This training highlights the importance of free and open source software (FOSS) and open hardware for health sciences.

By the end of this training, learners should be able to:

• Understand the importance of free and open source software (FOSS) for health sciences
• Be aware of the widely used FOSS tools for data analysis and visualization
• Understand the importance of open hardware for health research

Training outline

• The potential of FOSS tools
• Finding commonly used FOSS tools
• Using collaborative tools and platforms (e.g. GitHub, interactive notebooks)
• Virtual REsearch Environments (VRE) for health research
• Open hardware

Resources for facilitators and learners

Online courses

• The Carpentries. Welcome – Introduction to Open Data Science with R.
• Foundations of data analysis with R – The GRAPH Courses
• Chang, Winston. Cookbook for R.
• Oxford Population Health. FoSSA: Fundamentals of Statistical Software & Analysis – The GRAPH Courses.

Publications and blogs

• Niezen, G., Eslambolchilar, P., Thimbleby, H. 2016. "Open-Source Hardware for Medical Devices." BMJ Innovations. https://doi.org/10.1136/bmjinnov-2015-000080
• Heath, V. 2020. Open-Source Medical Hardware: What You Should Know and What You Can Do. Creative Commons.

Videos, webinars, online tutorials

• Bülau, Konstatin, Dege, Lion. 2022. APIs - Interfacing Tools and Services.
  

• Bonaretti, S. 2020. Why We Should Use Jupyter Notebook in Medical Image Analysis. TORW2020.
  

• CINECA Project. 2022. Text Mining Tools for Cleaning Cohort Data.
  

• Parrot, Scott. 2023. How To Extract Data from Systematic Review and Meta-Analysis.
  

• Jap, Jens. 2018. Abstrackr: Collaborative Open-Source Analysis Tool for Systematic Reviews.
  

• Washington State University Libraries. Using Zotero for Systematic Reviews. Google Docs.
  

• Berlin Institute of Health at Charité. BIH/Charité Virtual Research Environment.

• The Open Source Hardware Association. 2022. Open Hardware and Health Technology: A Panel Discussion.
  

• National Library of Medicine. 2021. NCBI Minute: Using NCBI Datasets Command-Line Tools to Access Data and Metadata for Genomes.
  

• BrainModes. 2020. What Is The Virtual Research Environment? (English).
  

Library guides

• Stansfield, C., Gough, D., Bangpan, M., Bhimani, N. 2021. Systematic Reviews. London: UCL Library Services

Curated lists of tools

• Awesome Health
• Wellcome / EPSRC Centre for Interventional and Surgical Sciences. WEISS Open Source Tools.
• National Library of Medicine. Data & Software - Site Guide.