Open Methods and Tools

In addition to data sharing, the openness of research relies on sharing of materials.


A reagents is a substance, compound or mixture that can be added to a system in order to create a chemical or other reaction. Reagents can be deposited with repositories like Addgene, The Bloomington Drosophila Stock Center, and ATCC to make them easily accessible to other researchers. License your materials so they can be reused by other researchers.


A protocol describes a formal or official record of scientific experimental observations in a structured format. Deposit virtual protocols for citation, adaptation, and reuse using

Notebooks, containers, software, and hardware

Sharing software used for research (whether computational in nature, or that relies on any software-based analysis/interpretation) is a necessary, though not sufficient, condition for reproducibility.

Reproducible analysis is aided by the use of literate programming, container technology, and virtualization.

Having the research software on GitHub is just the first part; it is equally important to have a published and persistent identifier associated with it, such as a DOI.

In addition to sharing your code and data, also share your Jupyter notebooks, Docker images, or other analysis materials or software dependencies. Share notebooks with Open services such as mybinder that allow for public viewing and execution of the entire notebook on shared resources. Containers and notebooks can be shared with Rocker or Code Ocean.

Read-only protocols should be deposited in your disciplines registry such as and SocialScienceRegistry or a general registry like Open Science Framework. Many journals, such as Trials, JMIR Research Protocols, or Bio-Protocol, will publish your protocol.

Open-source software

Publicly shared software is not actually open source unless accompanied by a suitable license, because by default software (along with any other creative work) falls under exclusive copyright to the creators, meaning no one else can use, copy, distribute, or modify your work (

Instead, you should choose an appropriate license for your software, based on what you would prefer to let others do (or prevent them from doing) with your code. site is a helpful resource to differentiate between licenses, although it does not feature every available or popular open-source license. Once you select a license, put the text—edited to include the author name(s) and year—in the software repository as a plaintext LICENSE file.

Although sharing software in any form is better than not sharing it, your software will have more impact and be more easily used by others—and your future self!—if you include documentation. This can include helpful comments in the code that explain why you did something (rather than what you did, which should be evident), an informative README file that describes what your software does and gives some helpful information (e.g., how to install, how to cite, how to run, important dependencies), tutorials/examples, and/or API documentation (which may be automatically generated from properly formatted comments in the code).

Missing or inaccessible dependencies or insufficient documentation of the computational environment are very common barriers to reuse and reproducibility. One approach to address these barriers is to share your code with your computational environment using container technology.

Open Licensing and File Formats

A license is a legal document that grants specific rights to user to reuse and redistribute a material under some conditions. Any right that is not granted by default by the licensor through the license can be asked. Licenses can be applied to any material (e.g., sound, text, image, multimedia, software) where some exploitation or usage rights exist.

Free content licenses are licenses that grant permission to access, re-use, and redistribute material with few or no restrictions. Those licenses range from very open to very restrictive. The more restrictions, the more difficult it becomes to combine differently licenses content—thus potentially preventing interoperability.

A file format is a standard way that information is encoded for storage in a computer file; however, not all formats have freely available specification documents, partly because some developers view their specification documents as trade secrets.

The most used licenses for scientific content are Creative Commons licenses. In general, a CC BY license (requiring only attribution) is a good option for works such articles, books, working papers, and reports while a dedication to the public domain using CC Zero (CC0) is recommended for datasets and databases.

Within the context of Open Science, and for optimal long-term archiving, files should not be compressed and should avoid proprietary or patent-encumbered formats and in favor of open formats based on documented standards. This ensures the access and re-usability of the content. Only unencrypted files should be published and archived.