sharing, publishing, archiving

URL to lesson:
https://github.com/Reproducible-Science-Curriculum/rr-publication

To the extent possible under law, the person who associated CC0 with this work has waived all copyright and related or neighboring rights to this work. This work is published from: United States.

sharing, publishing, archiving

• shared could mean I emailed it to you ;)
• publish : citable artifact, discoverable
• archive : long-term preservation

• why publish?
• what materials do we need to publish?
• when do we make them available?
• who are we sharing with?
• where do we publish various outputs?
• how do we prepare materials for publication?

For the remaining slides we are going to assume that we are at the point of publication.

• funding agency / journal requirement
• community expects it
• increased visibility / citation

• funding agency / journal requirement
• community expects it
• increased visibility / citation
• better research

• funding agency / journal requirement
• community expects it
• increased visibility / citation
• better research
• more efficient, less redundant science
  • by allowing others to build upon our work

Catalog the artifacts you produced this morning.

• What needs to be published?
• What does not need to be published?
• Anything that cannot be published?

• Domain-specific data repository (GenBank, PDB)
• Source code hosting service (GitHub, Bitbucket)
• Generic repository (Dryad, Figshare, Zenodo)
• Institutional repository
• Sharing services (RPubs, iPython Notebook Viewer, Dropbox, Google Drive)

Discuss: Contrast with journal supplementary materials.

• is there a domain specific repository?
• what are the backup & replication policies?
• is there a plan for long-term preservation?
• can people find your materials?
• is it citable? (does it provide DOIs)
• is your purpose archival, sharing or publication?

• top-level README that describes the data or software package
• list files and naming conventions
• describe abbreviations, column names, etc
• installation and usage instructions for software
  • create separate INSTALL if long
• citation instructions
  • consider creating a CITATION file
• contribution instructions
  • Github will automatically link to CONTRIBUTING file for new issues and pull requests

Documenting your research:

• collect all of the to-be-archived artifacts from the preceding lesson into a directory
• write a README file that describes the contents of the directory

The Open Definition sets out principles that define “openness” in relation to data and content. It makes precise the meaning of “open” in the terms open data, open content, and open source:

“Open means anyone can freely access, use, modify, and share for any purpose (subject, at most, to requirements that preserve provenance and openness).”

or more succinctly:

“Open data and content can be freely used, modified, and shared by anyone for any purpose”

CC0 enables scientists, educators, artists and other creators and owners of copyright- or database-protected content to waive those interests in their works and thereby place them as completely as possible in the public domain, so that others may freely build upon, enhance and reuse the works for any purposes without restriction under copyright or database law.

Dryad’s use of CC0 to make the terms of reuse explicit has some important advantages:

• Interoperability: Since CC0 is both human and machine-readable, other people and indexing services will automatically be able to determine the terms of use.
• Universality: CC0 is a single mechanism that is both global and universal, covering all data and all countries. It is also widely recognized.
• Simplicity: There is no need for humans to make, or respond to, individual data requests, and no need for click-through agreements. This allows more scientists to spend their time doing science.

From the Panton Principles:

[…] in the scholarly research community the act of citation is a commonly held community norm when reusing another community member’s work.

Community norms can be a much more effective way of encouraging positive behaviour, such as citation, than applying licenses. A well functioning community supports its members in their application of norms, whereas licences can only be enforced through court action and thus invite people to ignore them when they are confident that this is unlikely.

• Licenses, copyright, terms of use are complicated issues.
• There are legal implications to your choices.
• Citation is a professional norm in science.
  • We have good systems for ensuring proper citation.
  • Would you try to sue someone in court who fails to cite you properly?
• Keep it simple by putting the least-restrictive license possible

Let scientists do science without having to talk to lawyers.