The Hub is looking for testers!
If you're interested in using the latest version of the SHADE app, which is free, open to all and easy to use, write to shiny-stats@pasteur.fr
Combining statistics and biology: an imperative for the quality of experimental results
Since 2018, Institut Pasteur's Bioinformatics and Biostatistics Hub has been collaborating with the Pasteurian animal facilities and the Comité d'Éthique en Expérimentation Animale (CETEA) n°89 to evaluate the statistical aspects of Project Authorization Requests (DAP) in animal experimentation. These experts' review of the sections on statistical approaches and analyses (3.3.6.2 "Reduction strategies") revealed that they are often poorly filled, and that it is essential to initiate collaboration between statisticians and biologists right from the experimental design phase.
Indeed, neglecting this step can lead to major problems in terms of the quality of experimental results, including :
- statistical confusion between experimental factors and technical effects,
- an inflation of false positives,
- a general lack of robustness and reproducibility of results (or data).
In addition to the scientific issues linked to reproducibility, this also raises ethical questions about the appropriate use of animal models in research.
"SHADE” : experimental design optimization at the click of a button
To meet these challenges, research engineers Emeline Perthame, Pascal Campagne and Elise Jacquemet, from the Institut Pasteur's Bioinformatics and Biostatistics Hub, have collaborated with Marion Bérard, Deputy Head of the Central Animal House and CETEA Scientific Secretary, to develop an experimental planning software package called SHADE (SHiny Application for Designs of Experiments).
This application allows to :
- Calculate the number of subjects required for an animal experiment ("Power analysis")
- Automatically write the corresponding paragraph for DAPs
Developed to meet the needs of users and project leaders, and to fill the gaps left by existing systems, SHADE is proving to be an indispensable experimental planning tool. The interface enables "power analyses" to be carried out to determine the number of animals required according to the test to be carried out and the variations expected (e.g. weight loss, tumor size, etc.), thus guaranteeing sufficient statistical power to detect a given effect size.
DAP simplification and optimization with SHADE
The SHADE application automatically writes a concise text - available in French and English - for section 3.3.6.2 "Reduction strategies" of the DAPs. This text is structured around important concepts and keywords, such as the test used, variables, expected differences, test power and number of animals required. This feature simplifies the drafting of DAPs by researchers, facilitates rereading by reviewers and improves evaluation by CETEA, while guaranteeing the accuracy of statistical data and optimizing the use of animals.
Since its adoption in March 2019, the SHADE application has made a real improvement to Institut Pasteur's animal experimentation statistics. It has simplified and clarified the statistical aspects for project sponsors, while facilitating the Project Authorization Request process. It has also made it possible to consolidate experimental designs, by taking into account factors such as the influence of sex and the "cage effect".
Experimental planning accessible to all: adopt the SHADE reflex
The SHADE application is free and does not require an account (it does not store any data). It is already available to everyone at shade.pasteur.fr. It stands out for its simplicity and speed of use compared with other experimental planning software. Designed for non-statisticians, SHADE is intended for use by all project managers - whether or not they use animals - at the experimental design stage.
A webinar has been organized by FC3R on December 7 to demonstrate its use.
An even more ergonomic software interface will be available in early 2024. Thereafter, videoconference training and video tutorials should be available. A French version of the English tutorial is also planned.
In the course of its collaboration with animal houses, CETEA and researchers on the Pasteur campus, the Hub has set up numerous other initiatives in support of research. Meet us on December 7 to find out more!