Browse
Submit Data
Databases
API
Help

Dataset Information

20 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Thou Shalt Be Reproducible! A Technology Perspective.

ABSTRACT: This article elaborates on reproducibility in psychology from a technological viewpoint. Modern open source computational environments are shown and explained that foster reproducibility throughout the whole research life cycle, and to which emerging psychology researchers should be sensitized, are shown and explained. First, data archiving platforms that make datasets publicly available are presented. Second, R is advocated as the data-analytic lingua franca in psychology for achieving reproducible statistical analysis. Third, dynamic report generation environments for writing reproducible manuscripts that integrate text, data analysis, and statistical outputs such as figures and tables in a single document are described. Supplementary materials are provided in order to get the reader started with these technologies.

SUBMITTER: Mair P

PROVIDER: S-EPMC4943952 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Thou Shalt Be Reproducible! A Technology Perspective.

Mair Patrick P

Frontiers in psychology 20160714

This article elaborates on reproducibility in psychology from a technological viewpoint. Modern open source computational environments are shown and explained that foster reproducibility throughout the whole research life cycle, and to which emerging psychology researchers should be sensitized, are shown and explained. First, data archiving platforms that make datasets publicly available are presented. Second, R is advocated as the data-analytic lingua franca in psychology for achieving reproduc ...[more]

PMID: 27471486

Similar Datasets

Everything Matters: The ReproNim Perspective on Reproducible Neuroimaging.

Project description:There has been a recent major upsurge in the concerns about reproducibility in many areas of science. Within the neuroimaging domain, one approach is to promote reproducibility is to target the re-executability of the publication. The information supporting such re-executability can enable the detailed examination of how an initial finding generalizes across changes in the processing approach, and sampled population, in a controlled scientific fashion. ReproNim: A Center for Reproducible Neuroimaging Computation is a recently funded initiative that seeks to facilitate the "last mile" implementations of core re-executability tools in order to reduce the accessibility barrier and increase adoption of standards and best practices at the neuroimaging research laboratory level. In this report, we summarize the overall approach and tools we have developed in this domain.

| S-EPMC6374302 | biostudies-other

Thou shalt versus thou shalt not: a meta-synthesis of GPs' attitudes to clinical practice guidelines.

Project description:BackgroundGPs' adherence to clinical practice guidelines is variable. Barriers to guideline implementation have been identified but qualitative studies have not been synthesised to explore what underpins these attitudes.AimTo explore and synthesise qualitative research on GPs' attitudes to and experiences with clinical practice guidelines.Design of studySystematic review and meta-synthesis of qualitative studies.MethodPubMed, CINAHL, EMBASE, Social Science Citation Index, and Science Citation Index were used as data sources, and independent data extraction was carried out. Discrepancies were resolved by consensus. Initial thematic analysis was conducted, followed by interpretative synthesis.ResultsSeventeen studies met the inclusion criteria. Five were excluded following quality appraisal. Twelve papers were synthesised which reported research in the UK, US, Canada, and the Netherlands, and covered different clinical guideline topics. Six themes were identified: questioning the guidelines, GPs' experience, preserving the doctor-patient relationship, professional responsibility, practical issues, and guideline format. Comparative analysis and synthesis revealed that GPs' reasons for not following guidelines differed according to whether the guideline in question was prescriptive, in that it encouraged a certain type of behaviour or treatment, or proscriptive, in that it discouraged certain treatments or behaviours.ConclusionPrevious analyses of guidelines have focused on professional attitudes and organisational barriers to adherence. This synthesis suggests that the purpose of the guideline, whether its aims are prescriptive or proscriptive, may influence if and how guidelines are received and implemented.

| S-EPMC2084137 | biostudies-literature

Tissue Barrier-on-Chip: A Technology for Reproducible Practice in Drug Testing.

Project description:One key application of organ-on-chip systems is the examination of drug transport and absorption through native cell barriers such the blood-brain barrier. To overcome previous hurdles related to the transferability of existing static cell cultivation protocols and polydimethylsiloxane (PDMS) as the construction material, a chip platform with key innovations for practical use in drug-permeation testing is presented. First, the design allows for the transfer of barrier-forming tissue into the microfluidic system after cells have been seeded on porous polymer or Si3N4 membranes. From this, we can follow highly reproducible models and cultivation protocols established for static drug testing, from coating the membrane to seeding the cells and cell analysis. Second, the perfusion system is a microscopable glass chip with two fluid compartments with transparent embedded electrodes separated by the membrane. The reversible closure in a clamping adapter requires only a very thin PDMS sealing with negligible liquid contact, thereby eliminating well-known disadvantages of PDMS, such as its limited usability in the quantitative measurements of hydrophobic drug molecule concentrations. Equipped with tissue transfer capabilities, perfusion chamber inertness and air bubble trapping, and supplemented with automated fluid control, the presented system is a promising platform for studying established in vitro models of tissue barriers under reproducible microfluidic perfusion conditions.

| S-EPMC9323870 | biostudies-literature

Structure of human ATG9A: how holey art thou?

Project description:Several studies have provided insight into the unique intracellular localization, dynamic trafficking and diverse repertoire of binding partners of Atg9/ATG9, but structural details of the protein have remained elusive. Guardia and colleagues now report the structure of human ATG9A to a resolution of 2.9 Å, revealing, among other features, an elaborate system of tunnels permeating the ATG9A protein complex.

| S-EPMC7595600 | biostudies-literature

Deciphering next-generation pharmacogenomics: an information technology perspective.

Project description:In the post-genomic era, the rapid evolution of high-throughput genotyping technologies and the increased pace of production of genetic research data are continually prompting the development of appropriate informatics tools, systems and databases as we attempt to cope with the flood of incoming genetic information. Alongside new technologies that serve to enhance data connectivity, emerging information systems should contribute to the creation of a powerful knowledge environment for genotype-to-phenotype information in the context of translational medicine. In the area of pharmacogenomics and personalized medicine, it has become evident that database applications providing important information on the occurrence and consequences of gene variants involved in pharmacokinetics, pharmacodynamics, drug efficacy and drug toxicity will become an integral tool for researchers and medical practitioners alike. At the same time, two fundamental issues are inextricably linked to current developments, namely data sharing and data protection. Here, we discuss high-throughput and next-generation sequencing technology and its impact on pharmacogenomics research. In addition, we present advances and challenges in the field of pharmacogenomics information systems which have in turn triggered the development of an integrated electronic 'pharmacogenomics assistant'. The system is designed to provide personalized drug recommendations based on linked genotype-to-phenotype pharmacogenomics data, as well as to support biomedical researchers in the identification of pharmacogenomics-related gene variants. The provisioned services are tuned in the framework of a single-access pharmacogenomics portal.

| S-EPMC4118603 | biostudies-literature

Progress and Perspective of CRISPR-Cas9 Technology in Translational Medicine.

Project description:Translational medicine aims to improve human health by exploring potential treatment methods developed during basic scientific research and applying them to the treatment of patients in clinical settings. The advanced perceptions of gene functions have remarkably revolutionized clinical treatment strategies for target agents. However, the progress in gene editing therapy has been hindered due to the severe off-target effects and limited editing sites. Fortunately, the development in the clustered regularly interspaced short palindromic repeats associated protein 9 (CRISPR-Cas9) system has renewed hope for gene therapy field. The CRISPR-Cas9 system can fulfill various simple or complex purposes, including gene knockout, knock-in, activation, interference, base editing, and sequence detection. Accordingly, the CRISPR-Cas9 system is adaptable to translational medicine, which calls for the alteration of genomic sequences. This review aims to present the latest CRISPR-Cas9 technology achievements and prospect to translational medicine advances. The principle and characterization of the CRISPR-Cas9 system are firstly introduced. The authors then focus on recent pre-clinical and clinical research directions, including the construction of disease models, disease-related gene screening and regulation, and disease treatment and diagnosis for multiple refractory diseases. Finally, some clinical challenges including off-target effects, in vivo vectors, and ethical problems, and future perspective are also discussed.

| S-EPMC10477906 | biostudies-literature

Technology Considerations for Enabling eSource in Clinical Research: Industry Perspective.

Project description:BackgroundThe technological complexities and broad operational scope of eSource impede coordinated, inter-organizational action on advancing at-scale solutions.MethodsWe introduce an architectural framework for articulating technological considerations across organizations. The architecture neither implies nor endorses solution implementations; rather, it proposes solution functionality based upon principles and good clinical practices.ResultsKey technology considerations include patterns of anticipated use, implications to the current state of clinical trial operations, and the need for new technologies (i.e., IoT, Big Data, Predictive Analytics).ConclusionTechnology considerations drive implications beyond technology-influencing regulatory, process, and ethical realms of clinical research.

| S-EPMC7458892 | biostudies-literature

Thou Shalt Not Bear False Witness Against Null Hypothesis Significance Testing.

Project description:Null hypothesis significance testing (NHST) has been the subject of debate for decades and alternative approaches to data analysis have been proposed. This article addresses this debate from the perspective of scientific inquiry and inference. Inference is an inverse problem and application of statistical methods cannot reveal whether effects exist or whether they are empirically meaningful. Hence, raising conclusions from the outcomes of statistical analyses is subject to limitations. NHST has been criticized for its misuse and the misconstruction of its outcomes, also stressing its inability to meet expectations that it was never designed to fulfil. Ironically, alternatives to NHST are identical in these respects, something that has been overlooked in their presentation. Three of those alternatives are discussed here (estimation via confidence intervals and effect sizes, quantification of evidence via Bayes factors, and mere reporting of descriptive statistics). None of them offers a solution to the problems that NHST is purported to have, all of them are susceptible to misuse and misinterpretation, and some bring around their own problems (e.g., Bayes factors have a one-to-one correspondence with p values, but they are entirely deprived of an inferential framework). Those alternatives also fail to cover a broad area of inference not involving distributional parameters, where NHST procedures remain the only (and suitable) option. Like knives or axes, NHST is not inherently evil; only misuse and misinterpretation of its outcomes needs to be eradicated.

| S-EPMC5991793 | biostudies-literature

SOCIETAL PERSPECTIVE ON COST DRIVERS FOR HEALTH TECHNOLOGY ASSESSMENT IN SINDH, PAKISTAN.

Project description:Understanding cost-drivers and estimating societal costs are important challenges for economic evaluation of health technologies in low- and middle-income countries (LMICs). This study assessed community experiences of health resource usage and perceived cost-drivers from a societal perspective to inform the design of an economic model for the Community Level Interventions for Pre-eclampsia (CLIP) trials.Qualitative research was undertaken alongside the CLIP trial in two districts of Sindh province, Pakistan. Nine focus groups were conducted with a wide range of stakeholders, including pregnant women, mothers-in-law, husbands, fathers-in-law, healthcare providers at community and health facility-levels, and health decision/policy makers at district-level. The societal perspective included out-of-pocket (OOP), health system, and program implementation costs related to CLIP. Thematic analysis was performed using NVivo software.Most pregnant women and male decision makers reported a large burden of OOP costs for in- and out-patient care, informal care from traditional healers, self-medication, childbirth, newborn care, transport to health facility, and missed wages by caretakers. Many healthcare providers identified health system costs associated with human resources for hypertension risk assessment, transport, and communication about patient referrals. Health decision/policy makers recognized program implementation costs (such as the mobile health infrastructure, staff training, and monitoring/supervision) as major investments for the health system.Our investigation of care-seeking practices revealed financial implications for families of pregnant women, and program implementation costs for the health system. The societal perspective provided comprehensive knowledge of cost drivers to guide an economic appraisal of the CLIP trial in Sindh, Pakistan.

| S-EPMC5934709 | biostudies-other

"Holographic" Autostereoscopic Displays: A Perspective on Their Technology and Potential Impact in Chemistry.

Project description:The three-dimensional arrangement of atoms in molecules is essential for understanding their properties and behavior. Traditional 2D representations and digital 3D models presented on 2D media often fall short in conveying the complexity of molecular structures. Autostereoscopic displays, often marketed as "holographic" displays, pose a potential solution to this challenge. These displays, with their multi-view and single-view configurations, promise to advance chemistry education and research by offering accurate 3D representations with depth and parallax. In this perspective, I delve into the possibilities and limitations of autostereoscopic displays in chemistry, discussing the underlying technology and potential applications, from research to teaching and science communication. Multi-view autostereoscopic displays excel in facilitating collaborative work by enabling multiple viewers to simultaneously perceive the same 3D structure from different angles. However, they currently suffer from low resolution and high cost, which could limit their immediate widespread adoption. Conversely, single-view autostereoscopic displays with eye-tracking, while limited to one viewer at a time, provide higher resolution at a lower cost, thus suggesting that they might become the technology of the future given the balance of price to performance. Despite current limitations, autostereoscopic displays possess undeniable potential for shaping the future of chemistry education and research.

| S-EPMC10946886 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data