Practical Guides: CRS Primers

Gorka Fraga González, Fabio Molo, Leonhard Held

Individual participant data meta-analysis (IPDMA) can provide high-quality evidence in any area where data from individual participants in multiple studies can be combined. However, conducting an IPDMA remains a complex and resource-intensive process that requires careful planning. This primer collects relevant resources and practical advice, and outlines the steps for planning and conducting an IPDMA.

Peter Degen, Christian Meesters, Gorka Fraga González, Samuel Pawel, Fabio Molo

This primer introduces the use of workflow managers to create reproducible, portable, and scalable data analysis pipelines. We begin by outlining common benefits of workflow managers, followed by an introduction to Make as a foundational automation tool to illustrate core workflow concepts. We then introduce Snakemake and Nextflow, two popular, modern workflow managers designed for complex, data-intensive scientific workflows.

Gorka Fraga González, Andrew Clark, Eva Furrer, Leonhard Held

The aim of this primer is to help researchers get started with long-term archiving of their research data. We introduce different types of data archives, describe steps to prepare data for archiving, and provide a use case from a real study.

Sarah R. Haile, Malwina Kowalska, Hester van de Wiel, Markus Golder, Leonhard Held, Ulrike Held

A clinical research project has been completed in Switzerland — can data from it be shared, for example alongside a publication or to other interested researchers? This primer gives an overview of the legal basis in Switzerland for sharing data originating from clinical research projects, and outlines key considerations for data sharing, including informed consent, anonymization / pseudonymization, licenses and repositories.

Hester van de Wiel, Cora Burgwinkel, Leonhard Held

This primer provides an overview of sharing clinical trial data. It describes the process of how to prepare and how to deposit clinical trial data for sharing. Essential factors for clinical data sharing are highlighted, such as informed consent, anonymization, and data sharing platforms. Additionally, it describes how to request and use shared data.

Gorka Fraga González, Francesco Garassino, Fabio Molo, Steffen Bollmann, Eva Furrer

This primer discusses the use of software containers to improve computational reproducibility. It introduces the main elements of a container and different workflows for using them in scientific data analysis. An overview of software tools and a simple example help researchers in getting started with containers.

Charlotte Micheloud, Leonhard Held

This primer explains what replication studies are and presents several replication success criteria used in practice. Original and replication studies from large-scale replication projects are used to illustrate the properties of the different criteria.

Hester van de Wiel, Gorka Fraga González, Eva Furrer, Leonhard Held

This primer discusses file naming conventions (FNC) which help to achieve an organized and accessible collection of files. Implementing an effective FNC from the outset of a research project ensures better data organization, accessibility, and reproducibility, aligning with the FAIR principles for data management and facilitating collaboration among researchers.

Marianna Rosso, Leonhard Held

This primer dives into the world of data visualization as it explores its role in academia, enabling researchers and students to explore multidimensional datasets, uncover patterns, and communicate findings in an impactful way to a broad audience. Here, we present five principles of data visualization and provide a curated list of resources.

Felix Hofmann, Samuel Pawel, Melanie Röthlisberger, Leonhard Held

How can researchers and students use modern digital tools for collaboration? This primer gives an overview of various useful tools that can increase productivity and reproducibility.

Simon Schwab, Frank Ruschitzka, Gerhard Rogler, Leonhard Held

This primer explains what observational studies in clinical research are, and discusses reporting of such studies. A simple checklist is presented to help researchers stay on top of their reporting.

Benjamin Victor Ineichen, Martina Gosteli, Ulrike Held

This primer discusses the relevance of systematic reviews and provides an overview of the steps to conduct a rigorous preclinical or clinical systematic review.

Charlotte Micheloud, Stefanie von Felten, Leonhard Held

This primer was developed during the preparations of a Lab Pitch and discusses the design and analysis of cross-over trials.

Felix Hofmann, Samuel Pawel, Monika Hebeisen, Leonhard Held

Our first primer gives you a first taste of "Dynamic reporting": What it is? Why it is useful? and How you can use it.