EDUCATIONAL CORNER

Tools for Researchers
A teaching tool about the fickle p-value and other statistical principles based on real-life data
March 30, 2021

A poor understanding of what results from statistical tests do and do not mean and an over-reliance on p-values is seen…

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How to organize data in a spreadsheet?
December 18, 2020

Spreadsheets are widely used as a digital tool to capture, organize, process and archive information. However, to organize the information provided…

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Successful adaption of the EQIPD Quality System to specific research needs
December 18, 2020

The EQIPD Quality System is the result of a collaborative effort between several people and organizations, yet it cannot address all…

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Ten simple rules on how to write a standard operating procedure
October 8, 2020

The long-term accessibility of research data is fundamental in the economy of the research production process. However, the availability of data…

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EQIPD: PAASP’s contribution to the new Quality System for preclinical research
October 8, 2020

EQIPD (European Quality In Preclinical Data) is a project that was funded by the Innovative Medicine Initiative with the vision to enable a…

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Signing digitally with Microsoft
August 17, 2020

A. Background & Definitions Microsoft Office (incl. Word, Excel and PowerPoint) offers the possibility to create a digital signature (digital ID) as…

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R script BestDose
August 17, 2020

library(scales)library(ggplot2) ## sample sizen1 <- 8n2 <- 16n3 <- 32n4 <- 64 ## iterations m <- 500yfig <- vector()xfig <- vector()facetfig…

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Risk‐of‐bias VISualization (robvis): An R package and Shiny web app for visualizing risk‐of‐bias assessments
August 17, 2020

There is currently no generic tool for producing figures to display and explore the risk‐of‐bias assessments that routinely take place as…

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Octopus: The primary research record
May 28, 2020

Created in partnership with the UK Reproducibility Network, the Octopus platform is free to use and publishes all kinds of scientific…

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Using Microsoft OneNote as an ELN
May 28, 2020

Electronic research data documentation can be achieved with either comprehensive software applications or “do-it-yourself” solutions. Whereas the first is often quite…

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Sample Size Matters – An App Exploring Sample Size and Power
March 31, 2020

Problems with statistical analysis and data visualization in published papers (REF1, REF2, REF3, REF4) have led to calls to improve training for biomedical scientists….

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The Embassy of Good Science – An online platform fostering research integrity
March 31, 2020

By Iris Lechner The field of research integrity is growing substantially. An increasing number of guidelines and initiatives to foster responsible research…

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Biological vs technical replicates: Now from a data analysis perspective: R script
March 31, 2020

This is the R Script referenced in the blog post LINK

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Biological vs technical replicates: Now from a data analysis perspective
March 31, 2020

We have discussed this topic several times before (HERE and HERE). There seems to be a growing understanding that, when reporting an experiment’s…

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Is N-Hacking Ever OK? A simulation-based study
January 2, 2020

After an experiment has been completed and analyzed, a trend may be observed that is “not quite significant”. Sometimes in this…

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Thoughts on How Institutions Can Promote a Culture of Research Integrity
November 22, 2019

By Dr. Michael Lauer (NIH) Link to web page

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Toward Good In Vitro Reporting Standards
November 22, 2019

Many areas of biomedical science have developed reporting standards and checklists to support the adequate reporting of scientific efforts, but in…

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New Handbook of Experimental Pharmacology focusing on Good Research Practice
November 22, 2019

The Handbook of Experimental Pharmacology is one of the most authoritative and influential book series in pharmacology. It provides critical and…

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fiddle: the file drawer data liberation effort tool
August 12, 2019

fiddle is a free, open source “matchmaking” tool designed to help researchers to identify the publication format that will work best for…

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Want to learn about EQIPD?
August 7, 2019

A series of videos is published about EQIPD by the ECNP network. The first video gives a brief introduction by Dr…

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Updated review of electronic laboratory notebooks (ELNs) published by LabsExplorer
May 22, 2019

LabsExplorer has recently published an updated review on electronic lab notebooks. The first review was published in 2017 (LINK) giving a…

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MANILA – A web tool for designing reproducible and transparent preclinical intervention studies
May 22, 2019

Teemu D. Laajala1,21: University of Turku, Turku (Finland), Department of Mathematics and Statistics2: University of Colorado, Denver (CO, US), Anschutz Medical…

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FAIRsharing as a community approach to standards, repositories and policies
May 22, 2019

We say we need standards, but do we use them?The scientific community, funders and publishers endorse the concept that common data…

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Within-subject study designs: Latin Square?
March 11, 2019

In within-subject study designs (also known as the cross-over), subjects may be given sequences of treatments with the intent of studying…

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Why we need to report more than ’Data were Analyzed by t-tests or ANOVA’
March 11, 2019

In this article,Weissgerber et al. present findings suggesting that scientific publications are often lacking sufficient information about the statistical methods used,…

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Visualization of Biomedical Data
March 11, 2019

The rapid increase in volume and complexity of biomedical data requires changes in research, communication, and clinical practices. This includes learning…

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Workshop at ERA-NET Neuron meeting
January 30, 2019

ERA-NET Neuron organised a workshop research data quality on January 22nd, 2019 in Bonn. PAASP Team members, Anton Bespalov and Martin…

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Collection of resources for the use of R in study design and analysis
December 20, 2018

In the recent report on „Digital tools and services to support research replicability and verifiability”, Caroline Skirrow and Markus Munafó have argued that…

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Digital tools and services to support research replicability and verifiability
December 20, 2018

Digital tools hold promise for improving replicability and verifiability of scientific research. In this paper, the availability and use of such…

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Power analysis for two-sided t-test
December 20, 2018

The example below does not require any additional R packages to be installed (i.e. runs with the basic R installation).This example…

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Useful Tools and Resources November 2018
November 17, 2018

A new video resource for introductory training on the 3Rs The NC3R published a new educational video on the 3Rs (replacement,…

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Simple changes of individual studies can improve the reproducibility of the biomedical scientific process as a whole
November 17, 2018

Today, the probability of successfully publishing negative/null results in biomedical research is lower than that for positive results. For instance, negative…

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New tutorial video by the NC3R
September 14, 2018

The NC3R published a new educational video on the 3Rs (replacement, refinement and replacement) on their web page. It is a…

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NC3R Workshop: ‘Improving peer review of in vivo research proposals’
September 10, 2018

On May 9th, 2018, a workshop hosted by the NC3Rs about „Improving peer review of in vivo research proposals“ and included…

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“How to pick an electronic laboratory notebook?
September 10, 2018

Commentary about the Nature-Toolbox article by Roberta Kwok (August 6th, 2018) Laboratory Notebooks (LN) play a key role in research since…

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Genetic and transcriptional evolution alters cancer cell line drug response
September 10, 2018

In this paper, published in Nature, the authors analysed how different cancer cells are – not so much from the original…

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A repository for protocols – protocols.io
August 22, 2018

Lenny Teytelman wrote in a Nature – World View article about the necessity to share experimental protocols to be able to…

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Unambiguous identification of antibodies, cell lines and organisms around the globe: A call for the Research Resource ID
August 21, 2018

Unambiguous identification of antibodies, cell lines and organisms around the globe: A call for the Research Resource ID The reproducibility crisis…

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FAIR and ALCOAplus – data management principles
August 13, 2018

Data recording practices play a central element in research and can vary largely from lab to lab and researcher to researcher….

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Bayes’ Theorem: How do we weigh evidence to make decisions?
July 20, 2018

In this clearly and graphically explained educational video, Amber Biology offers an intuitive introduction to Bayes’ Theorem, using biomarkers and ovarian cancer…

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Four simple ways to increase power without increasing the sample size
July 9, 2018

Underpowered experiments have three problems: true effects are harder to detect, the true effects that are detected tend to have inflated…

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Recommendations for the Design and Analysis of In Vivo Electrophysiology Studies
July 9, 2018

Recommendations for the Design and Analysis of In Vivo Electrophysiology Studies The Journal of Neuroscience has recently released a series of…

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Newly developed ‘Harmonized animal research reporting principles’ (HARRP) published
July 9, 2018

The International Council for Laboratory Animal Science (ICLAS) has recently published Harmonized Animal Research Reporting Principles (HARRP), the first step of…

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New research platform Springer Nature Experiments
July 9, 2018

On 2018 July 25th, the SpringerProtocols.com platform will be deactivated and replaced by the new research platform Springer Nature Experiments, a…

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How to grow a healthy lab
June 6, 2018

A healthy research environment is fundamental to good science. However, this is an aspect that is rarely discussed. That’s partly because…

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What exactly is N in cell culture and animal experiments?
June 6, 2018

“Accurate Design of in vitro experiments – Why does it matter?” was the name of a previous post (LINK) from our…

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Improving Reproducibility in Research – a Healthcare Triage series
March 30, 2018

This episode is part of Healthcare Triage’s series on Improving Reproducibility in Research. The Introduction to the series can be found…

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All preclinical trials should be registered in advance in an online registry
February 27, 2018

The Food and Drug Administration Act of 2007 established requirements for the preregistration of clinical trials and also set penalties for…

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Abstract Sifter: a comprehensive front-end system to PubMed
February 27, 2018

In this article, Nancy Baker and colleagues introduce the Abstract Sifter, a Microsoft Excel based application that enhances existing search capabilities…

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Simple statistics
February 1, 2018

This website was published by Tom MacWright and contributers to provide a library of statistical methods in readible JavaScript. This detailed…

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PAASP and Phinnex
December 19, 2017

PAASP, Henrich Pharma Consulting and Global Clinical Trials (GCT) are the founding members of the Pharma Innovation Excellence (PHINNEX) consortium What…

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The Experimental Design Assistant
November 10, 2017

Addressing the common problems that researchers encounter when designing and analyzing animal experiments will improve the reliability of in vivo research….

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Simple Randomisation
October 11, 2017

A randomization tool for the daily routine The case study in this Newsletter illustrates very well the importance of study subject…

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Block randomisation
October 11, 2017

In this section we provide information about useful tools for designing and analyzing experiments – instruments and equipment, which we at…

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Tools and resources – September 2017
September 28, 2017

In this Newsletter issue, we introduce helpful resources for educational and training purposes, which were recently published and which all address…

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Useful Tools in Newsletter September 2017
September 19, 2017

In this Newsletter issue, we introduce helpful resources for educational and training purposes, which were recently published and which all address…

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Webinar bei Martin Michel
January 30, 2017

Prof. Dr. Martin Michel presented the November Cohen Veterans Bioscience Webinar on November 16th from 12 pm noon – 1 pm ET. Martin…

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Accurate design of in vitro experiments – why does it matter?
August 24, 2016

Good statistical design is a key aspect of meaningful research. Elements such as data robustness, randomization and blinding are widely recognized…

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Searching for significance
August 20, 2016

To examine associations between urinary chemical concentrations and adult health status, the US Centers for Disease Control and Prevention (CDC) measured…

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Block randomization: R code
July 22, 2016

There are a variety of free online tools that can be easily accessed to address various data analysis needs, such as…

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E-Learning tools and MOOCs II
May 22, 2016

E-learning platforms and Massive Open Online Courses (MOOCs) are picking up momentum in popularity and are an emerging new model for…

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E-learning tools and MOOCs
April 22, 2016

E-learning platforms and Massive Open Online Courses (MOOCs) are picking up momentum in popularity and are an emerging new model for…

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