Collaborative writing of scientific papers

We will look at Authorea, one of the platforms for creating scientific papers online in a collaborative way. Then we will look at what is Markdown and how do we use it on Authorea. Finally, we will look at one aspect of open access, particularly licensing, i.e. what can happen with the paper after it is published.

Tools

Authorea

Authorea is freemium cloud platform for writing scientific articles. Try writing a document at:

https://www.authorea.com/

Note: When creating account or article on Authorea, use your institutional (NCSU) email, but don't send announcement about it to all people in the institution (which is something Authorea may do by default if you won't say no).

Markdown

Markdown is a way how include things such a headings and lists into a documents while still keeping it as a simple text file. Generally speaking, Markdown is a markup language like HTML but simpler (and also less powerful).

In Authorea, go to Insert -> Markdown and type or copy paste there the following text:

# This is a heading

This is *emphasis*.

* This is a list.
* Of different items.
Markdown when edited in the text editor (or Markdown mode in Authorea)

Markdown when edited in the text editor (or Markdown mode in Authorea)

Markdown when rendered (e.g. after converting to HTML)

Markdown when rendered (e.g. after converting to HTML)

Open access and licenses

Publishing an article as open access is usually achieved by licensing it using one of the Creative Commons licenses.

For example, MDPI uses CC BY (Creative Commons Attribution License). In a description of an article MDPI says:

This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

CC BY is also used, for example, by PLOS and it is the most common license used for open access articles.

Another license commonly used for open access articles is CC BY-NC (Creative Commons Attribution-NonCommercial License) sometimes combined also with ND (NoDerivatives) part (CC BY-NC-ND or CC BY-ND) preventing commercial use and modifications. What that exactly means in each particular case is often hard to determine [Redhead, 2012], but it is clear that these licenses doen't fulfill the Open Definition:

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

The "preservation of provenance" part is for example the attribution in CC BY and the "preservation of openness" part can be found for example in CC BY-SA (Creative Commons Attribution-ShareAlike License). CC BY-SA is sometimes used for open access articles and is quite commonly used in general, for example at Wikipedia. The CC BY-SA license requires that the derived works are distributed only under the same or similar license.

Creative Common licenses have both "human-readable summaries" ("plain English") and a full legal language license documents.

Resources

Texts

Videos

References

Assignment

Write a paragraph or two using about Authorea or Creative Commons into the following documents. Use Markdown to write it. Include a heading of the topic you are writing about and some other formating. Pick a topic which is not yet described by other student.

If writing about Authorea the topics may include: using Markdown, using the default editor, using LaTeX, including figures, tables, exports, imports, account policies and payments, etc. Try out the feature as you are writing about it. If writing about Creative Commons, the topics may include: description of a specific license, advantages and disadvantages, use cases, etc. Feel free to search for existing texts and draw from them (and cite and quote them).

You will need to request access by emailing the class instructor (vpetras). The links to the documents follow.

Authorea: https://www.authorea.com/users/23014/articles/195127-title

Creative Commons: https://www.authorea.com/users/23014/articles/195129-title