Abstract

The "face" of scholarly publishing and outputs are changing. it is not unusual to find journal articles that are primary studies and secondary data and opinion (well-considered, and evidence backed opinions) presented in the space of the same journal. This was not the norm even a decade ago. In addition to this, the rapid expansion of the web as a medium of expression of scholarly communication has resulted in a new format. Hence blogs and primary and secondary analyses jostle for their spaces in the same ecosystem. 
As much as this has expanded, the tools to produce that knowledge is still to catch up. While there are some advances in the form of entirely web based online writing that enables people to collaborate and write freely on the web, the norm still is to produce outputs for the paper version. The screen is almost like an "extension" of the paper. Happily, with the extension of the web and appearance of small screen based tablets and phones, this trend is changing as well. 
In this publication, we are going to explore the new authoring tool Authorea that allows a space to write online papers and presentation of those papers on the site as well. We shall review its properties in terms of integrating LaTeX and markdown as well as simple markup based writing that enables a tight integration of different forms of writing and data presentation. This article is both a musing and a "how to" for Authorea as it stands today. 

Introduction

Changing face of scholarly publishing

The interface of Authorea is really simple. If you opt for the new "beta" style of writing, then you are all set. All you need to do is to set up your headings, and your thoughts and you should be able to write easily. We can write almost any form of text in Authorea. One idea might be to start with Authorea and then fine tune for further distrintion or writing long, complicated pieces with Overleaf, where you can port Authorea document as a Latex document and then open in Overleaf to finish it. 

Mechanics of Writing 

In general, when you write any document, you will be able to structure your thoughts in the fom of headings, and hen then, once the headings are all in place, fill in the headings and sections that you create with paragraphs of thought that are relevant for hat that puarti particular section and continue. For a shorter text such as an article, this would be the case; for a longer form of your writing, your setions sections and headers take the shape of your chapter heaed headers. Thus, if you were to writ write something like a thesis, you will would be using the headers or the section headers as your chapter headings and continue to write. 
Having said that, for academic writing, we need some more e things to worry about . Every fact that you state in an academic dcu documen m document must be accounted for, or at least you should be able to identify an evidn evidence to state your fact. Second, as academic writing is vetted in fo one form or another, therefore, this form of writing is open to scrutiny of facts and interpretations that you state. Also, bea e because of this reason, in academic wrii writing, you are restricted to state facts and interpretations rather than your opinions. This essentially means that ou wi you will depend on diagrams and analyses particularly when you write tet texts in epidemiology or health sciences. Third, most academic writing involves long tracts of passae passages where he the author is engaged in discussions, debates, discuri discursive writing where he or she draws from oher other people's writings, other diagrams, his o or her own analyses, previous writings, summaries, and othe other forms of evidene evidence and sources to substantiate the text he or she should write. To make it easy for readers to in understand the key points, an authors would like to abbreviate information or abridge or paraphrs paraphrase in the form of tables, and figures that explain or inform. These fiure figures could be in the form of flowcharts, or diagrams, or even perhaps in the form of graphs and charts that are developed on the fly. 
Given these different requirements, it is important 

Need for a simple integrated system to write scholarly paper

With the need for writing academic papers involving the following elements:
1. Paragraphs that woud would enable tightly linked sentences that provide the structure of the paper
  1. Paragraphs that provide the structure of the ag arguments
  2. Citations that provide links and cross linking to the sources from the where the facts are taken
  3. Structures such as lists and bullet points that help to pare down complex ideas to sipler simpler digestible units
  4. Tanles Tables and chrt charts that provide analytical contexts
  5. Diagrams nd and Flow charts that provide explanatory context to the text being written
  6. A neat set of headers that help to hold the structure in place
it is not easy to see It is no Most available word processing applications by themselves are not very intuitive to meet all these requirements that are needed to write a scholarly paper. The most popular application, Word, for example, is quite elegant in its design andn very responsive in the fo way it lets a user write free text, and also how tables and figures can be imported and embedded in the document. Howeer, it is not very intuitive for a writer to writ write or include equations and special symbols nd and the writer will have to spend time and energy to locate the symbols in the crumbs presented on the softeare to identify the symbols nand buuild the equation. build the equations or insert these sumbols to make them work. Another format is LaTeX, the elegant typesetting system. 
While LaTeX is elegant and very powerful tpe tupe tp typesetting system and is also dependn based on lain plain text and therefore very intuitive, it is not very easy to use. The numerous symbols and characters that one need to remeber remember in order to accomplish relti relatively sm simple tasks such as write a table or insert an environment such as an image is not very easy for a novice to wlear learn and then again, it is not e very easy to remember and use on a daily basis. As a result, many new writers who have started out with the ad process of academic riting writing tend to avoid writing in LaTeX. We ba Web based and rich text formatting of LaTeX helps to overcome some of these initial hindrances, but then again, adoption level is not very high. 
h The third type of format that has increasingly gained adoption in web writing in particular is using markdown formatted wiritng. This is a an elegant format of writinng particularly for web and very easy to master and use. The headers setio sections can be easily used with ah hash marks or singe single and double underlines, text emphasis with bold or italics are easy to am master, the lists and of various forms such as bullet lists and enumerated lists are easy to write and intuitive to set up. Yet due to its design restrictions, pure markdown is limited s as in markdown it is not very intuitive to add citations, and making table is impossile. The only way There hae have been further development of markdown in recent years to include scholarly markdown and that community ensures that it is possible to create tables relatively easily by using bar lines an and simple t straight lines. 
Therefore, a truly intuitive system of writng would n integrate everyting, i.e.,
Getting all of these features w under one roof is something of a holy grail of writing. So lets see what alternatives do we have at the moment. 

State of the science as it exists now