Introduction to this course

  • This material is developed for mid-career and senior researchers in biomedical and biosciences fields.
  • This training aims to build a shared understanding and facilitate the integration of computational reproducibility in data science.

Better and faster research !

  • motivations

What is special in data science project ?

  • content organisation

Reproducibility

  • Version controlled repository help record different contributions and contributor information openly.
  • Open Science is an umbrella term that involve different practices for research in the context of different research objects.
  • Online Persistent Identifiers or Digital Object Identifiers are useful for releasing and citing different versions of research objects.

An introduction to version control

  • version control
  • git

Setting up a computational project

  • Shared repository with well structured and organised files are crucial for starting a project
  • Documentation is as important as data and code to understand the different aspects of the project and communicate about the research.
  • Licencing and open science practices allow proper use and reuse of all research objects, hence should be applied in computational research from the start.

Implementing tools and methods during the project

  • Make group leaders familiar with practices that are crucial for their teams to develop reproducible code.
  • Encourage researchers to think about code reproducibility through quality check, testing, sharing their code as well as a research environment.
  • Introduce Continuous Integration for automating the testing process.

Research Data Management

  • Good research data management practices esures findability of your research data.
  • Storing, regular backing-up and archiving prevents data loss.
  • Sharing all types of research data transparently makes them easier to understand and reuse by others.
  • Gives fair recognition to people generating, handling and using data, and further stimulates collaboration with others.

Fostering documentation

  • Version controlled repository help record different contributions and contributor information openly.
  • Open Science is an umbrella term that involve different practices for research in the context of different research objects.
  • Online Persistent Identifiers or Digital Object Identifiers are useful for releasing and citing different versions of research objects.

Scientific rigour with code

  • statistics

Coding basics

  • First key point. Brief Answers to questions. (FIXME)

Code testing and Review

  • There are many benefits of code review and this should be implemented and practised in research team culture as early and as frequently as possible.
  • Synchronous code review creates opportunities for researchers to get feedback and learn from others in real-time.
  • Asynchronous code review is a good practice when working with busy researchers or collaborators in different time zones.

Code Modularity

Publication and release

  • First key point. Brief Answer to questions. (FIXME)

Open Science Practices

  • Version controlled repository help record different contributions and contributor information openly.
  • Open Science is an umbrella term that involve different practices for research in the context of different research objects.
  • Online Persistent Identifiers or Digital Object Identifiers are useful for releasing and citing different versions of research objects.

Data and code citation

  • First key point. Brief Answer to questions. (FIXME)