Practicing Open Science

[written for upper level Biology students, reprinted from my Animal Behavior course site]

What is Open Science?

Open Science is about sharing all of your scientific work openly with others: your ideas, your hypotheses, your methods, your data, your analyzed results, and your research publications. Dan Gezelter, in his piece, What Exactly is Open Science? states four fundamental goals for open science:

  • Transparency in experimental methodology, observation, and collection of data
  • Public availability and re-usability of scientific data
  • Public accessibility and transparency of scientific communication
  • Using web-based tools to facilitate scientific collaboration

But Why Do Science Openly?

Scientists often keep their work private and worry about getting “scooped” for a variety of reasons. But there are a number of advantages that many see to scientific research being performed in the open, some of these include:

  • Science now is slow, wasteful, and locked away
  • Ruled by commercial interests
  • Reproducibility crises, questionable research practices
  • Make scientific practice more effective by increasing collaboration, transparency of the review process
  • Inclusivity
  • Increase our range and extent of knowledge, amplify collective intelligence, increase cognitive diversity
  • Real breakthroughs need to come through diverse teams of collaborators who share data, not individual superstars
  • Declining funding for basic science and for higher education, increasing corporatization of academia, decreasing public trust

Sources: To cure brain diseases, neuroscientists must collaborate: That’s why I’m giving my data away; Open Science and OER : Closing the LoopOpen Science MOOCA new paradigm for the scientific enterprise: nurturing the ecosystem

OK, Let’s do this! But how?

There are many ways to put all of your methods and protocols on the open web. You can upload your material to one or more sites for Open Lab Notebooks, Open Methods, Open Protocols, or post your work on your own site (or both).

This is an example of an open lab notebook on openlabnotebooks.org posted by a researcher who works on modeling diseases of the brain through STEM cells. As he states on his site: “…we can’t do this alone.”

Other sites include: the Center for Open Science and Protocols.io

Open Science is connected to other components of the Open Ecosystem

Open Data is an important piece of Open Science. Javiera Atenas and Leo Havemann define Open Data as “an umbrella term describing openly-licensed, interoperable, and reusable datasets which have been created and made available to the public…” (Interoperable means that the data can be read, used and exchanged between multiple systems, programs.) There are hundreds of thousands of open datasets provided by various government agencies, professional organizations and individuals. Some examples of places to find open data include: DataWorld, the U.S. Center for Disease Control, and BISON- Biodiversity Information Serving our Nation.

Open Access refers to the publication of journal articles that are freely available to others on the web. You may have noticed that often when you are doing library research, the journal article that you want to read costs money and you have to click on some link to pay for it before you can read it. This is what is referred to as being “locked behind a paywall”. Open Access means that the reader does not have to pay (that doesn’t mean that no one paid). Some journals are Open Access journals so that all of the articles within them are openly available. Some paywalled journals give authors the option to pay a fee to make their article open access to readers. There are also non-open-access articles that students can read “for free” (using your sign-in credentials) because our library has paid to access them.

The word “publication” is broadening as authors can choose to self-publish on their own sites instead of a peer-reviewed journal, or to put their work in databases or repositories that do not require a review process before submission. These are referred to as preprints. An open access preprint server for Biology is BioRxiv. (pronounced bio-archive). A preprint is a full draft of a research paper that is shared publicly before it has been peer reviewed. There may be pro’s and con’s to this. Such work may be reviewed later by a larger audience of readers allowing the author to get broader feedback and to make revisions continuously as opposed to a one time review by a small group of peers reviewing the paper in anonymity. Open Annotation tools can provide a way for scientists and others to openly review papers and materials that are not traditionally published, or before the work goes to publication. The tool Hypothes.is is broadly used for web annotation and they have a BioScience portal.

Note to my science students: You always have choices. But if you see the value, you can practice open science by sharing all stages of your research project openly. You can share your project ideas and hypotheses with others so they can help you refine them. You can share your data and engage in collaboration and conversations about the analyses and interpretations of your data, and the conclusions that you may draw with others in the class and with people (other students, scientists, anyone interested) outside of our classroom.