTS: CREDO, a Customizable, REproducible, DOcker file generator for bioinformatics applications, has been developed as a tool to moderate reproducibility issues by building and distributing docker containers with embedded bioinformatics tools. CREDO simplifies the process of generating Docker images, facilitating reproducibility and efficient research in bioinformatics. The crucial step in generating a Docker image is creating the Dockerfile, which requires incorporating heterogeneous packages and environments such as Bioconductor and Conda. CREDO stores all required package information and dependencies in a Github-compatible format to enhance Docker image reproducibility, allowing easy image creation from scratch. The user-friendly GUI and CREDO's ability to generate modular Docker images make it an ideal tool for life scientists to efficiently create Docker images. Overall, CREDO is a valuable tool for addressing reproducibility issues in bioinformatics research and promoting open science practices.


Assuntos
Biologia Computacional , Software , Reprodutibilidade dos Testes , Biologia Computacional/métodos
10.
BMC Genomics ; 25(1): 694, 2024 Jul 15.
Artigo em Inglês | MEDLINE | ID: mdl-39009985

RESUMO

Animals plastically adjust their physiological and behavioural phenotypes to conform to their social environment-social niche conformance. The degree of sexual competition is a critical part of the social environment to which animals adjust their phenotypes, but the underlying genetic mechanisms are poorly understood. We conducted a study to investigate how differences in sperm competition risk affect the gene expression profiles of the testes and two brain areas (posterior pallium and optic tectum) in breeding male zebra finches (Taeniopygia castanotis). In this pre-registered study, we investigated a large sample of 59 individual transcriptomes. We compared two experimental groups: males held in single breeding pairs (low sexual competition) versus those held in two pairs (elevated sexual competition) per breeding cage. Using weighted gene co-expression network analysis (WGCNA), we observed significant effects of the social treatment in all three tissues. However, only the treatment effects found in the pallium were confirmed by an additional randomisation test for statistical robustness. Likewise, the differential gene expression analysis revealed treatment effects only in the posterior pallium (ten genes) and optic tectum (six genes). No treatment effects were found in the testis at the single gene level. Thus, our experiments do not provide strong evidence for transcriptomic adjustment specific to manipulated sperm competition risk. However, we did observe transcriptomic adjustments to the manipulated social environment in the posterior pallium. These effects were polygenic rather than based on few individual genes with strong effects. Our findings are discussed in relation to an accompanying paper using the same animals, which reports behavioural results consistent with the results presented here.


Assuntos
Tentilhões , Transcriptoma , Animais , Masculino , Tentilhões/genética , Tentilhões/fisiologia , Testículo/metabolismo , Perfilação da Expressão Gênica , Comportamento Sexual Animal , Colículos Superiores/metabolismo , Espermatozoides/metabolismo , Comportamento Social
11.
Am J Epidemiol ; 2024 May 23.
Artigo em Inglês | MEDLINE | ID: mdl-38794897

RESUMO

Real-world evidence (RWE) studies are increasingly used to inform policy and clinical decisions. However, there remain concerns about the credibility and reproducibility of RWE studies. Observational researchers should highlight the level of transparency of their studies by providing a succinct statement addressing study transparency with the publication of every paper, poster, or presentation that reports on a RWE study. In this paper, we propose a framework for an explicit transparency statement that declares the level of transparency a given RWE study has achieved across five key domains: 1) protocol, 2) pre-registration, 3) data, 4) code sharing, and 5) reporting checklists.

12.
Proc Biol Sci ; 291(2021): 20231422, 2024 Apr 30.
Artigo em Inglês | MEDLINE | ID: mdl-38654647

RESUMO

Researchers in the biological and behavioural sciences are increasingly conducting collaborative, multi-sited projects to address how phenomena vary across ecologies. These types of projects, however, pose additional workflow challenges beyond those typically encountered in single-sited projects. Through specific attention to cross-cultural research projects, we highlight four key aspects of multi-sited projects that must be considered during the design phase to ensure success: (1) project and team management; (2) protocol and instrument development; (3) data management and documentation; and (4) equitable and collaborative practices. Our recommendations are supported by examples from our experiences collaborating on the Evolutionary Demography of Religion project, a mixed-methods project collecting data across five countries in collaboration with research partners in each host country. To existing discourse, we contribute new recommendations around team and project management, introduce practical recommendations for exploring the validity of instruments through qualitative techniques during piloting, highlight the importance of good documentation at all steps of the project, and demonstrate how data management workflows can be strengthened through open science practices. While this project was rooted in cross-cultural human behavioural ecology and evolutionary anthropology, lessons learned from this project are applicable to multi-sited research across the biological and behavioural sciences.


Assuntos
Ciências do Comportamento , Coleta de Dados , Humanos , Coleta de Dados/métodos , Comparação Transcultural , Projetos de Pesquisa , Ecologia/métodos
13.
Brief Bioinform ; 23(1)2022 01 17.
Artigo em Inglês | MEDLINE | ID: mdl-34850820

RESUMO

Data resources are essential for the long-term preservation of scientific data and the reproducibility of science. The SIB Swiss Institute of Bioinformatics provides the life science community with a portfolio of openly accessible, high-quality databases and software platforms, which vary from expert-curated knowledgebases, such as UniProtKB/Swiss-Prot (part of the UniProt consortium) and STRING, to online platforms such as SWISS-MODEL and SwissDrugDesign. SIB's mission is to ensure that these resources are available in the long term, as long as their return on investment and their scientific impact are high. To this end, SIB provides its resources, in addition to stable financial support, with a range of high-quality, innovative services that are, to our knowledge, unique in the field. Through this first-class management framework with central services, such as user-centric consulting activities, legal support, open-science guidance, knowledge sharing and training efforts, SIB supports the promotion of excellence in resource development and operation. This review presents the ecosystem of data resources at SIB; the process used for the identification, evaluation and development of resources; and the support activities that SIB provides. A set of indicators has been put in place to select the resources and establish quality standards, reflecting their multifaceted nature and complexity. Through this paper, the reader will discover how SIB's leading tools and databases are fostered by the institute, leading them to be best-in-class resources able to tackle the burning matters that society faces from disease outbreaks and cancer to biodiversity and open science.


Assuntos
Biologia Computacional , Ecossistema , Animais , Bases de Dados de Proteínas , Estágios do Ciclo de Vida , Reprodutibilidade dos Testes
14.
Magn Reson Med ; 91(5): 1803-1821, 2024 May.
Artigo em Inglês | MEDLINE | ID: mdl-38115695

RESUMO

PURPOSE: K trans $$ {K}^{\mathrm{trans}} $$ has often been proposed as a quantitative imaging biomarker for diagnosis, prognosis, and treatment response assessment for various tumors. None of the many software tools for K trans $$ {K}^{\mathrm{trans}} $$ quantification are standardized. The ISMRM Open Science Initiative for Perfusion Imaging-Dynamic Contrast-Enhanced (OSIPI-DCE) challenge was designed to benchmark methods to better help the efforts to standardize K trans $$ {K}^{\mathrm{trans}} $$ measurement. METHODS: A framework was created to evaluate K trans $$ {K}^{\mathrm{trans}} $$ values produced by DCE-MRI analysis pipelines to enable benchmarking. The perfusion MRI community was invited to apply their pipelines for K trans $$ {K}^{\mathrm{trans}} $$ quantification in glioblastoma from clinical and synthetic patients. Submissions were required to include the entrants' K trans $$ {K}^{\mathrm{trans}} $$ values, the applied software, and a standard operating procedure. These were evaluated using the proposed OSIP I gold $$ \mathrm{OSIP}{\mathrm{I}}_{\mathrm{gold}} $$ score defined with accuracy, repeatability, and reproducibility components. RESULTS: Across the 10 received submissions, the OSIP I gold $$ \mathrm{OSIP}{\mathrm{I}}_{\mathrm{gold}} $$ score ranged from 28% to 78% with a 59% median. The accuracy, repeatability, and reproducibility scores ranged from 0.54 to 0.92, 0.64 to 0.86, and 0.65 to 1.00, respectively (0-1 = lowest-highest). Manual arterial input function selection markedly affected the reproducibility and showed greater variability in K trans $$ {K}^{\mathrm{trans}} $$ analysis than automated methods. Furthermore, provision of a detailed standard operating procedure was critical for higher reproducibility. CONCLUSIONS: This study reports results from the OSIPI-DCE challenge and highlights the high inter-software variability within K trans $$ {K}^{\mathrm{trans}} $$ estimation, providing a framework for ongoing benchmarking against the scores presented. Through this challenge, the participating teams were ranked based on the performance of their software tools in the particular setting of this challenge. In a real-world clinical setting, many of these tools may perform differently with different benchmarking methodology.


Assuntos
Meios de Contraste , Imageamento por Ressonância Magnética , Humanos , Reprodutibilidade dos Testes , Imageamento por Ressonância Magnética/métodos , Software , Algoritmos
15.
Magn Reson Med ; 91(5): 1787-1802, 2024 May.
Artigo em Inglês | MEDLINE | ID: mdl-37811778

RESUMO

PURPOSE: To create an inventory of image processing pipelines of arterial spin labeling (ASL) and list their main features, and to evaluate the capability, flexibility, and ease of use of publicly available pipelines to guide novice ASL users in selecting their optimal pipeline. METHODS: Developers self-assessed their pipelines using a questionnaire developed by the Task Force 1.1 of the ISMRM Open Science Initiative for Perfusion Imaging. Additionally, each publicly available pipeline was evaluated by two independent testers with basic ASL experience using a scoring system created for this purpose. RESULTS: The developers of 21 pipelines filled the questionnaire. Most pipelines are free for noncommercial use (n = 18) and work with the standard NIfTI (Neuroimaging Informatics Technology Initiative) data format (n = 15). All pipelines can process standard 3D single postlabeling delay pseudo-continuous ASL images and primarily differ in their support of advanced sequences and features. The publicly available pipelines (n = 9) were included in the independent testing, all of them being free for noncommercial use. The pipelines, in general, provided a trade-off between ease of use and flexibility for configuring advanced processing options. CONCLUSION: Although most ASL pipelines can process the common ASL data types, only some (namely, ASLPrep, ASLtbx, BASIL/Quantiphyse, ExploreASL, and MRICloud) are well-documented, publicly available, support multiple ASL types, have a user-friendly interface, and can provide a useful starting point for ASL processing. The choice of an optimal pipeline should be driven by specific data to be processed and user experience, and can be guided by the information provided in this ASL inventory.


Assuntos
Processamento de Imagem Assistida por Computador , Imageamento Tridimensional , Marcadores de Spin , Processamento de Imagem Assistida por Computador/métodos , Imageamento Tridimensional/métodos , Artérias , Imagem de Perfusão , Circulação Cerebrovascular , Imageamento por Ressonância Magnética/métodos , Perfusão
16.
BMC Med Res Methodol ; 24(1): 93, 2024 Apr 22.
Artigo em Inglês | MEDLINE | ID: mdl-38649798

RESUMO

BACKGROUND: The dissemination of clinical trial results is an important scientific and ethical endeavour. This survey of completed interventional studies in a French academic center describes their reporting status. METHODS: We explored all interventional studies sponsored by Rennes University Hospital identified on the French Open Science Monitor which tracks trials registered on EUCTR or clinicaltrials.gov, and provides an automatic assessment of the reporting of results. For each study, we ascertained the actual reporting of results using systematic searches on the hospital internal database, bibliographic databases (Google Scholar, PubMed), and by contacting all principal investigators (PIs). We describe several features (including total budget and numbers of trial participants) of the studies that did not report any results. RESULTS: The French Open Science Monitor identified 93 interventional studies, among which 10 (11%) reported results. In contrast, our survey identified 36 studies (39%) reporting primary analysis results and an additional 18 (19%) reporting results for secondary analyses (without results for their primary analysis). The overall budget for studies that did not report any results was estimated to be €5,051,253 for a total of 6,735 trial participants. The most frequent reasons for the absence of results reported by PIs were lack of time for 18 (42%), and logistic difficulties (e.g. delay in obtaining results or another blocking factor) for 12 (28%). An association was found between non-publication and negative results (adjusted Odds Ratio = 4.70, 95% Confidence Interval [1.67;14.11]). CONCLUSIONS: Even allowing for the fact that automatic searches underestimate the number of studies with published results, the level of reporting was disappointingly low. This amounts to a waste of trial participants' implication and money. Corrective actions are needed. TRIAL REGISTRATION: https://osf.io/q5hcs.


Assuntos
Ensaios Clínicos como Assunto , Humanos , Centros Médicos Acadêmicos/estatística & dados numéricos , Ensaios Clínicos como Assunto/estatística & dados numéricos , Ensaios Clínicos como Assunto/métodos , Ensaios Clínicos como Assunto/economia , França , Projetos de Pesquisa , Inquéritos e Questionários , Estudos Transversais
17.
BMC Med Res Methodol ; 24(1): 152, 2024 Jul 17.
Artigo em Inglês | MEDLINE | ID: mdl-39020325

RESUMO

When different researchers study the same research question using the same dataset they may obtain different and potentially even conflicting results. This is because there is often substantial flexibility in researchers' analytical choices, an issue also referred to as "researcher degrees of freedom". Combined with selective reporting of the smallest p-value or largest effect, researcher degrees of freedom may lead to an increased rate of false positive and overoptimistic results. In this paper, we address this issue by formalizing the multiplicity of analysis strategies as a multiple testing problem. As the test statistics of different analysis strategies are usually highly dependent, a naive approach such as the Bonferroni correction is inappropriate because it leads to an unacceptable loss of power. Instead, we propose using the "minP" adjustment method, which takes potential test dependencies into account and approximates the underlying null distribution of the minimal p-value through a permutation-based procedure. This procedure is known to achieve more power than simpler approaches while ensuring a weak control of the family-wise error rate. We illustrate our approach for addressing researcher degrees of freedom by applying it to a study on the impact of perioperative p a O 2 on post-operative complications after neurosurgery. A total of 48 analysis strategies are considered and adjusted using the minP procedure. This approach allows to selectively report the result of the analysis strategy yielding the most convincing evidence, while controlling the type 1 error-and thus the risk of publishing false positive results that may not be replicable.


Assuntos
Pesquisadores , Humanos , Pesquisadores/estatística & dados numéricos , Projetos de Pesquisa , Interpretação Estatística de Dados , Pesquisa Biomédica/métodos , Modelos Estatísticos , Complicações Pós-Operatórias/prevenção & controle
18.
Pharmacoepidemiol Drug Saf ; 33(6): e5815, 2024 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-38783412

RESUMO

Electronic health records (EHRs) and other administrative health data are increasingly used in research to generate evidence on the effectiveness, safety, and utilisation of medical products and services, and to inform public health guidance and policy. Reproducibility is a fundamental step for research credibility and promotes trust in evidence generated from EHRs. At present, ensuring research using EHRs is reproducible can be challenging for researchers. Research software platforms can provide technical solutions to enhance the reproducibility of research conducted using EHRs. In response to the COVID-19 pandemic, we developed the secure, transparent, analytic open-source software platform OpenSAFELY designed with reproducible research in mind. OpenSAFELY mitigates common barriers to reproducible research by: standardising key workflows around data preparation; removing barriers to code-sharing in secure analysis environments; enforcing public sharing of programming code and codelists; ensuring the same computational environment is used everywhere; integrating new and existing tools that encourage and enable the use of reproducible working practices; and providing an audit trail for all code that is run against the real data to increase transparency. This paper describes OpenSAFELY's reproducibility-by-design approach in detail.


Assuntos
COVID-19 , Registros Eletrônicos de Saúde , Software , Humanos , Reprodutibilidade dos Testes , COVID-19/epidemiologia , Projetos de Pesquisa
19.
Pharmacoepidemiol Drug Saf ; 33(3): e5728, 2024 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-37984998

RESUMO

PURPOSE: The use of open-source programming languages can facilitate open science practices in real-world evidence (RWE) studies. Real-world studies often rely on using big data, which makes using such languages complicated. We demonstrate an efficient approach that enables RWE researchers to use R to undertake RWE analysis tasks from cohort building to reporting. METHODS: Using the Merative Marketscan data (2017-2019), we developed an R function to transform the data into parquet format to be used in R. Then, we compared the differences in data size before and after transformation. We compared the performance of the transformed data in R to the original data in terms of numerical consistency and running times required to complete simple exploratory tasks. To show how the transformed databases can be used in practice, we conducted a simplified replication of an active comparator new user study from the literature. All codes are available on GitHub. RESULTS: Our approach exhibited high efficiency in data storage, as evidenced by the converted data size, which ranged from 10% to 43% of that of the original data files. The runtime of the exploratory tasks in R generally outperformed that of the original data with SAS. We showed, through example, how the converted data can be efficiently used to implement an RWE study. CONCLUSION: We demonstrate a free and efficient solution to facilitate the use of open-source programming languages with big real-world databases, which can facilitate the adoption of open science practices.


Assuntos
Análise de Dados , Armazenamento e Recuperação da Informação , Humanos , Bases de Dados Factuais
20.
Clin Trials ; 21(1): 40-50, 2024 02.
Artigo em Inglês | MEDLINE | ID: mdl-37904489

RESUMO

INTRODUCTION: Neurofibromatosis 1 and schwannomatosis are characterized by potential lifelong morbidity and life-threatening complications. To date, however, diagnostic and predictive biomarkers are an unmet need in this patient population. The inclusion of biomarker discovery correlatives in neurofibromatosis 1/schwannomatosis clinical trials enables study of low-incidence disease. The implementation of a common data model would further enhance biomarker discovery by enabling effective concatenation of data from multiple studies. METHODS: The Response Evaluation in Neurofibromatosis and Schwannomatosis biomarker working group reviewed published data on emerging trends in neurofibromatosis 1 and schwannomatosis biomarker research and developed recommendations in a series of consensus meetings. RESULTS: Liquid biopsy has emerged as a promising assay for neurofibromatosis 1/schwannomatosis biomarker discovery and validation. In addition, we review recommendations for a range of biomarkers in clinical trials, neurofibromatosis 1/schwannomatosis-specific data annotations, and common data models for data integration. CONCLUSION: These Response Evaluation in Neurofibromatosis and Schwannomatosis consensus guidelines are intended to provide best practices for the inclusion of biomarker studies in neurofibromatosis 1/schwannomatosis clinical trials, data, and sample annotation and to lay a framework for data harmonization and concatenation between trials.


Assuntos
Neurilemoma , Neurofibromatoses , Neurofibromatose 1 , Neurofibromatose 2 , Neoplasias Cutâneas , Humanos , Neurofibromatose 1/diagnóstico , Neurofibromatose 2/diagnóstico , Neurofibromatose 2/patologia , Neurofibromatoses/diagnóstico , Neurofibromatoses/terapia , Neurofibromatoses/patologia , Biomarcadores
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