Countway and protocols.io logosThe protocols.io platform is a free and open access repository for recording and sharing detailed up-to-date research methods and protocols. It allows researchers to easily create, edit, share, and get credit for their protocols, and provides an open access hub for scientists to communicate improvements and corrections to scientific methods. The platform is useful for researchers in any discipline that uses a step-by-step methodology, such as biology, chemistry, neuroscience, engineering, data science, and other computational or life science fields.

Countway Library supports free Premium individual and team accounts for Harvard Medical School, Harvard School of Dental Medicine and Harvard T.H. Chan School of Public Health faculty, students and staff. Benefits of premium accounts include:

  • Premium users can create unlimited private protocols
  • Premium team workspaces can invite other academic or industry collaborators at no additional charge
  • If a premium workspace administrator graduates or leaves, they can reassign the workspace to another affiliated member
  • Premium users can export all their workspace protocols and records in bulk as PDF or JSON files
  • Backup snapshots of the entire protocols.io database are made every sixty (60) seconds, going back three (3) days

Learn more on our organization landing page.

Getting Started

Important Details

Below are some key details about the Countway license and protocols.io. If you have any additional questions, please do not hesitate to contact the Publishing and Data Services Team.

  1. What are the key benefits of the pilot for the LMA community? This pilot will focus on a major barrier to reproducible research: the creation and sharing of detailed methods in published articles (see Plan to replicate 50 high-impact cancer papers shrinks to just 18). We aim to chisel away at this barrier by having Harvard researchers identify precisely the steps of their performed experiments. The pilot should increase adoption of protocols.io for internal organization and tracking of research methods at each LMA school, and subsequently will lead to better reporting and more reproducible publications from the Harvard research community.
  2. How does protocols.io work? How do I login? The protocols.io platform includes a public repository of methods. All public content is CC-BY. Users can create, publish and read public protocols at no cost. However, there is a fee for creating private areas for method collaboration. This is included in the protocols.io Premium features. These features include private groups to organize, discuss, and collaborate around methods. The Countway pilot will allow all HMS, HSDM, and HSPH faculty, students and staff to access these Premium features at no fee during the license period. To sign-up, you just need to visit the protocols.io website and Sign in with SSO to verify your HarvardKey credentials.
  3. Can I create computational/bioinformatics protocols? protocols.io allows you to capture all the details of computational analyses (parameters, specifics of the pipelines, versions and locations of datasets, software, etc.) Others who wish to run your method will then have a step-by-step pipeline to follow and can capture output files alongside each run. Sharing computational workflows on protocols.io is not meant to replace GitHub or Jupyter Notebooks, but to work in tandem with links to those platforms. See examples of computational pipelines shared on protocols.io.
  4. What happens after the pilot? There is no obligation for campuses or researchers to pay any fees. At the end of the pilot period, in the event of contract cancellation or non-renewal, Harvard users will have the option of paying for the individual and team accounts directly. Note that no additional private content will be allowed to be created within protocols.io without a paid subscription. The costs for Premium features are listed on the website.
  5. How will non-LMA school collaborators be handled? During the pilot, premium team accounts created by HMS/HSDM/HSPH users will not be limited members from those schools. Academic or industry collaborators are free to join such private groups at no additional charge.
  6. How reliable is protocols.io? Is the content archived? All content created in protocols.io is licensed CC-BY. Public content in protocols.io is archived in CLOCKSS, and there is a free public API allowing a snapshot of the entire protocols.io public content at any time. PDFs and JSON files of all public protocols are also mirrored in the open and searchable GitHub repository. For private protocols, every researcher can export all of their protocols and records in bulk as PDF or JSON files; there is also integration with Google Drive, Drop Box, and Box for single-click export from protocols.io.
  7. Should I worry about scooping or a journal rejecting my manuscript if the method is shared before submission? Posted protocols are analogous to preprints rather than a formal prior publication, therefore it won't disqualify you from publishing the method as part of a research paper. To date, we have never been made aware of a journal rejecting a submission because the protocol was already published. But if you're not ready to make your protocol public, you have the option to share your protocol privately with specific individuals or groups, or you can use the 'Reserve DOI' option. to share a private link with a journal until your article is accepted. See the help page for more information.

Find the complete collection of FAQs on the protocols.io website.

Feedback is welcome

We welcome feedback and requests; they are critical for continuing to strengthen the protocols.io pilot and ensuring that it makes Harvard researchers’ lives easier. To offer suggestions or for more information, please contact protocols.io support.