Open By Design¶

This guide was prepared by the Center for Open and REproducible Science (CORES). See the full list of contributors below.

THIS IS CURRENTLY A WORK IN PROGRESS

See the Guide for Contributors if you wish to contribute to this project.

What is “open science”?¶

At its core, the term “open science” embodies a fundamental set of values regarding how scientific research should be pursued:

Transparency and openness: The products of scientific research (including data, code, and publications) should be shared as openly as possible.
Reproducibility: Scientific practices should prioritize rigor and reproducibility, even when they conflict with other considerations or incentives.
Diversity and inclusion: The scientific process should be open to all, and diversity within the scientific community should be both pursued and celebrated.
Community-mindedness: Scientists should coordinate and cooperate rather than compete.

These values have been expressed through a number of specific practices aimed at improving the credibility and effectiveness of the scientific enterprise:

Open access publication: The knowledge outputs of scientific research (including publications) should be openly accessible to the world, without restrictions based on commercial interest. This access should occur as early in the process of publication as possible, such as through the posting of preprints to public preprint servers.
Open data, code, and research materials: The data underlying any scientific publication and the code used to analyze those data should be accessible as widely as possible, in line with the FAIR Principles (Findable, Accessible, Interoperable, and Reusable)
Openness by design: The next generation of researchers should be trained and supported to do transparent and reproducible science from day one — that is, to be “open science natives”.
Evidence syntheses: Individual studies should be viewed as building blocks that inform our cumulative scientific knowledge, rather than as individually conclusive. To this end, outputs of individual studies should be made available in a manner that facilitates evidence syntheses such as meta-analyses and replication attempts.

This guide aims to provide researchers with the resources necessary to implement open science practices within their own research.

Check out Easing Into Open Science: A Tutorial for Graduate Students

The components of open science practice¶

This guide is organized according to a number of different aspects of open science practices:

Pre-registration
Reproducible data analysis
Reproducible modeling
Reproducible manuscript
Reproducible project
Code sharing
Data sharing
Open access publication

We also discuss several topics of the open science infrastructure:

Computer literacy
Programming
Project management

We have included some more general suggestions:

Joining the culture of open science

Why should I do it?¶

As the availability of large datasets, powerful computational algorithms, and enormous computing power continues to expand and influence public policy and medical practice, it is crucial our research practices adapt to our evolving society. To do this, we need increased transparency and reproducibility in our scientific research. This is the ultimate goal of the open science movement. As scientists, we need to promote the integrity and public credibilty of science.

How this book is organized¶

We have organized this book to describe several open science practices with domain-specific examples of how they have been applied. These examples are critical for illustrating how to implement open science practices into your research workflow. Please feel free to add an example of incorporating these open science practices in your work!

We understand the barrier to applying open science practices can be steep. In an effort to reduce the barrier to entry, we have a section to introduce you to several topics of the open science infrastructure. Developing and honing these skills will further strengthen your open science prowess.

Contributors ✨¶

Thanks goes to these wonderful people who contributed to the development of this guide (emoji key):

_{Russ Poldrack} 🎨 🖋 📆	_{Catherine Thomas} 🖋	_{Erik Santoro} 🖋	_{Chris Markiewicz} 🖋	_henrymj 🖋	_{Oscar Esteban} 🖋
_{McKenzie Paige Hagen} 🖋	_bissettp 🖋	_MatildeVaghi 🖋	_{Franklin Feingold} 🖋🎨📆	_ghuckins 🖋	_{waltersjonathon} 🖋
_Shashank 🖋	_{ihandleyminer} 🖋	_masaba 🖋	_{Alex Cionca} 🖋