Draft: Notes on Writing and Publishing Workflow

Notes on Writing and Publishing Workflow

The world of scholarly publishing is changing. It’s almost like a new paradigm of publishing is opening before us. Open access publishing has made it easy for almost anyone with ideas to make it available to as wide an audience as one wants because the article or the idea itself is free to access by anyone.

Compared with toll access and its trappings, this suggests a new way of doing things. The question still persists as to what are some of the ways where people can publish beta ideas, make it open and invite potential scholars and friends to come and comment on it and take it from a stage of beta or alpha ideas to work till a publishable structure is established. It turns out that there are different ways of doing this. I found a few tools very interesting and intuitive to work with. There are social aspects to this publishing and these are also open for business in the sense it is possible to submit it to other people’s review and get more ideas and refine them. There are risks that people might steal your ideas, mix them and share them for their own fulfilment without paying you any attribution. Unfortunately that is a genuine risk. That said, here are some tools that can be used to build scholarly publishing workflow.

Collaborative Authoring Software

A couple of collaborative authoring software come to mind. Both are great. The first one that comes to mind is Authorea. Authorea is a free open website where anyone can register to obtain a free account and then get started to publish one’s own article.

There are two flavours to write. One of them is to write using Markdown, a typing process that is very intuitive and easy and uses plain text. I use plain text in almost all my writings and it synchronizes well with the email style of writing. You use simple texts to format your writing. For more information on markdown see John Gruber’s page on markdown formatted writing.

The other writing style that Authorea supports is LaTeX, a typesetting system that enables anyone to write again in plain text and typeset papers. I have found that the way to work best with Authorea is to invite your fellow authors or coauthors, and get them started with an account. Basically, you can start with an abstract or summary page, and then start with the process of writing. The tables in Authorea are based on LaTeX tables, which can sometimes be a little tedious to work with, unless one is familiar with typesetting LaTeX tables. The figures are easy to work with. Here is my working flow with Authorea:

1. I usually start setting up a file structure in the layout.md file that is contained I the folder space.

2. In the layout.md, I put in the sequence of the files (either latex files or markdown files that will be added to the main body of the text)

3. We keep writing and adding figures and tables as needed. (This is the bit I need to work on)

4. Keep the citations in the citation tab or search for citations within Authorea itself.

The next collaborating authoring tool that comes to mind for scientific scholarly writing is Overleaf. Overleaf is great and is based on LaTeX alone. The beauty of Overleaf is the number of templates and publishing opportunities and a nice formatting system that takes the tedium of publishing using LaTeX. In my opinion, this would be a killer app if we had some way of integrating Markdown in it for publishing. It’d be similarly nice if Authorea were to pay attention to the templating or direct publishing to open access or toll access publishing journals. Google Docs for that matter is also excellent in allowing real time collaboration where two individuals can simultaneously work on a document. Google Docs also tightly integrates with Google Scholar, a great source of literature and bibliographic information and also indeed with the search facility in general. However, I am not sure the extent to which Google Scholar can be easily used for typesetting ideas and expressions and tightly integrating with Epidemiology and statistical workflow.

Publishing Workflow

Two shining examples are PeerJ and my new found The Winnower. PeerJ in particular shines with its preprint system where an article or indeed any piece of work can be hosted and others can be invited to come and view and comment on it, and then the Winnower system goes a step ahead in letting people directly publish, review, and comment and then revise the manuscript based on these comments. It’s a world where your publishing and scholarly communication workflow can be integrated with crowd ideas and comments and can be further embellished.

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